Probing the recognition surface of a DNA triplex: Binding studies with intercalator-neomycin conjugates

Article abstract of DOI:10.1021/bi100071j

Thermodynamic studies on the interactions between intercalator-neomycin conjugates and a DNA polynucleotide triplex [poly(dA)·2poly(dT)] were conducted. To draw a complete picture of such interactions, naphthalene diimide-neomycin (3) and anthraquinone-ne

Full text of DOI:10.1021/bi100071j

5540 Biochemistry 2010, 49, 5540–5552
DOI: 10.1021/bi100071j
Probing the Recognition Surface of a DNA Triplex: Binding Studies with
Intercalator-Neomycin Conjugates†
Liang Xue,‡ Hongjuan Xi, Sunil Kumar, David Gray, Erik Davis, Paris Hamilton, Michael Skriba, and Dev P. Arya*
‡
Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634 Present address:
Department of Chemistry, University of the Pacific, Stockton, CA 95211.
Received January 15, 2010; Revised Manuscript Received May 14, 2010
ABSTRACT: Thermodynamic studies on the interactions between intercalator-neomycin conjugates and a DNA
polynucleotide triplex [poly(dA) 2poly(dT)] were conducted. To draw a complete picture of such interactions,
3
naphthalene diimide-neomycin (3) and anthraquinone-neomycin (4) conjugates were synthesized and used
together with two other analogues, previously synthesized pyrene-neomycin (1) and BQQ-neomycin (2)
conjugates, in our investigations. A combination of experiments, including UV denaturation, circular dichroism
(CD) titration, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC), revealed
that all four conjugates (1-4) stabilized poly(dA) 2poly(dT) much more than its parent compound, neomycin.
3
UV melting experiments clearly showed that the temperature (Tm3f2) at which poly(dA) 2poly(dT) dissociated
3
into poly(dA) poly(dT) and poly(dT) increased dramatically (>12 °C) in the presence of intercalator-
3
neomycin conjugates (1-4) even at a very low concentration (2 μM). In contrast to intercalator-neomycin
conjugates, the increment of Tm3f2 of poly(dA) 2poly(dT) induced by neomycin was negligible under the same
3
conditions. The binding preference of intercalator-neomycin conjugates (1-4) to poly(dA) 2poly(dT) was
also confirmed by competition dialysis and a fluorescent intercalator displacement assay. Circular dichroism
3
titration studies revealed that compounds 1-4 had slightly larger binding site size (∼7-7.5) with poly(dA)
3
2poly(dT) as compared to neomycin (∼6.5). The thermodynamic parameters of these intercalator-neomycin
conjugates with poly(dA) 2poly(dT) were derived from an integrated van’t Hoff equation using the Tm3f2 values,
3
the binding site size numbers, and other parameters obtained from DSC and ITC. The binding affinity of all tested
ligands with poly(dA) 2poly(dT) increased in the following order: neomycin < 1 < 3 < 4 < 2. Among them, the
3
binding constant [(2.7 ( 0.3) ꢀ 108 M-1] of 2 with poly(dA) 2poly(dT) was the highest, almost 1000-fold greater
3
than that of neomycin. The binding of compounds 1-4 with poly(dA) 2poly(dT) was mostly enthalpy-driven and
3
gave negative ΔCp values. The results described here suggest that the binding affinity of intercalator-neomycin
conjugates for poly(dA) 2poly(dT) increases as a function of the surface area of the intercalator moiety.
3
Targeting the major groove of the DNA duplex with a single-
stranded DNA to produce a DNA triple-helical structure has
aroused much interest, especially in the past two decades, since its
discovery in the 1950s (1). Such recognition obeys well-defined
base pairing rules by making specific hydrogen bond contacts
between nucleobases of the third strand and substituents on
the exposed faces of the Watson-Crick base pairs, known as
the purine and pyrimidine motifs, which have been examined by
many investigators (2-6). DNA triple-helical structures formed
in vivo under physiological conditions have been observed and
named “H-DNA”, yet much remains to be learned about their
biological functions (7, 8). A well-designed synthetic DNA
oligonucleotide [also known as triplex-forming oligonucleotide
(TFO)]1 binds to DNA duplex in a sequence-specific manner.
Evidence suggesting that TFOs can effectively block the binding
of a variety of proteins to DNA duplexes raises the level of
importance of their potential therapeutical uses. Examples of
triplex formation that inhibit cleavage of DNA mediated by
topoiosomerase II and interfere with the unwinding function of
DNA helicases are well-documented (9, 10). Several groups have
revealed inhibition of transcription by blockage of DNA or RNA
polymerase using the triplex strategy in the promoter (P1) of the
c-myc oncogene (11, 12) and in the R subunit of the interleukin-2
receptor (IL-2RR) (13, 14).
In spite of its promising sequence-specific recognition of DNA
duplex, the triplex formation strategy, also known as Antigene,
has some limitations (3, 15). A DNA triplex is more difficult to
form than a DNA duplex because of the electrostatic repulsions
between the negatively charged backbone(s) of TFO and the
DNA duplex. In addition, the formation of the DNA triplex is
energetically less favorable, and the resulting DNA triplex is less
stable than its counterpart duplex.
Over the years, several strategies for overcoming the instabi-
lity of the DNA triplex, such as modification of nucleobases and
backbone groups of TFO (16-18) and utilization of small
binding molecules (19-22), have been investigated. Interest-
ingly, many DNA duplex intercalators have been found to
stabilize DNA triple-helical structures, although the selectivity
of these molecules between the DNA triplex and duplex is
†We are grateful for support of this research by the National Science
Foundation (CHE/MCB-0134972) and the National Institutes of Health
(R15CA125724).
*To whom correspondence should be addressed. E-mail: dparya@
clemson.edu. Phone: (864) 656-1106. Fax: (864) 656-6613.
1Abbreviations: FID, fluoroscent intercalator displacement; TFO,
triplex-forming oligonucleotide; BQQ, benzoquinoquinoxaline.
r
pubs.acs.org/Biochemistry
Published on Web 05/25/2010
2010 American Chemical Society

Article
Biochemistry, Vol. 49, No. 26, 2010 5541
F
IGURE 1: Structures of neomycin and intercalator-neomycin conjugates.
subtle (23). Helene and co-workers rationally designed and
synthesized benzopyridoindole derivatives, which prefer to bind
the DNA triplex over the duplex and increase the rate of triplex
formation (24, 25). We have reported the discovery of the first
DNA triplex-specific groove binder, neomycin [an antibiotic
(Figure 1)] (26, 27). Our results showed that among all the
aminoglycosides, neomycin specifically stabilizes DNA triple-
neomycin seems not to alter the selective binding of neomycin to
the DNA triplex over the duplex. The observed enhancement of
DNA triplex stabilization by 1 and 2 is attributed to the “dual
recognition mode”, in which the neomycin moiety binds in the
Watson-Hoogsteen groove when the intercalator inserts between
the proximate base triplets to provide additional stabilization.
Further understanding of interactions of intercalator-
neomycin conjugates with DNA triplexes can be achieved by
acquiring thermodynamic parameters of their binding events. For
a complete study, we in this period have synthesized two addi-
tional intercalator-neomycin conjugates, naphthalene diimide-
neomycin (3) and anthraquinone-neomycin (4). We probe the
surface area of the DNA triplex using compounds 1-4 with
varying surfaces for stacking between the DNA triplets (Figure 1).
Fluorescent intercalator displacement (FID) assays were first
performed to estimate the relative affinities of these ligands for the
DNA triplex. The binding enthalpies, entropies, and equilibrium
constants of these intercalator-neomycin conjugates (1-4) with
helical structures such as poly(dA) 2poly(dT), AT-rich or mixed
3
base of DNA oligonucleotide triplexes, and a 12-mer intramole-
cular DNA triplex while having a weaker effect or no effect on
DNA duplexes (26). Furthermore, modeling studies of a system
including neomycin and a (dT)10 (dA)10 (dT)10 DNA triplex
3
3
suggest that neomycin most likely binds in the Watson-
Hoogsteen groove of the DNA triplex with its ring I sitting in the
center of the groove and rings II and IV bridging the two
pyrimidine strands together (27). These reports expanded the
number of nucleic acids that aminoglycosides have been shown to
bind and suggested that the aminoglycoside preference is for
smaller A-form major grooves (28-43). Further expanding the
family of DNA triplex binding ligands based on the structure of
neomycin was achieved by conjugating intercalators such as
pyrene and BQQ with neomycin to yield pyrene-neomycin (1)
and BQQ-neomycin (2) conjugates (Figure 1). UV denaturation
and circular dichroism studies of DNA triplexes with 1 and 2
reveal that these two conjugates enhance the stabilization of DNA
triplexes much more than their parent compound, neomy-
cin (44, 45). In addition, covalent attachment of intercalators to
a DNA polynucleotide triplex, poly(dA) 2poly(dT) were derived
3
from an integrated van’t Hoff equation (46) to exploit the effect of
the intercalator moiety and the important factors on the stabiliza-
tion of the DNA triplex.
EXPERIMENTAL PROCEDURES
General Methods. Unless otherwise specified, chemicals
were purchased from Aldrich (St. Louis, MO) or Fisher Scien-
tific (Pittsburgh, PA) and used without further purification.

