Towards sequence selective DNA binding: Design, synthesis and DNA binding studies of novel bis-porphyrin peptidic nanostructures

Article abstract of DOI:10.1039/b803281e

A new series of peptidic nanostructures bearing two intercalating moieties was designed and synthesized to achieve selective recognition of DNA sequences. A cationic porphyrin was attached to a glutamic acid side chain and the latter introduced into a pep

Full text of DOI:10.1039/b803281e

View Article Online / Journal Homepage / Table of Contents for this issue
www.rsc.org/obc
Volume 6 | Number 14 | 21 July 2008 | Pages 2445–2640
ISSN 1477-0520
FULL PAPER
Eric Biron and Normand Voyer
Towards sequence selective DNA
binding: design, synthesis and DNA
binding studies of novel bis-porphyrin
peptidic nanostructures
2WT\XRP[ꢀBRXT]RT
In this issue...
1477-0520(2008)6:14;1-J

PAPER
www.rsc.org/obc | Organic & Biomolecular Chemistry
Towards sequence selective DNA binding: design, synthesis and DNA binding
studies of novel bis-porphyrin peptidic nanostructures†
Eric Biron and Normand Voyer*
Received 26th February 2008, Accepted 2nd April 2008
First published as an Advance Article on the web 9th May 2008
DOI: 10.1039/b803281e
A new series of peptidic nanostructures bearing two intercalating moieties was designed and
synthesized to achieve selective recognition of DNA sequences. A cationic porphyrin was attached to a
glutamic acid side chain and the latter introduced into a peptidic sequence by standard solid-phase
peptide synthesis methodology. Conformation of the hydrosoluble peptidic structures bearing two
cationic porphyrins was studied by circular dichroism. Using UV–visible spectroscopy and induced
circular dichroism, we demonstrate that the compounds are fully intercalated upon binding to
double-stranded DNA and that the compounds exhibit a tremendous preference for GC over AT
sequences for intercalation.
Our approach to achieve sequence selective DNA binding is to
Introduction
use engineerable peptidic frameworks to orient properly two DNA
The development of nanoscale tools having specific applications
intercalating moieties. The distance between the intercalating units
is of great interest in many areas of science. One application of ut-
can be easily modified and this variation should provide sequence
most importance is to develop molecular tools able to probe a spe-
cific nucleic acid sequence at the genome wide scale.1,2 Such func-
tional supramolecular tools have extremely interesting biomedical
preferences among the synthesized bis-intercalator peptides.
Among the available intercalating moieties, the cationic meso-
tetrakis(4-N-methylpyridiniumyl)porphyrin (TMPyP) was chosen
applications and could be used in biosensors, for diagnostic and
because of its high affinity for DNA and its well known DNA-
as therapeutic agents.1–3 Impressive advances in the design of
sequence-selective DNA-binding agents have been achieved dur-
ing the last decade. For example, pyrrole–imidazole polyamides
that can be programmed to recognize specific DNA sequences with
affinities and specificities comparable to DNA binding proteins
have been developed.2,4 Other successful approaches include pep-
tide nucleic acids (PNAs),5 Cu2+-mediated assembly of bipyridine–
Hoechst ligand molecules,6 triple-helix-forming oligonucleotides,7
modified zinc-finger proteins,8 and other molecules such as other
minor-groove binders and intercalators.9
Intercalation of small aromatic molecules in double-stranded
DNA (dsDNA) is an extremely efficient binding mode.10,11 Nu-
merous compounds, including some natural products and some
clinically used chemotherapeutic agents, interact with DNA by in-
tercalating one or more aromatic groups between base pairs of the
double helix.10–12 Whereas initial studies focused on molecules with
a single intercalating moiety,11 the promise of improved sequence
specificity has led researchers to investigate compounds that
contain more than one intercalating group.13,14 Bis-intercalating
compounds showed higher DNA binding affinities and slower
dissociation rates than the corresponding monomers.10,15 Over the
past two decades, a great number of dimeric forms of DNA in-
tercalators, such as bis-acridinecarboxamides, bis-naphthalimides,
bis-imidazoacridones has been developed as potential anticancer
drugs.13–16
binding properties.17,18 We now report the solid-phase synthesis,
conformational studies and DNA-binding properties of a new
series of bis-porphyrin peptides.
Results and discussion
Design
The starting point for the design of a versatile peptidic scaffold
was based on work previously reported, by our group20 and
others,21 for the construction of engineerable peptidic frameworks.
The general concept of this work was to use a-helical peptidic
structures as scaffolds to orient multiple macrocyclic ligands on
top of each other. One major advantage of using this strategy is
the possibility to easily vary the distance between the intercalating
moieties and their orientation simply by changing their position in
the peptidic sequence. In this case, hydrosolubility of the peptidic
framework is a very important prerequisite to allow DNA-binding
in aqueous media and prevent aggregation. Unfortunately, most
of the amino acids that induce an a-helix are hydrophobic (ala,
leu, etc.). To avoid this inconvenience, the peptidic framework was
also based on the stabilized hydrosoluble a-helices reported by
Marqusee and Baldwin.19 It was shown that a 17-mer alanine-
based peptide 1 containing three glutamic–lysine residue pairs
spaced by 4 residues readily forms an a-helix in water (Fig. 1).
Under an a-helix structure, the Glu−-(i + 4)Lys+ ion pairs or salt
bridges stabilize the helix and confer the hydrosolubility.
De´partement de chimie and CREFSIP, Faculte´ des sciences et de ge´nie,
Universite´ Laval, Que´bec, Que´bec, Canada G1K 7P4. E-mail: normand.
voyer@chm.ulaval.ca; Fax: 1-418-656-7916; Tel: 1-418-656-3613
† Electronic supplementary information (ESI) available: UV–vis spectra
of DNA titrations and ICD spectra of peptides 6–12 with poly(dGdC)2,
poly(dAdT)2 and CT-DNA. See DOI: 10.1039/b803281e
On the other hand, the intercalating units are attached to
the peptidic structure via an amide bond to glutamic acid side
chains. This modified glutamic acid can be introduced into
the peptide simply by replacing an alanine (Fig. 1). To do so,
This journal is
The Royal Society of Chemistry 2008
Org. Biomol. Chem., 2008, 6, 2507–2515 | 2507
©