5542 Biochemistry, Vol. 49, No. 26, 2010
Xue et al.
Neomycin sulfate was purchased from ICN Biomedicals (Solon,
OH) and was used without further purification. Mini-dialysis
flotation devices were acquired from Pierce (Rockford, IL).
Polynucleotides were purchased from GE Healthcare (Piscataway,
NJ). The concentrations of the polynucleotide solutions were
determined by UV spectroscopy, using the following molar
extinction coefficients: ε264 = 8520 M-1 cm-1 base-1 for poly-
2.03 (m, 2H), 1.94 (m, 1H), 1.40 (m, 54H); MS (MALDI-TOF)
calcd for C74H113N9O27S2Naþ (M þ Na)þ 1646.86, found
1647.19.
(iv) Preparation of 4. In a 10 mL round-bottom flask, 4a
(7.1 mg, 0.090 mmol) was dissolved in a 1:1 TFA/CH2Cl2 mixture
(2 mL) and the solution stirred at room temperature for 3 h.
The solvent was removed under vacuum, and the residue
was dissolved in deionized water (20 mL). The aqueous layer
was washed with ether (3 ꢀ 20 mL). Lyophilization yielded 3 as a
(dT), and ε260 = 6000 M-1 cm-1 bp-1 for poly(dA) poly(dT).
3
Oligonucleotides were synthesized and purified by IDT
(Coralville, IA). 1H NMR spectra were recorded on a JEOL
(Tokyo, Japan) ECA 500 MHz FT-NMR spectrometer. MS
(MALDI-TOF) spectra were recorded using a Kratos (Columbia,
MD) analytical KOMPACT SEQ mass spectrometer. UV spectra
were recorded on a Varian (Walnut Creek, CA) Cary 1E UV-vis
spectrophotometer. FID assays were conducted using a Photon
Technology International (Lawrenceville, NJ) instrument. Iso-
thermal titration calorimetric measurements were performed on a
MicroCal (Piscataway, NJ) VP-ITC isothermal titration calori-
meter. Circular dichroism spectra were recorded on a JASCO
(Easton, MD) J-810 spectropolarimeter equipped with a thermo-
electrically controlled cell holder. Differential scanning calori-
metric measurements were taken on a MicroCal VP-DSC
differential scanning calorimeter.
1
yellow solid (9 mg, 90%): H NMR (CD3OD) δ 8.60 (s, 1H),
8.20-8.40 (m, 4H), 7.8-7.84 (m, 2H), 5.40 (br, 1H), 5.37 (m,
1H), 5.11 (m, 1H), 4.90 (m, 1H), 4.50 (m, 2H), 4.23 (m, 1H), 4.09
(m, 2H), 3.82 (m, 4H), 3.76 (m, 2H), 3.67 (m, 2H), 3.44-3.56
(m, 8H), 3.00-3.30 (m, 10H), 2.84-2.86 (m, 4H), 2.70-2.78
(m, 6H), 2.69 (m, 4H), 2.35 (m, 6H), 2.03 (m, 2H), 1.94 (m, 1H);
MS (MALDI-TOF) calcd for C44H65N9O15S2Naþ (M þ Na)þ
1047.2, found 1046.9.
Preparation of Poly(dA) 2Poly(dT). The poly(dA) poly-
3
3
(dT) duplex (100 μM/triplet) and poly(dT) (100 μM/triplet) were
dissolved in a mixture (1.5 mL) of sodium cacodylate (SC,
10 mM, pH 6.8), KCl (150 mM), and EDTA (0.5 mM). The
mixture was heated at 90 °C for 10 min, slowly cooled to room
temperature, and incubated at 4 °C for 12 h to maximize the
extent of DNA triplex formation.
(i) Preparation of 3a. To an anhydrous pyridine solution
(2 mL) of compound 12 (18 mg, 0.014 mmol) were added
compound 5 (7.6 mg, 0.015 mmol) and DMAP (catalytic
amount). After the mixture had been stirred under N2 at room
temperature overnight, the organic solvent was removed under
vacuum. Flash chromatography of the residue (6% MeOH in
CH2Cl2) yielded the desired product as a white solid (15 mg,
Isothermal Titration Calorimetry (ITC). Into a mixture
(1.42 mL) of a poly(dA) 2poly(dT) DNA solution (100 μM),
3
sodium cacodylate (10 mM, pH 6.8), KCl (150 mM), and EDTA
(0.5 mM) in a sample cell at 20 °C was constantly injected an
aliquot of a mixture (10 μL) of the ligand of interest (1-200 μM),
sodium cacodylate (10 mM, pH 6.8), KCl (150 mM), and EDTA
(0.5 mM) through a rotary syringe. The interval between each
injection was 300 s, and the duration of each injection was
20 s. The syringe rotated at 260 rpm. The calorimetric spectrum
was recorded after each injection and was processed using
Origin version 5.0. The spectra obtained from injection of the
ligand solution at the same concentration into a buffer solution
[10 mM sodium cacodylate, 150 mM KCl, and 0.5 mM EDTA
(pH 6.8)] at 20 °C were used as blanks. Integration of the area
under each heat burst curve yielded the heat given off upon each
injection.
1
86%): Rf = 0.33 (silica gel, 6% MeOH in CH2Cl2); H NMR
(CD3OD) δ 8.74-8.77 (m, 4H), 5.40 (br, 1H), 5.37 (m, 1H), 5.11
(m, 1H), 4.90 (m, 1H), 4.23 (m, 1H), 4.09 (m, 2H), 3.82 (m, 4H),
3.76 (m, 2H), 3.67 (m, 2H), 3.44-3.56 (m, 6H), 3.00-3.30
(m, 9H), 2.84-2.86 (m, 4H), 2.70-2.78 (m, 6H), 2.69 (m, 4H),
2.35 (m, 6H), 2.03 (m, 2H), 1.94 (m, 1H), 1.40 (m, 54H); MS
(MALDI-TOF) calcd for C77H119N11O28S2 1610.96, found
1611.56.
(ii) Preparation of 3. In a 10 mL round-bottom flask, 3a
(15 mg, 0.090 mmol) was dissolved in a 1:1 TFA/CH2Cl2 mixture
(2 mL) and the solution stirred at room temperature for 3 h. The
solvent was removed under vacuum, and the residue was
dissolved in deionized water (20 mL). The aqueous layer was
washed with ether (3 ꢀ 20 mL). Lyophilization yielded 3 as a
yellow solid (9 mg, 90%): 1H NMR (CD3OD) δ 8.74-8.77
(m, 4H), 5.40 (br, 1H), 5.37 (m, 1H), 5.11 (m, 1H), 4.90 (m, 1H),
4.90 (q, 2H) 4.23 (m, 2H), 4.09 (m, 2H), 3.82 (m, 6H), 3.76 (m,
6H), 3.67 (m, 2H), 3.44-3.56 (m, 6H), 3.00-3.30 (m, 12H),
2.84-2.86 (m, 6H), 2.70-2.78 (m, 8H), 2.69 (m, 4H), 2.45 (m,
2H), 2.03 (m, 2H), 1.94 (m, 1H), 1.45 (m, 2H).
To calculate the actual heat produced from binding of ligand
to DNA triplex, the following equation was used.
ΔHactual ¼ ΔHmeasured - ΔHblank
where ΔHactual is the actual heat produced by the binding of
ligand to the DNA triplex, ΔHmeasured is the measured heat from
the titration curve, and ΔHblank is the heat produced from
injection of ligand into the buffer solution (blank).
UV Denaturation. The UV denaturation samples (1 mL)
were prepared by mixing the poly(dA) 2poly(dT) DNA (15 μM/
3
(iii) Preparation of 4a. To an anhydrous pyridine solution
(5 mL) of compound 12 (10.7 mg, 0.008 mmol) were added
compound 6 (9.3 mg, 0.027 mmol) and DMAP (catalytic
amount). After the mixture had been stirred at room temperature
overnight, the organic solvent was removed under vacuum. Flash
chromatography of the residue (5% MeOH in CH2Cl2) yielded
the desired product as a white solid (7.1 mg, 86%): Rf = 0.60
triplet), sodium cacodylate (10 mM, pH 6.8), KCl (150 mM),
EDTA (0.5 mM), and one of the intercalator-neomycin con-
jugates (1-4) at various concentrations (0, 1, 2, 4, 10, 15, and
25 μM). The UV melting spectra of these samples in 1 cm path
length quartz cuvettes were recorded at 260 and 280 nm as a
function of temperature (5-95 °C, heating rate of 0.2 °C/min).
The melting temperature was determined as the one that has the
peak value in the first derivative of the melting curve.
1
(silica gel, 10% MeOH in CH2Cl2); H NMR (CD3OD) δ 8.60
(s, 1H), 8.20-8.40 (br, 1H), 5.37 (m, 1H), 5.11 (m, 1H), 4.90
(m, 1H), 4.23 (m, 1H), 4.09 (m, 2H), 3.82 (m, 4H), 3.76 (m, 2H),
3.67 (m, 2H), 3.44-3.56 (m, 6H), 3.00-3.30 (m, 9H), 2.84-
2.86 (m, 4H), 2.70-2.78 (m, 6H), 2.69 (m, 4H), 2.35 (m, 6H),
Circular Dichroism (CD) Titration Measurements. Into
a mixture (1.8 mL) of a poly(dA) 2poly(dT) DNA solution
(50 μM/base triplet), sodium cacodylate (10 mM, pH 6.8), KCl
3
(150 mM), and EDTA (0.5 mM) in a 1 cm path length quartz