Fig. 1 Sequences of the alanine-based hydrosoluble a-helical peptides;
(a) 17-mer peptide designed by Marqusee and Baldwin;19 (b) peptide 1
bearing two porphyrins. The dashed lines represent ion pair formation
under an a-helical structure. (Ac = acetate.)
porphyrin modified glutamic acids are synthesized beforehand and
introduced into the peptide during solid-phase synthesis. Another
important feature in the design of a bis-intercalator peptide is the
positioning of the intercalating units into the peptidic sequence.
We found that to orient the intercalating units on the same side of
the a-helix, they would have to be introduced at positions 4 and
15 in a 17-mer peptide (Fig. 2) and at positions 2 and 16 in an
18-mer peptide. It can be easily observed that simply by changing
the position of the intercalating units into the peptidic sequence,
the distance between them is also modified. For example, if the
peptidic framework adopts an a-helical conformation, the distance
between the intercalating moieties is, when calculated with 0.15 nm
per amino acid,22 1.65 nm for the 17-mer and 2.10 nm for the 18-
mer.
Fig. 2 17-Mer peptide 2 bearing two porphyrins; (a) side view; (b) top
view.
The influence of the peptidic framework rigidity was also
an interesting feature to investigate. More adaptable (flexible)
peptidic frameworks composed only of glycine were designed.
The distance between the intercalating units was varied simply
by changing the number of glycines between them.
Synthesis
The first step of the synthesis was to prepare the porphyrin
modified glutamic acids. N-Fmoc glutamic acids bearing a
porphyrin were synthesized as previously described.23 Briefly, 5-
(4-nitrophenyl)-10,15,20-tris(4-pyridinyl)porphyrin was prepared
using the classical Adler–Longo procedure by refluxing a mix-
ture of 4-nitrobenzaldehyde (1.75 eq.), 4-pyridinecarboxaldehyde
(3 eq.) and pyrrole (4 eq.) in the presence of acetic anhydride
(Ac2O) in propionic acid (Scheme 1).24 After purification by silica
gel chromatography, the nitro group was reduced by means of
stannous chloride in 6 N HCl to yield quantitatively the 5-(4-
aminophenyl)-10,15,20-tris(4-piridinyl)porphyrin 3. The coupling
reaction was achieved by activating the carboxylic function of
N-Boc-glutamic acid methyl ester with ethylchloroformate in
Scheme 1 Reagents, conditions and yields: (i) CH3CH2CO2H–Ac2O
reflux, 1.5 h; 8%; (ii) SnCl2, 6 N HCl; 98%; (iii) (a) ClCOOEt, TEA, DCM,
0
0
◦C, 30 min, (b) 3, TEA, DCM, 0 ◦C, 2 h; 80%; (iv) 1 N NaOH, THF,
◦C, 30 min; 90%; (v) 4M HCl–dioxane, 30 min; 99%; (vi) Fmoc-OSu,
DIEA, MeCN–H2O (9 : 1), 3 h; 80%.
dichloromethane in the presence of triethylamine (TEA), followed
by addition of 3.23,24 The fully protected modified amino acid 4 was
2508 | Org. Biomol. Chem., 2008, 6, 2507–2515
This journal is
The Royal Society of Chemistry 2008
©