Article
Biochemistry, Vol. 49, No. 26, 2010 5543
Scheme 1 a
a(a) 2,4,6-Triisopropylbenzenesulfonlyl chloride, pyridine, room temperature; (b) 1,2-aminothiolethane, Na, EtOH; (c) TCDP, DCM,
room temperature; (d) 7 or 8, CH2Cl2; (e) TFA/CH2Cl2.
cuvette at 20 °C were injected aliquots (0.6-40 μL) of the
intercalator-neomycin stock aqueous solution. The solution
was then mixed by gentle inversion of the close capped cuvette
several times. The interval between each injection was 10 min.
The circular dichroism spectra were recorded as a function of
wavelength (200-350 nm).
A concentrated solution of compound (100 μM to 10 mM)
was added, and the fluorescence was measured after incubation
at 10 °C for 5 min. The addition of compound was continued
until the fluorescence reached saturation. For all titrations, final
concentrations were corrected for dilution (<5% of the total
volume).
Competition Dialysis Measurements. Nucleic acid solu-
tions were prepared in phosphate buffer (8 mM, pH 7.0) and NaCl
(185 mM) to yield a final concentration of 75 μM (per monomeirc
unit of each polymer). The nucleic acid solution (200 μL) was
placed into a mini-dialysis unit and then allowed to equilibrate
against a phosphate buffer (400 mL) of ligand (1 μM) at room
temperature for 72 h. At the end of the experiment, nucleic acid
samples (180 μL) were carefully removed and were taken to a
final concentration of sodium dodecyl sulfate [SDS, 1% (w/v)].
After equilibration for 2 h, the concentration of ligand was
determined spectroscopically. An appropriate correction was
made due to volume changes.
For the FID assay using the plate reader, the procedures were
as follows. The solution of poly(dA) 2poly(dT) was incubated
3
with thiazole orange for 30 min prior to use for FID titration.
Each well of a 96-well plate was loaded with a poly(dA) 2poly(dT)
3
solution (200 μL each). A concentrated solution of ligand (1-8)
(9.35-935 μM) was added, and the fluorescence was measured after
incubation for 5 min. The 96-well plate was read in triplicate on a
Cary eclipse plate reader fluorometer with advanced reads software
(excitation at 504 nm, emission at 532 nm, 430-1100 nm cutoff
filter) (no ligand, 100% fluorescence; no DNA, 0% fluorescence).
Fluorescence readings are reported as percent fluorescence relative
to control wells.
The following nucleic acids (47) were used in the experiments:
16S A-site rRNA, i-motif, poly(dA) poly(rU), poly(rA)
3
3
RESULTS AND DISCUSSION
poly(dT), poly(dG) poly(rC), poly(dA-dT), Clostridium perfrin-
3
gens DNA, Micrococcus lysodeikticus DNA, calf thymus DNA,
Synthesis of Naphthalene diimide-Neomycin and
Anthraquinone-Neomycin Conjugates. We recently prepared
two intercalator-neomycin conjugates (1 and 2) by tethering the
intercalator moiety at the 50-OH position of neomycin (44, 45).
The synthesis of 3 and 4 in the study presented here adopted the
same synthetic strategy, in which the 50-OH position of neomycin
was selected to tether the intercalators because of the ease of
modification at this position (45, 48, 49). Typically, reaction of
t-Boc-protected neomycin with 2,4,6-triisopropylbenzenesulfonlyl
chloride was followed by treatment of 1,2-aminothiolethane to
yield compound 11 (Scheme 1). The amino group of 11 was
further converted into an isothiocyanate group by reaction with
poly(dA) 2poly(dT), poly(dA) poly(dT), poly(dA), poly(dT),
3
3
poly(rA) 2poly(rU), poly(rA) poly(rU), poly(rA), and poly(rU).
3
3
Fluorescence Intercalator Displacement Assay (FID).
Thiazole orange (700 nM) was dissolved in a buffer solution
[10 mM sodium cacodylate, 150 mM KCl, and 0.5 mM EDTA
(pH 6.8 or 5.5)], and its fluorescence was recorded (excitation at
504 nm, emission at 520-600 nm). The triplex deoxynucleotide
hairpin 50-dA12-x-dT12-x-dT12-30 (where x is hexaethylene glycol)
was added to the thiazole orange solution to yield a final DNA
concentration of 100 nM (per strand), and the fluorescence was
measured again and normalized to 100% relative fluorescence.

5544 Biochemistry, Vol. 49, No. 26, 2010
Xue et al.
F
IGURE 2: Graphical representationofthe thiazoleorangedisplacementassay. (A) Raw emissiondataof1.25μM thiazoleorangeuponexcitation
at 534 nm with buffer only (O) and after addition of 0.88 μM poly(dA) 2poly(dT) triplex (b). The BQQ-neomycin conjugate was then titrated
3
from 0.25 μM to 1.06 mM. (B) Decrease in the fluorescence intensity of the complex (DNA-thiazole orange) upon addition of aliquots of
the BQQ-neomycin conjugate. (C) Assuming a linear relationship between the changes in fluorescence intensity with the fraction of thiazole
orange displaced results in an S-shaped binding isotherm. This graph allows determination of the concentration of ligands needed to displace half
of the thiazole orange from the DNA triplex. Buffer conditions: 150 mM KCl, 10 mM SC, 0.5 mM EDTA, pH 6.8, 0.88 μM poly(dA) 2poly(dT)/
3
base triplet, 1.25 μM TO.
1,10-thiocarbonyldi-2-(1H)-pyridone (TCDP) to yield 12 (37).
Table 1: AC50 Values for Binding of Various Neomycin Conjugates to the
DNA Triplexa
Subsequently reacting 12 with an intercalator (7 or 8) yielded 3a
or 4a, with a thiourea linkage in decent yields. Treatment of 3a
and 4a with trifluoroacetic acid (TFA) removed the acid labile
Boc-protecting groups to produce 3 and 4, respectively, in quanti-
tative yields. It is noteworthy that compound 12 has broad app-
lications in terms of conjugation of neomycin with other moieties
containing amino groups (Scheme 1) (37, 50).
FID Assay as a Rapid Probe for Conjugate Affinities.
The fluorescence intercalator displacement (FID) method, a
technique complementing the limitations of ITC in calculating
the intrinsic affinities, has been introduced by Boger (51). In this
method, an intercalator such as ethidium bromide (EB) or
thiazole orange (TO) intercalates into a DNA triplex to form a
complex solution. The bound intercalator fluoresces more sig-
nificantly than the free intercalator. Titration of a competitive
ligand that has a high binding affinity for the DNA triplex into
the solution will in principle displace the bound intercalator. The
amount of displaced bound intercalator can be measured as a
function of the decrease in fluorescence; ethidium bromide, which
intercalates into nucleic acids with a moderate affinity (51), is
known to be displaced by a competitive ligand. Thiazole orange
was used in our assay because it gave much greater fluorescence
enhancement (3000-fold increment) upon intercalation into
DNA than ethidium bromide (20-fold increment) (52).
aminoglycoside
conjugate
AC50 (50-dA12-x-
dT12-x-dT12-30)
AC50 [poly(dA)
2poly(dT)]
3
6
1.59 ( 0.04 μM
4.4 ( 0.7 μM
7.2 ( 0.9 μM
124 ( 18 nM
138 ( 20 nM
366 ( 13 nM
1.56 ( 0.29 μM
3.0 ( 0.6 μM
8
7
2
379 ( 86 nM
4
713 ( 123 nM
1.78 ( 0.32 μM
5.37 ( 1.46 μM
47.4 ( 2.1 μM
1
3
neomycin
aBuffer conditions: 150 mM KCl, 10 mM SC, 0.5 mM EDTA, and 100
nM 50-dA12-x-dT12-x-dT12-30/strand with 700 nM TO or 0.88 μM poly-
(dA) 2poly(dT)/base triplet with 1.25 μM TO.
3
affinity was observed in the experiments with the 50-dA12-x-dT12-
x-dT12-30 triplex. The AC50 of neomycin (47.4 μM) is approxi-
mately 100-fold higher than that of 2 (379 nM) and approxi-
mately 50-fold higher than that of 4 (713 nM). Surprisingly, the
AC50 value of 1 is smaller than that of 3 even though 3 has a larger
surface area for interaction with DNA than 1. It is noteworthy
that the trend of AC50 values for intercalators follows the same
pattern observed for intercalator-neomcyin conjugates. In parti-
cular, the rationally designed triplex-specific ligand BQQ has the
lowest AC50 value, indicating the highest affinity for the DNA
triplex among the tested intercalators. When the FID experi-
The displacement assays were first performed as complete
titrations on a fluorometer (Figure 2) and were then run (in
triplicate) on a 96-well plate reader at a salt concentration of
ments were conducted with the poly(dA) poly(dT) duplex,
3
150 mM KCl (Figure 1a-c). The polynucleotide triplex poly(dA)
thiazole orange could not be displaced by 10 mM neomycin,
suggesting that the affinity of the aminoglycoside is 2-3 orders of
magnitude lower for the AT-rich DNA duplex than for the AT-
rich DNA triplex.
3
2poly(dT) and a smaller intramolecular triplex hairpin
50-dA12-x-dT12-x-dT12-30 were used to assess the affinities of
the conjugates. The AC50 values reported in Table 1 represent the
ligand concentrations required to displace 50% of thiazole
orange from the triplex, as measured by a 50% reduction of
the initial bound thizaole orange fluorescence. The AC50 values
for different intercalators and intercalator-neomycin conjugates
are listed in Table 1. 2 has the lowest AC50 value among all
the intercalator-neomycin conjugates, suggesting that it binds
to the DNA triplex more tightly than other conjugates. The
UV Denaturation of Poly(dA) 2Poly(dT) with Inter-
3
calator-Neomycin Conjugates. The thermal stability of DNA
triple-helical structures can be examined using UV denatura-
tion. Biphasic transitions are commonly observed when the UV
spectrum of the DNA triplex is monitored as a function of
temperature, which represents dissociation of the DNA triplex
into its counterpart duplex at lower temperatures and further
dissociation of the resulting DNA duplex into single-stranded
structures at higher temperatures. Measuring the melting tem-
peratures of the DNA triplex in the presence of binding ligands is
rank order for binding to poly(dA) 2poly(dT) given by the
3
AC50 values is as follows: neomycin (3 μM) < 3 (1.56 μM) < 1
(366 nM) < 4 (138 nM) < 2 (124 nM). A similar trend in binding

Article
Biochemistry, Vol. 49, No. 26, 2010 5545
Table 2: UV Melting Temperatures Recorded When Poly(dA) 2Poly(dT)
3
Dissociated in the Presence of Intercalator-Neomycin Conjugates (1-4) at
Various Concentrationsa
concentration (μM)
Tm3f2
Tm2f1
1
0
1
2
4
34
72
72
72
73
43
56
59
2
3
0
2
4
34
72
-
-
80 (Tm3f1
)
)
86 (Tm3f1
F
IGURE 3: Representative UV melting profiles of poly(dA) 2poly-
3
0
1
2
4
34
54
65
70
72
72
73
75
(dT) at 260 nm in the absence (9) and presence of neomycin [4 μM
([)], neomycin and 7 [4 μM each (1)], 7 [4 μM (b)], and 3 [4 μM (2)].
Experimental conditions: sodium cacodylate buffer (10 mM, pH 6.8),
KCl (150 mM), and EDTA (0.5 mM). [DNA] = 15 μM per base
triplet. The y-axis has been artificially offset to differentiate the
melting curves.
4
0
1
2
4
34
60
68
74
72
74
74
80
2poly(dT) increases in the following order: neomycin < 1 < 3 <
4 < 2. Interestingly, the strength of stabilizing poly(dA) 2poly-
3
(dT) by intercalators 5, 6, 7, and 8 at 4 μM showed the same order
exhibited by intercalator-neomycin conjugates (Tables 1 and 2
of the Supporting Information), suggesting that the increasing
surface area of the intercalator moiety is clearly an important
factor in recognition of the DNA triplex.
aTm3f2 is thehe melting temperature representing the dissociation of
poly(dA) 2poly(dT) to poly(dA) poly(dT) and poly(dT). Tm2f1 is the
3
3
melting temperatures representing the dissociation of poly(dA) poly(dT)
3
to poly(dA) and poly(dT).
Competition Dialysis of Intercalator-Neomycin Conju-
gates with Different Structures of Nucleic Acids. Competi-
tion dialysis is a quick and convenient method developed by
Chaires (47, 54) for simultaneously determining the binding
preference of ligands for different structures of nucleic acids.
The nucleic acid solutions (75 μM per monomeric unit of each
polymer) in mini-dialysis units are allowed to equilibrate against
a large excess of the desired ligand (1 μM). After the bound ligand
had dissociated from nucleic acids via use of a surfactant (SDS),
the concentration of the ligand was measured spectroscopically.
The amount of detected ligand in each nucleic acid solution
corresponds to its binding affinity for this nucleic acid. Our
previous competition dialysis study revealed that 2 binds pre-
ferentially to DNA or RNA triple-helical structures while having
minimum binding to the corresponding single-stranded and
duplex nucleic acids. In this study, competition dialysis experi-
ments with 1, 3, and 4 as well as their corresponding intercalators
(5, 7, and 8) against 20 different types of nucleic acids, including
G-quadruplex and triplex, were conducted.
a quick and unambiguous way to simultaneously determine
the relative strength of ligands on stabilization of the DNA
triplex and the selectivity of ligands between the DNA triplex
and duplex. A DNA polynucleotide triplex such as poly(dA)
3
2poly(dT) was used as a model DNA triplex in UV denaturation
because of its clear transitions of triplex into duplex and duplex
into random coil structures. Under our experimental condi-
tions, in the absence of ligands, the melting temperatures of
poly(dA) 2poly(dT) dissociating into poly(dA) poly(dT) and
3
3
poly(dT) and poly(dA) poly(dT) dissociating into poly(dA)
3
and poly(dT) were 34 and 72 °C, respectively. Our UV denatura-
tion results suggested that all four intercalator-neomycin con-
jugates dramatically stabilized poly(dA) 2poly(dT) and had little
effect on its duplex, poly(dA) poly(dT) (Table 2). Among the four,
compound 2 exhibited the greatest stabilization on poly(dA)
3
3
3
2poly(dT). In the presence of 2 (4 μM), only one melting transi-
tion at 86 °C was observed (Figure 1 of the Supporting Informa-
tion), indicating the merging of triplex to duplex and duplex to
single-strand transitions (53). In contrast, the UV melting tem-
peratures representing the triplex to duplex transition in the
presence of neomycin, 1, 3, and 4 at the same concentration
(4 μM) were 40, 58, 70, and 74 °C, respectively (Table 2). In all
cases, the changes in DNA duplex melting temperature were
The concentration of the ligand in each individual nucleic
acid solution is determined via subtraction of the ligand concen-
tration in the calf thymus DNA solution, a typical B-form nucleic
acid structure (Figure 4). Calf thymus DNA is chosen because
according to the UV denaturation studies, these intercalator-
neomycin conjugates have minimal binding affinity for it. Our
results show that in general, compounds 1, 3, and 4 do
not bind to single-stranded nucleic acids. Just like 2, all three
intercalator-neomycin conjugates tested here bind preferentially
subtle. The stabilization of poly(dA) 2poly(dT) seems to result
3
from the covalent attachement of the intercalator and neomycin
since a mixture of intercalator and neomycin does not show the
equivalent stabilization. For instance, the melting temperature
of poly(dA) 2poly(dT) in the presence of 7 (4 μM) and neomycin
to poly(dA) 2poly(dT) while having little binding affinity for
3
3
(4 μM) was 50 °C, ∼20 °C lower than that in the presence of 3
poly(dA) poly(dT). This observation unambiguously supports
3
at the same concentration (4 μM) (Figure 3). All of the described
our previous conclusions that intercalator-neomycin conjugates
favor triple-helical DNA structures. Compounds 1 and 4 bind to
results here indicate that the strength of stabilizing poly(dA)
3

5546 Biochemistry, Vol. 49, No. 26, 2010
Xue et al.
F
IGURE 4: Competition dialysis results of 1, 3, and 4 as well as their corresponding intercalators 5, 7, and 8 (1 μM) with various types of nucleic
acids (75 μM). Buffer: Na2HPO4 (6 mM), NaH2PO4 (2 mM), Na2EDTA (1 mM), NaCl (185 mM), and pH 7.0.
poly(dG) poly(dC), while 3 does not bind to it at all. All three
intercalator-neomycin conjugates to some extent have binding
UV Thermal Denaturation, CD, and Fluorescence Spec-
troscopy. To understand the binding of our intercalator-
3
affinity for DNA-RNA hybrid sequences, such as poly(dA)
neomycin conjugates with poly(dA) 2poly(dT), we sought to
3
3
poly(rU), which are know to be A-form nucleic acid struc-
tures (49).The competition dialysis results for the intercalators
(5, 7, and 8) show patterns different from those of 1, 3, and 4,
suggesting that the selectivity in binding of 1, 3, and 4 to different
nucleic acids results from the combination of groove binding and
stacking interactions, not simply from the base stacking interac-
tions of the intercalator.
investigate the binding site sizes of 1-4 with poly(dA) 2poly(dT)
3
using UV thermal denaturation and circular dichroism (CD)
spectroscopy. Binding of the intercalator-neomycin conjugates
(1-4) with poly(dA) 2poly(dT) slightly altered the conforma-
3
tion of the DNA triplex secondary structure, which was conse-
quently detected by circular dichroism spectroscopy. A much
larger change in Tm was observed using thermal denaturation
studies (Table 2). Tm changes varied linearly with an increase in
concentration of the intercalator-neomycin conjugates, and a
Determining the Binding Site Size of Intercalator-
Neomycin Conjugates with Poly(dA) 2Poly(dT) Using
3