obtained in 80% yield. Methyl ester cleavage on 4 was performed
with 1 N NaOH in THF followed by Boc deprotection with 4 M
HCl in 1,4-dioxane and reprotection using Fmoc-OSu to give 5
in very good yield after purification by short column silica gel
chromatography.
peptides were obtained in good yields (25–38% overall yield)
and in a highly pure form after purification. Peptide purity was
determined by HPLC and ESI-MS was used for characterization.
Conformational studies
The bis-intercalator peptides were synthesized on Wang resin
following standard Fmoc strategy solid-phase peptide synthesis
(Scheme 2).25 The first amino acid, Fmoc-Ala-OH, was at-
tached to the resin via activation with diisopropylcarbodiimide
(DIC) and 1-hydroxybenzotriazole (HOBt) in the presence of
diisopropylethylamine (DIEA) in DMF. Fmoc deprotection was
performed twice using a 20% piperidine solution in DMF for
15 minutes. Each standard Fmoc-protected amino acid (Ala,
Gly, Lys(Boc), and Glu(Ot-Bu)) was coupled in a 5-fold excess
by activating with DIC-HOBt-DIEA in DMF. The modified
amino acid 5 was coupled in a reduced 1.5-fold excess to the
amino free resin-bound peptide using O-(7-azabenzotriazol-1-yl)-
1,1,3,3-tetramethyluronium hexafluorophosphate (HATU) in the
presence of DIEA in DMF for 3 h.23 The final amino acid was
N-Boc protected to generate free peptides after cleavage under
acidic conditions. Most conveniently, N-methylation of the pyridyl
groups was carried out directly on solid-phase with an excess of
iodomethane in DMF.23 Finally, methylated peptides were cleaved
from the resin using a mixture of trifluoroacetic acid (TFA),
triisopropylsilane (TIS) and water (95 : 2.5 : 2.5). Synthesized
Conformational analyses of peptides 2, 6–8 were performed using
circular dichroism (CD) to demonstrate the helical structure of
the peptidic frameworks. CD spectra were recorded for peptides 2,
6–8 at 50 lM in a buffer solution (Tris·HCl 10 mM, NaCl 50 mM,
EDTA 1 mM, pH 7.0) (Fig. 3). Highly populated helical structures
were observed for peptides 2 and 6 with negative maxima at 206
and 222 nm and a positive maximum at 191 nm, whereas peptide
7 showed weaker ellipticity and peptide 8 showed no ellipticity.
These results suggest that only peptides 2 and 6 are long enough
to form a stable a-helix structure in water. The same curves were
observed for peptides in which the porphyrin modified amino acids
have been replaced by alanines. This last experiment confirmed
that the presence of porphyrin units does not affect the structure
of the peptidic framework.
DNA binding studies
We have previously demonstrated that a cationic porphyrin
attached to a peptide maintains its DNA binding properties.23
DNA binding studies with peptides 2, 6–12 were performed to
Scheme 2 Synthesis of bis-cationic porphyrin peptides 2, 6–12. Reagents and conditions: (i) Fmoc-Ala-OH, DIC, HOBt, DIEA, DMF, 24 h; (ii) 20%
piperidine–DMF, 2 × 15 min; (iii) 5, HATU, DIEA DMF, 3 h; (iv) Fmoc-Ala-OH or Fmoc-Glu(OtBu)-OH or Fmoc-Lys(Boc)-OH or Boc-Ala-OH,
DIC, HOBt, DIEA, DMF, 1 h; (v) CH3I, DMF, 24 h; (vi) TFA–TIS–H2O (95 : 2.5 : 2.5), 4 h.
This journal is
The Royal Society of Chemistry 2008
Org. Biomol. Chem., 2008, 6, 2507–2515 | 2509
©