Article
Biochemistry, Vol. 49, No. 26, 2010 5547
F
(dT) as determined by UV thermal denaturation. (C) Plot for the determination of the binding site of poly(dA) 2poly(dT) and naphthalene
IGURE 5: (A and B) Representative plots for the determination of binding site sizes of intercalator-neomycin conjugates with poly(dA) 2poly-
3
3
diimide. The graph shows the change in fluorescence of naphthalene diimide when it is titrated with poly(dA) 2poly(dT). Naphthalene diimide
was excited at 356 nm, and the emission scans were recorded from 370 to 500 nm: 15 μM poly(dA) poly(dT)/base triplet, 0.5-15 μM
3
3
naphthalene diimide, 10 °C. n is the number of base triplets per drug. Buffer conditions: sodium cacodylate (10 mM), EDTA (0.5 mM), KCl
(150 mM), and pH 5.5.
plot of Tm versus ligand concentration was made to determine the
binding site size. A transition point resulting from the slope
change was clearly observed in all of the plots, when the primary
(KT) at different temperatures for analysis of interactions bet-
ween the intercalator-neomycin conjugate and poly(dA)
3
2poly(dT) were further derived from the following integrated
available sites in poly(dA) 2poly(dT) were saturated by the
van’t Hoff equation using the calculated KT values.
3
m
intercalator-neomycin conjugate. Our results suggest that the
binding site sizes of 1-4 with poly(dA) 2poly(dT) are 7, 7.5, 7.5,
KT
m
3
KT
¼
ꢀ
ꢁ
ΔCp=R
and 7.5, respectively (Figure 5). The values of binding site size
described here are reasonable compared to that of neomycin and
conjugates (∼6-6.5) reported previously using CD spectroscopy
(27, 44, 45). The observed similarity in binding site sizes implies
a similarity in the binding modes of compounds 1-4 with
Tm
T
ΔCpTð1=Tm - 1=TÞ
- 1=TÞe
T =Rð1=Tm
e- ΔH
where ΔHT is the observed enthalpy change associated with the
binding of an intercalator-neomycin conjugate to poly(dA)
2poly(dT) and ΔCp is the heat capacity change for binding. ΔHT
was determined using isothermal titration calorimetry (ITC), in
which small aliquots of a buffered intercalator-neomycin con-
jugate were injected into a solution containing a large excess of
3
poly(dA) 2poly(dT).
3
Extrapolating Thermodynamic Parameters from the
Interactions between Intercalator-Neomycin Conjugates
and Poly(dA) 2Poly(dT). Our ultimate understanding of
3
interactions between intercalator-neomycin conjugates and
poly(dA) 2poly(dT) in terms of possible numbers of binding
3
poly(dA) 2poly(dT) is achieved by acquiring a complete set of
3
sites. ΔCp was derived from the slope of the linear relationship in
which the binding enthalpy (ΔHT) was plotted as a function of
temperature (T).
thermodynamic parameters. A method for extrapolating thermo-
dynamic parameters from experimental data was developed and
optimized by McGhee and others (46, 55); they used the
following equation.
All of the experiments used for calculations of thermodynamic
parameters were conducted at two different pH values (6.8 and
5.5). The ΔHHS values measured by DSC for the dissociation of
poly(dA) 2poly(dT) into poly(dA) poly(dT) and poly(dT) at pH
1
1
R
-
¼
lnð1 þ KT LÞ
m
Tm0 Tm
nðΔHHS
Þ
3
3
5.5 and 6.8 were 1.67 and 1.59 kcal/mol, respectively (Figure 6),
where Tm0 is the melting temperature representing the dissocia-
tion of the DNA triplex into the duplex in the absence of ligand,
Tm is the melting temperature representing the dissociation of the
DNA triplex into the duplex in the presence of an intercalator-
neomycin conjugate, R is the gas constant, ΔHHS is the enthalpy
change corresponding to the dissociation of the DNA triplex
into the duplex in the absence of ligand, L is the free ligand
concentration at Tm which is estimated to be one-half of the total
drug concentration, and n is the binding site size. The melting
temperatures were determined using UV spectroscopy as de-
scribed above. The enthalpy change (ΔHHS) was measured using
differential scanning calorimetry (DSC), in which the heat
produced from the dissociation of the DNA triplex was plotted
as a function of temperature (20-90 °C). The binding site size
was obtained from UV thermal denaturation and CD titration
experiments as described above. After this equation had been
suggesting that poly(dA) 2poly(dT) was more stable at a lower
3
pH. This observation is consistent with the common belief that
the stability of the DNA triplex increases with a decrease in pH
because of suppression of the electrostatic repulsions between
DNA backbones under lower-pH conditions. A similar trend
was observed for the dissociation of poly(dA) poly(dT) into
3
poly(dA) and poly(dT), in which the ΔHHS value at pH 5.5 (5.00
kcal/mol) was 150 cal/mol higher than that at pH 6.8 (4.87 cal/mol).
Figure 7a shows the CD spectra of the preformed poly-
(dA) poly(dT) duplex and poly(dA) 2poly(dT) triplex in the
3
3
absence (scans a and c) and presence of the tightest binding
ligand 2, BQQ-neomycin (scans b and d). The duplex and triplex
DNA have signature CD spectra which have been preserved
upon addition of the conjugate, suggesting that little conforma-
tional change takes place when drug is added. Figure 7a shows
that when ligand 2 (BQQ-neomycin) binds to the duplex or
triplex, no red or blue shift is observed in the CD spectrum of the
preformed duplex or triplex. Figure 7b shows the continuous
variation experiments with poly(dA) and poly(dT) in the absence
solved, the association constant at Tm (KT ) in the presence of the
m
intercalator-neomycin conjugate at a desired concentration was
obtained. The more meaningful and useful association constants

5548 Biochemistry, Vol. 49, No. 26, 2010
Xue et al.
F
conditions: sodium cacodylate (10 mM), EDTA (0.5 mM), and KCl (150 mM).
IGURE 6: DSC melting profile of poly(dA) 2poly(dT) in the absence of binding ligand at pH 5.5 (left) and pH 6.8 (right). Experimental
3
and presence of drug 3. All intercalators and conjugates exhibit
similar minima at 66% dT, suggesting that the three-strand DNA
triplex is present in solution in the absence and presence of the
drugs.
intrinsic interaction between the intercalator-neomycin conju-
gate and poly(dA) 2poly(dT) because neomycin is substantially
3
protonated at this pH value and thus the protonation heat is
minimized. However, studying such a binding event at pH 5.5 can
lead to some practical problems. The interactions between these
ITC experiments were conducted to determine the enthalpy
changes in the binding of intercalator-neomycin conjugates to
conjugates and poly(dA) 2poly(dT) intend to become more
3
poly(dA) 2poly(dT) at pH 5.5 and 6.8 (Figures 13-20 of the
entropy-driven at low pH; therefore, the intensity of ITC signals
decreases dramatically, necessitating the use of higher concentra-
tions of samples.
3
Supporting Information). The preformed DNA triplex solution
was incubated in a sample cell at the temperatures which were
lower than 20 °C to ensure the presence of DNA triplex (Tm
=
To calculate the ΔCp values, the enthalpy changes (ΔHT) were
plotted versus temperature and fitted via linear regression
analysis. The slope of linear fitting represents the ΔCp in the
34 °C). The enthalpy changes (ΔHT) were recorded as a heat
burst curve when small portions of the buffered intercalator-
neomycin conjugate were injected into the DNA solution. The
area under each heat burst curve was integrated and recorded as
the ΔHT values. For instance, when the pH of the solution was
5.5, the ΔHT values at 10 °C for neomycin, 1, 2, 3, and 4 were
-6.4 ( 0.1, -3.2 ( 0.1, -6.8 ( 0.1, -10.9 ( 0.2, and -15.9 ( 0.4
kcal/mol, respectively (Table 3). Under this condition, the ΔHT
values increased in the following order: 1 < 3 < 4 < 2 (which is
consistent with the order of DNA triplex stabilization derived
from UV denaturation experiments). A similar trend was also
observed when intercalator-neomycin conjugates were injected
binding of intercalator-neomycin conjugates to poly(dA)
3
2poly(dT) under this experimental condition. In all cases, nega-
tive ΔCp values were observed at pH 6.8 and 5.5 and the ΔCp
values are in general more negative at pH 6.8 than at pH 5.5
(Tables 3 and 4). Protonation heats at pH 6.8 yield a much higher
ΔCp value. In contrast, the relatively low ΔCp values at pH 5.5
indicate a more intrinsic drug-triplex interaction. Additionally,
the enthalpy changes in the binding of 3 and 4 with triplex
poly(dA) 2poly(dT) were -3.7 and -7.8 kcal/mol greater,
3
respectively, than those with the duplex poly(dA) poly(dT),
3
into the poly(dA) 2poly(dT) solution at different temperatures
suggesting that interactions between the intercalator-neomycin
conjugate and the DNA triplex are more enthalpy-driven than
those with the DNA duplex.
3
and pH values (Table 3). The enthalpy change in the binding
of neomycin to poly(dA) 2poly(dT) at pH 6.8 was somewhat
3
different from the trend observed in the UV denaturation
The binding constant of the intercalator-neomycin conjugate
experiments. Our UV melting studies suggest that 1 has a stron-
with poly(dA) 2poly(dT) was then derived using all the para-
3
ger stabilization effect on poly(dA) 2poly(dT) than neomycin
meters described above. At pH 5.5, all intercalator-neomycin
3
at pH 6.8. For instance, the melting temperature of poly(dA)
conjugates seemed to bind poly(dA) 2poly(dT) more tightly than
3
3
2poly(dT) in the presence of 1 (4 μM) was 24 °C higher than that
in the presence of neomycin. However, at pH 6.8, the enthalpy
neomycin. The calculated binding constants increased in the
order neomycin < 1 < 3 < 4 < 2, with values of (2.7 ( 0.3) ꢀ
108 M-1 for 2, (3.7 ( 0.1) ꢀ 107 M-1 for 3, (5.5 ( 0.3) ꢀ 106 M-1
for 4, (1.9 ( 0.1) ꢀ 106 M-1 for 1, and (2.4 ( 0.1) ꢀ 105 M-1 for
neomycin (Table 3). The binding constant of 2 with poly-
change for the binding of 1 to poly(dA) 2poly(dT) was 3.2 kcal/
3
mol lower than that for the binding of neomycin to poly-
(dA) 2poly(dT) even though 1 has greater DNA triplex stabili-
3
zation than neomycin. In contrast, at pH 5.5, the enthalpy change
(dA) 2poly(dT) is (2.7 ( 0.3) ꢀ 108 M-1, which is ∼1000-fold
3
for the binding of 1 to poly(dA) 2poly(dT) was 0.9 kcal/mol
higher than that of neomycin. This observed high binding
constant of 2 is consistent with our previously published result
which showed that 2 is a very potent DNA triplex binding ligand.
The rationally designed triplex-specific binding ligand, BQQ in 2,
may play an important role in promoting significant DNA triplex
3
greater than that for the binding of neomycin to poly(dA) 2poly-
3
(dT), which was consistent with the order in which 1 stabilizes
triplex more. In addition, the enthalpy changes for the binding of
the intercalator-neomycin conjugate with poly(dA) 2poly(dT)
3
at pH 6.8 were much greater than that for the corresponding
binding at pH 5.5. This observation is attributed to the binding-
linked neomycin protonation heat. The amino groups of neo-
mycin, according to their pKa values, are not completely proto-
nated at pH 6.8. The heat produced from such amine protonation
at pH 6.8 results in an overestimation of enthalpy changes (56).
The enthalpy change measured at pH 5.5 reflects more of an
binding. The binding constant of 2 with poly(dA) 2poly(dT)
3
is ∼7.3-, ∼49-, and ∼142-fold higher than those of 4, 3, and 1,
respectively. These data, in addition to our FID AC50 values,
allow us to quantitate the relative strength of binding of the
intercalators to poly(dA) 2poly(dT). The larger the surface area
3
of the intercalator, the higher the DNA triplex binding affinity of
its neomycin conjugate. Pyrene itself does not stabilize DNA

Article
Biochemistry, Vol. 49, No. 26, 2010 5549
F
(a) Poly(dA) 2poly(dT) triplex (no ligand) [a], poly(dA) 2poly(dT) triplex (0.13 equiv of 2) [b], poly(dA) poly(dT) duplex (no ligand) [c], and
IGURE 7: CD scans for the poly(dA) poly(dT) duplex and the poly(dA) 2poly(dT) triplex in the absence and presence of 2 (BQQ-neomycin).
3 3
3
3
3
poly(dA) poly(dT) duplex (0.13 equiv of 2) [d]. Experimental conditions: sodium cacodylate (10 mM), EDTA (0.5 mM), KCl (150 mM), 10 °C,
3
and pH 5.5. (b) Continuous variation scans (left) and A260 plot (right) of dA30 (1 μM/base) and dT30 (1 μM/base) in the absence of drug (top)
and presence of napthalenediimide-neomycin conjugate 3 (rbd = 7) (bottom). Experimental conditions: sodium cacodylate (10 mM), EDTA
(0.5 mM), KCl (150 mM), 15 °C, and pH 5.5.
triplexes; therefore, its conjugate 1 has the weakest triplex binding
ability among the four. The slight discrepancy between FID
results and calorimetric data, when comparing the affinities, can
be attributed to the differences in the nature and sensitivities of
the measurements, given that the affinities are quite comparable.
The FID assay, which indirectly measures the ligand affinities,

5550 Biochemistry, Vol. 49, No. 26, 2010
Xue et al.
Table 3: Thermodynamic Profiles of Intercalator-Neomycin Conjugates (1-4) and Intercalator 7 with Poly(dA) 2Poly(dT) at pH 5.5a
3
[KCl]
(mM)
ΔHwc
(kcal/mol)
Tm0
Tm
ΔH(10 °C)
(kcal/mol)
ΔH(15 °C)
(kcal/mol)
ΔH(20 °C)
(kcal/mol)
ΔCp
KT(20 °C)
(M-1
)
ligand
(°C)
(°C)
n
(cal mol-1 K-1
)
neomycin
140
150
150
150
150
150
1.70
1.67
1.67
1.67
1.67
1.67
31.4
33.8
33.8
33.8
33.8
31.0
34.4
49.5
55.4
64.0
68.8
37.2
6.8
7
-0.6 ( 0.1 (12 °C)
-1.5 ( 0.1
-2.4 ( 0.1
-
-
-1.31 ( 0.02
-1.64 ( 0.02
-2.8 ( 0.1
-6.4 ( 0.1
-9.7 ( 0.2
-87 ( 4
-10 ( 3
-40 ( 20
-110 ( 15
-220 ( 20
-131
(2.4 ( 0.1) ꢀ 105
(1.9 ( 0.1) ꢀ 106
(5.5 ( 0.3) ꢀ 106
(3.7 ( 0.1) ꢀ 107
(2.7 ( 0.3) ꢀ 108
1.89 ꢀ 105
1
3
4
2
7
7.5
7.5
7.5
4
-2.6 ( 0.1
-6.1 ( 0.2
-8.5 ( 0.4
-0.38 ( 0.07
-5.4 ( 0.2
-7.5 ( 0.4
-1.4 ( 0.1b
-0.81 ( 0.01
aExperimental condition: sodium cacodylate (10 mM), EDTA (0.5 mM), and KCl (150 mM). bCalculated at 23 °C.
Table 4: Thermodynamic Profiles of Intercalator-Neomycin Conjugates (1-4) with Poly(dA) 2Poly(dT) at pH 6.8a
3
[KCl]
(mM)
ΔHwc
(kcal/mol)
Tm0
Tm
ΔH(10 °C)
(kcal/mol)
ΔH(20 °C)
(kcal/mol)
ΔH(5 °C)
(kcal/mol)
ΔCp
KT(20 °C)
(M-1
)
ligand
(°C)
(°C)
n
(cal mol-1 K-1
)
neomycin
150
150
150
150
150
1.59
1.59
1.59
1.59
1.59
34.4
34.4
34.4
34.4
34.4
49.5
58.0
65.0
68.0
85.0
6.5
7
-6.4 ( 0.1
-3.2 ( 0.1
-6.8 ( 0.1
-10.9 ( 0.2
-15.9 ( 0.4
-7.5 ( 0.2
-3.7 ( 0.1
-7.8 ( 0.1
-12.7 ( 0.2
-19.3 ( 0.4
-8.2 ( 0.04
-
-8.3 ( 0.8
-14.5 ( 0.1
-21.1 ( 0.4
-116 ( 4
-45 ( 1
-104 ( 10
-231 ( 6
-346 ( 13
-
-
-
-
-
1
3
4
2
7.5
7.5
7.5
aExperimental condition: sodium cacodylate (10 mM), EDTA (0.5 mM), and KCl (150 mM).
F
IGURE 8: Thermodynamics of binding interactions of ligands with the poly(dA) 2poly(dT) triplex at pH 5.5. Red bars represent ΔG, blue bars
3
ΔH, and green bars TΔS. Experimental conditions: sodium cacodylate (10 mM), EDTA (0.5 mM), and KCl (150 mM).
shows a 2-4-fold higher affinity for 1 over 3, whereas data from
Table 3 show the opposite trend, with 3 showing a 2-fold higher
affinity. Additionally, the FID measurements were performed at
pH 6.8, whereas the affinities listed in Table 3 are reported at
pH 5.5. When the FID experiments were repeated at pH 5.5, simi-
lar trends were observed, with 3 (AC50 = 408 ( 70 nM) showing
a higher AC50 than 1 (AC50 = 240 ( 20 nM). The UV thermal
denaturation temperatures at both pH 6.8 and 5.5 (Tables 2 and
3) clearly show a much larger change in Tm3f2 for 3 over 1 (70 °C
vs 50 °C at pH 6.8 and 55.9 °C vs 49 °C at pH 5.5), suggesting that
3 stabilizes the DNA triplex better than 1 at the two pH values.
Figure 8 shows the distribution of thermodynamic properties
of ligand-triplex interactions as bar graphs. The free energy for
each of the ligand has been calculated from the binding constant
by using the Gibbs free energy equation. Free energy change (red
bars), enthalpy change (blue bars), and entropic contributions
(green bars) help summarize the contribution of the individual
ligands as well as the conjugates. Three different classes of ligands
are represented in the figure with respect to binding mode.
Neomycin is a major groove binder; naphthalene diimide is a
well-known intercalator, and neomycin conjugates bind through
the dual recognition mode (major groove and intercalation). The
plot in Figure 8 is a good starting point for understanding the
contribution of thermodynamic properties during the drug-
DNA binding interactions. It is clear from the figure that bind-
ing of neomycin (groove binder) as well as naphthalene diimide
(intercalator) is largely driven by enthalpy contributions. As we
go from 1 (pyrene-neomycin) to 2 (BQQ-neomycin), an in-
crease in intercalator surface area leads to an increase in the
enthalpy of interaction, which clearly leads to a more negative free
energy of binding. However, as seen from the free energies of
interaction of neomycin, 7, and 3, the free energy ΔG3-triplex is not
a sum of free energies ΔGneomycin-triplex and ΔG7-triplex, leading to
a ΔGcoupling of ∼5 kcal/mol. While ΔH3-triplex increases substan-
tially, the corresponding increase in ΔS3-triplex is not observed,
suggesting that the conjugate pays an entropic cost of covalently
bridging neomycin with the intercalator with the given linker
length. As we proceed to the higher-affinity conjugates 2 and 4,
the entropic contribution toΔGcomplexation decreases substantially.
The thermodynamics of interaction of ligands 5, 6, and 8 with the

Article
Biochemistry, Vol. 49, No. 26, 2010 5551
triplex could not be performed because of the poor solubility of
these compounds in aqueous solution. Further studies with
different linker lengths will be beneficial in maximizing the free
energies of interaction of the dual binding modes and are
currently being explored in our laboratories.
8. Agazie, Y. M., Lee, J. S., and Burkholder, G. D. (1994) Characteriza-
tion of a New Monoclonal Antibody to Triplex DNA and Immuno-
fluorescent Staining of Mammalian Chromosomes. J. Biol. Chem.
269, 7019–7023.
9. Kopel, V., Pozner, A., Baran, N., and Manor, H. (1996) Unwinding of
the Third Strand of a DNA Triple Helix, a Novel Activity of the SV40
Large T-Antigen Helicase. Nucleic Acids Res. 24, 330–335.
10. Spitzner, J. R., Chung, I. K., and Muller, M. T. (1995) Determination
of 50 and 30 DNA Triplex Interference Boundaries Reveals the Core
DNA Binding Sequence for Topoisomerase II. J. Biol. Chem. 270,
5932–5943.
CONCLUSIONS
Decades of work in the recognition of DNA triplexes have led
to the design of intercalators that preferentially bind to DNA
triplexes, while minimizing the binding to the DNA duplex.
Addition of a groove binding DNA triplex selective ligand such
as neomycin has allowed us to achieve DNA triplex affinities that
would be difficult to attain with a univalent binding mode
without sacrificing selectivity. Our results here provide a measure
of quantification of triplex binding when the ligand surface area
is increased in the following order: pyrene < naphthalene diimide
anthraquinone < BQQ. It is not a surprise that 2 is the most
potent DNA triplex stabilizing agent among all the intercalator-
neomycin conjugates in our study because the BQQ moiety (6) is
known as a rationally designed DNA triplex-specific binding
ligand. All of the other intercalators (pyrene, naphthalene diimide,
and anthraquinone) bind to the DNA duplex as well as the DNA
triplex to some extent. The conjugates containing the intercalator
and neomycin enhance the binding affinity of the DNA triplex
via a possible cooperative binding mode. Such a “dual binding
mode” may be useful in guiding the design of novel DNA triplex
binding ligands (and perhaps other nucleic acids). The thermo-
dynamic data also raise the possibility of tuning the DNA triplex
binding strength of neomycin conjugates by simply swamping the
intercalator moiety. A large data bank of DNA intercalators has
already been established; therefore, preparation of such conju-
gates for screening the nucleic acid binding ligands is practical.
Inspection of the ligand-triplex interaction thermodynamics
shows a clear additive effect of enthalpies of interaction, and
future studies with linker length optimization can lead to even
higher-affinity ligands.
11. Cooney, M., Czernuszewicz, G., Postel, E. H., Flint, S. J., and Hogan,
M. E. (1988) Site-Specific Oligonucleotide Binding Represses
Transcription of the Human c-Myc Gene in Vitro. Science 241,
456–459.
12. Postel, E. H., Flint, S. J., Kessler, D. J., and Hogan, M. E. (1991)
Evidence that a Triplex-Forming Oligodeoxyribonucleotide Binds to
the c-Myc Promoter in HeLa Cells, Thereby Reducing c-Myc mRNA
Levels. Proc. Natl. Acad. Sci. U.S.A. 88, 8227–8231.
13. Grigoriev, M., Praseuth, D., Guieysse, A. L., Robin, P., Thuong,
N. T., Helene, C., and Harel-Bellan, A. (1993) Inhibition of Gene
Expression by Triple Helix-Directed DNA Cross-Linking at Specific
Sites. Proc. Natl. Acad. Sci. U.S.A. 90, 3501–3505.
14. Grigoriev, M., Praseuth, D., Robin, P., Hemar, A., Saison-Behmoaras,
T., Dautry-Varsat, A., Thuong, N. T., Helene, C., and Harel-Bellan, A.
(1992) A Triple Helix-Forming Oligonucleotide-Intercalator Conju-
gate Acts as a Transcriptional Repressor Via Inhibition of NF κB
Binding to Interleukin-2 Receptor a-Regulatory Sequence. J. Biol.
Chem. 267, 3389–3395.
15. Murray, J. A. H. (1992) Antisense RNA and DNA, Wiley-Liss,
New York.
~
16. Avino, A., Grimau, M. G., Frieden, M., and Eritja, R. (2004)
Synthesis and Triple-Helix-Stabilization Properties of Branched Oli-
gonucleotides Carrying 8-Aminoadenine Moieties. Helv. Chim. Acta
87, 303–316.
17. Sollogoub, M., Dominguez, B., Brown, T., and Fox, K. R. (2000)
Synthesis of a Novel Bis-Amino-Modified Thymidine Monomer for
use in DNA Triplex Stabilisation. Chem. Commun. 23, 2315–2316.
18. Kawai, K., Saito, I., and Sugiyama, H. (1998) Stabilization of
Hoogsteen Base Pairing by Introduction of NH2 Group at the C8
Position of Adenine. Tetrahedron Lett. 39, 5221–5224.
19. Gianolio, D. A., Segismundo, J. M., and McLaughlin, L. W. (2000)
Tethered Naphthalene Diimide-Based Intercalators for DNA Triplex
Stabilization. Nucleic Acids Res. 28, 2128–2134.
ꢀ ꢁ
20. Sun, J., Carestier, T., and Helene, C. (1996) Oligonucleotide Directed
Triple Helix Formation. Curr. Opin. Struct. Biol. 6, 327–333.
21. Baudoin, O., Marchand, C., Teulade-Fichou, M.-P., Vigneron, J.-P.,
Sun, J.-S., Garestier, T., Helene, C., and Lehn, J.-M. (1998) Stabiliza-
tion of DNA Triple Helices by Crescent-Shaped Dibenzophenan-
throlines. Chem.;Eur. J. 4, 1504–1508.
SUPPORTING INFORMATION AVAILABLE
NMR spectra of 3 and 4, spectra for ITC experiments of
22. Robles, J., and McLaughlin, L. W. (1997) DNA Triplex Stabilization
using a Tethered Minor Groove Binding Hoechst 33258 Analogue.
J. Am. Chem. Soc. 119, 6014–6021.
23. Scaria, P. V., and Shafer, R. H. (1991) Binding of Ethidium Bromide
to a DNA Triple Helix. J. Biol. Chem. 266, 5417–5423.
24. Pilch, D. S., Martin, M. T., Nguyen, C. H., Sun, J. S., Bisagni, E.,
Garestier, T., and Helene, C. (1993) Self-Association and DNA-
Binding Properties of Two Triple Helix-Specific Ligands: Compar-
ison of a Benzo[e]Pyridoindole and a Benzo[g]Pyridoindole. J. Am.
Chem. Soc. 115, 9942–9951.
25. Escude, C., Nguyen, C. H., Mergny, J.-L., Sun, J.-S., Bisagni, E.,
Garestier, T., and Helene, C. (1995) Selective Stabilization of DNA
Triple Helices by Benzopyridoindole Derivatives. J. Am. Chem. Soc.
117, 10212–10219.
26. Arya, D. P., Jr., Coffee, R. L., Jr., Willis, B., and Abramovitch, A. I.
(2001) Aminoglycoside-Nucleic Acid Interactions: Remarkable
Stabilization of DNA and RNA Triple Helices by Neomycin.
J. Am. Chem. Soc. 123, 5385–5395.
27. Arya, D. P., Micovic, L., Charles, I., Jr., Coffee, R. L., Jr., Willis, B.,
and Xue, L. (2003) Neomycin Binding to Watson-Hoogsteen
(W-H) DNA Triplex Groove: A Model. J. Am. Chem. Soc. 125,
3733–3744.
28. Willis, B., and Arya, D. P. (2009) Triple Recognition of B-DNA.
Bioorg. Med. Chem. Lett. 19, 4974–4979.
29. Willis, B., and Arya, D. P. (2006) Major Groove Recognition of DNA
by Carbohydrates. Curr. Org. Chem. 10, 663–673.
30. Willis, B., and Arya, D. P. (2006) An Expanding View of Aminoglyco-
side-Nucleic Acid Recognition. Adv. Carbohydr. Chem. Biochem. 60,
251–302.
compounds 1-4 titrating into a large excess of poly(dA) 2poly-
3
(dT) at pH 5.5 and 6.8, and ΔCp plots. This material is available
free of charge via the Internet at http://pubs.acs.org.
REFERENCES
1. Felsenfeld, G., Davies, D., and Rich, A. (1957) Formation of a
Three Stranded Polynucleotide Molecule. J. Am. Chem. Soc. 79,
2023–2024.
2. Radhakrishnan, I., and Patel, D. J. (1994) Solution Structure of a
Pyrimidine Purine Pyrimidine DNA Triplex Containing T AT,
3
3
3
Cþ GC and G TA Triples. Structure 2, 17–32.
3
3
3. Praseuth, D., Guieysse, A. L., and Helene, C. (1999) Triple Helix
Formation and the Antigene Strategy for Sequence-Specific Control
of Gene Expression. Biochim. Biophys. Acta 1489, 181–206.
4. Beal, P. A., and Dervan, P. B. (1991) Second Structural Motif for
Recognition of DNA by Oligonucleotide-Directed Triple-Helix
Formation. Science 251, 1360–1363.
5. Chen, F. M. (1991) Intramolecular Triplex Formation of the Pur-
ine Purine Pyrimidine Type. Biochemistry 30, 4472–4479.
3
3
6. Radhakrishnan, I., and Patel, D. J. (1993) Solution Structure of a
Purine Purine Pyrimidine DNA Triplex Containing G GC and
T AT Triplexes. Structure 1, 135–152.
3
3
3
3
7. Michel, D., Chatelain, G., Herault, Y., and Brun, G. (1992) The Long
Repetitive Polypurine Polypyrimidine Sequence (Ttccc)48 Forms
DNA Triplex with Pu-Pu-Py Base Triplets In Vivo. Nucleic Acids
Res. 20, 439–443.

5552 Biochemistry, Vol. 49, No. 26, 2010
Xue et al.
31. Arya, D. P., and Willis, B. (2003) Reaching into the Major Groove of
B-DNA: Synthesis and Nucleic Acid Binding of a Neomycin-Hoechst
33258 Conjugate. J. Am. Chem. Soc. 125, 12398–12399.
32. Shaw, N. N., and Arya, D. P. (2008) Recognition of the Unique
Structure of DNA:RNA Hybrids. Biochimie 90, 1026–1039.
33. Shaw, N. N., Xi, H., and Arya, D. P. (2008) Molecular Recognition of
a DNA:RNA Hybrid: Sub-Nanomolar Binding by a Neomycin-
Methidium Conjugate. Bioorg. Med. Chem. Lett. 18, 4142–4145.
34. Arya, D. P. (2005) Aminoglycoside-Nucleic Acid Interactions: The
Case for Neomycin. Top. Curr. Chem. 253, 149–178.
35. Arya, D. P., Coffee, R. L., Jr., and Charles, I. (2001) Neomycin-Induced
Hybrid Triplex Formation. J. Am. Chem. Soc. 123, 11093–11094.
36. Charles, I., Xi, H., and Arya, D. P. (2007) Sequence-Specific Target-
ing of RNA with an Oligonucleotide-Neomycin Conjugate. Biocon-
jugate Chem. 18, 160–169.
37. Charles, I., Xue, L., and Arya, D. P. (2002) Synthesis of Amino-
glycoside-DNA Conjugates. Bioorg. Med. Chem. Lett. 12, 1259–
1262.
38. Xi, H., Gray, D., Kumar, S., and Arya, D. P. (2009) Molecular
Recognition of Single-Stranded RNA: Neomycin Binding to Poly(A).
FEBS Lett. 583, 2269–2275.
39. Arya, D. P., Coffee, R. L., Jr., and Xue, L. (2004) From Triplex to
B-Form Duplex Stabilization: Reversal of Target Selectivity by
Aminoglycoside Dimers. Bioorg. Med. Chem. Lett. 14, 4643–4646.
40. Arya, D. P., Coffee, R. L., Jr., and Willis, A., III (2001) Triple Helix
Stabilization by Aminoglycoside Antibiotics. Abstracts of Papers,
221st National Meeting of the American Chemical Society, San
Francisco, CARB-088.
41. Arya, D. P., and Coffee, R. L., Jr. (2000) DNA Triple Helix
Stabilization by Aminoglycoside Antibiotics. Bioorg. Med. Chem.
Lett. 10, 1897–1899.
45. Xue, L., Charles, I., and Arya, D. P. (2002) Pyrene-Neomycin
Conjugate: Dual Recognition of a DNA Triple Helix. Chem. Com-
mun. 1, 70–71.
46. Doyle, M. L., Brigham-Burke, M., Blackburn, M. N., Brooks, I. S.,
Smith, T. M., Newman, R., Reff, M., Stafford, W. F., Sweet, R. W.,
Truneh, A., Hensley, P., and O’Shannessy, D. J. (2000) Measure-
ment of Protein Interaction Bioenergetics: Application to Structural
Variants of Anti-sCD4 Antibody. Methods Enzymol. 323, 207–230.
47. Ren, J., and Chaires, J. B. (2001) Rapid Screening of Structurally Selective
Ligand Binding to Nucleic Acids. Methods Enzymol. 340, 99–108.
48. Kirk, S. R., Luedtke, N. W., and Tor, Y. (2000) Neomycin-Acridine
Conjugate: A Potent Inhibitor of Rev-RRE Binding. J. Am. Chem.
Soc. 122, 980–981.
49. Arya, D. P., Xue, L., and Willis, B. (2003) Aminoglycoside
(Neomycin) Preference is for A-Form Nucleic Acids, Not just
RNA: Results from a Competition Dialysis Study. J. Am. Chem.
Soc. 125, 10148–10149.
50. Charles, I., and Arya, D. P. (2005) Synthesis of Neomycin-DNA/
peptide Nucleic Acid Conjugates. J. Carbohydr. Chem. 24, 145–160.
51. Boger, D. L., Fink, B. E., Brunette, S. R., Tse, W. C., and Hedrick,
M. P. (2001) A Simple, High-Resolution Method for Establishing
DNA Binding Affinity and Sequence Selectivity. J. Am. Chem. Soc.
123, 5878–5891.
52. Boger, D. L., and Tse, W. C. (2001) Thiazole Orange as the Fluor-
escent Intercalator in a High Resolution Fid Assay for Determining
DNA Binding Affinity and Sequence Selectivity of Small Molecules.
Bioorg. Med. Chem. 9, 2511–2518.
53. Escude, C., Nguyen, C. H., Kukreti, S., Janin, Y., Sun, J.-S., Bisagni,
E., Garestier, T., and Helene, C. (1998) Rational Design of a Triple
Helix-Specific Intercalating Ligand. Proc. Natl. Acad. Sci. U.S.A. 95,
3591–3596.
42. Arya, D. P., Shaw, N., and Xi, H. (2007) Novel Targets for Amino-
glycosides. In Aminoglycoside Antibiotics: From chemical biology to
drug discovery (Arya, D. P., Ed.) pp 289-314, Wiley, New York.
43. Xi, H., and Arya, D. P. (2005) Recognition of Triple Helical Nucleic
Acids by Aminoglycosides. Curr. Med. Chem. Anticancer Agents 5,
327–338.
44. Arya, D. P., Xue, L., and Tennant, P. (2003) Combining the Best in
Triplex Recognition: Synthesis and Nucleic Acid Binding of a BQQ-
Neomycin Conjugate. J. Am. Chem. Soc. 125, 8070–8071.
54. Ren, J., and Chaires, J. B. (1999) Sequence and Structural Selectivity
of Nucleic Acid Binding Ligands. Biochemistry 38, 16067–16075.
55. McGhee, J. D. (1976) Theoretical Calculations of the Helix-Coil
Transition of DNA in the Presence of Large, Cooperatively Binding
Ligands. Biopolymers 15, 1345–1375.
56. Barbieri, C. M., and Pilch, D. S. (2006) Complete Thermodynamic
Characterization of the Multiple Protonation Equilibria of the
Aminoglycoside Antibiotic Paromomycin:
A Calorimetric and
Natural Abundance 15N NMR Study. Biophys. J. 90, 1338–1349.