isosbestic point throughout the titration, the optical contribution
certainly came from two distinct species, free and bound porphyrin
chromophores.28 In contrast, when poly(dAdT)2 was used, the
bathochromic shift and the hypochromicity were less important
(Fig. 4). These results were characteristic of a groove binding
mode.
Titration of compounds 2, 6–12 with poly(dGdC)2 showed also
an important decrease of the Soret band with strong bathochromic
shifts (Dkmax = 16–22 nm) and important hypochromicities (%H =
43.2–49.8) (Fig. 4 and Table 1). The hypochromicity was deter-
mined by the equation H = (Af − Ab)/(Af) × 100, where Af
and Ab represent the Soret absorbances of the free and bound
porphyrins, respectively. These results are characteristic of inter-
calative binding and demonstrate that both porphyrins intercalate
into GC-rich DNA since the spectral changes are comparable to
those of the monoporphyrin. No isosbestic points were observed
for peptides 2, 6–12, suggesting that the binding process is more
than two steps and can be explained in terms of a collaboration
effect. In contrast, during titration with poly(dAdT)2, the intensity
of the Soret band decreased much less for each compound studied.
Bathochromic shifts from 4 to 8 nm and hypochromicities from
3.6 to 23.1% were observed (Table 1). These spectral changes
indicate that peptides 2, 6–12 interact with AT-rich DNA by
groove binding. On the other hand, during titration with CT-
DNA, intermediate spectral changes with bathochromic shifts
from 8 to 14 nm and hypochromicities from 11.4 to 30.9% were
observed for compounds 2, 6–12 (Table 1). The intensity of the
Soret band of each bis-porphyrin peptide decreased together with
a red shift at the initial step, and then the intensity of the red
shifted peak increased with further DNA additions. These results
propose that in most cases, two modes of interaction are observed
and could be explained by the probability of the second porphyrin
finding a nearby GC-rich site for intercalation. When no GC-
rich site can be found for intercalation in the neighborhood, the
second porphyrin interacts with AT-rich sites via groove binding
or simply by outside binding. Once again, no isosbestic points
were observed for peptides 2, 6–12, suggesting a collaboration
effect. The obtained results demonstrate that the length and
structural properties of the peptidic framework do not seem to
play an important role in the mode of interaction with various
DNA.
Fig. 3 CD spectra of compounds 2, 6–8 (50 lM) in a buffer solution
Tris·HCl 10 mM, NaCl 50 mM, EDTA 1mM, pH 7.0.
investigate the mode of interaction, the selectivity (GC vs. AT), and
the impact of the distance between the intercalating units as well as
the influence of the peptidic framework (rigidity vs. adaptability).
The modes of interaction of porphyrins with DNA have been
studied by several groups and their results established three
types of binding modes: intercalative binding, groove binding,
and outside binding.26 Intercalative binding has been found to
occur dominantly at GC-rich regions, groove binding at AT-
rich regions, and outside binding at both GC-rich and AT-rich
regions.18,27 During spectrophotometric titration with DNA, the
intercalated porphyrin species has the following characteristics:
(i) a large red shift of the Soret band (≥15 nm),28,29 (ii) substantial
hypochromicity (≥35%),28,29 and (iii) an induced negative CD
band in the Soret region.18,29,30 In contrast, the groove binding
porphyrin species has the following characteristics: (i) a small red
shift in the Soret band (≤8 nm),28,29 (ii) little hypochromicity or
hyperchromicity of the Soret maximum,28,29 and (iii) an induced
positive CD band in the Soret region.18,28,29 On the other hand, the
outside binding porphyrin species is characterized by an induced
conserved Soret region.30
Interaction of peptides 2, 6–12 with various types of DNA (calf
thymus DNA (CT-DNA), poly(dAdT)2 and poly(dGdC)2) was
examined by spectrophotometric titration in the Soret region (UV
and CD). The extraordinary extinction coefficient of the Soret
band for the cationic porphyrins allowed spectrophotometric de-
tection of porphyrin–DNA interactions at very low concentration
(5 lM). Visible spectra of compounds 2, 6–12 were recorded in the
presence of an increasing amount of DNA in a TE buffer (Tris·HCl
10 mM, NaCl 50 mM, EDTA 1 mM, pH 7.0) at 1/R values up to
50, where R denotes input ratio of [porphyrin] : [base pairs]).29,30
It has been shown previously that during titration with GC rich
DNA (CT-DNA and poly(dGdC)2), an important bathochromic
shift (Dkmax) and hypochromicity (H) with one set of isosbestic
points were observed for the Soret band of the cationic mono-
porphyrin H2TMPyP (Fig. 4).23 These results corresponded to
an intercalative binding and because of the presence of an
Induced circular dichroism (ICD) in the Soret region is very
helpful for analysis of the binding mode of an achiral porphyrin
to chiral DNA.18,31 Peptides 2, 6–12 did not show any ICD in the
Table 1 UV–Vis spectral changes of peptides 2, 6–12 in the presence of
DNA
Poly(dGdC)2
Poly(dAdT)2
CT-DNA
Peptide
Dkmax
%H
Dkmax
%H
Dkmax
%H
H2TMPyP
20 nm
20 nm
18 nm
16 nm
20 nm
22 nm
18 nm
18 nm
22 nm
51.5
44.6
45.5
44.9
47.3
43.2
44.5
49.8
49.0
8 nm
8 nm
6 nm
4 nm
8 nm
6 nm
8 nm
6 nm
8 nm
26.7
3.6
8.1
10.0
16.8
23.1
18.1
14.9
5.4
16 nm
8 nm
8 nm
43.5
26.5
25.3
26.6
11.4
30.9
28.8
28.7
28.2
2
6
7
8 nm
8
12 nm
10 nm
12 nm
10 nm
14 nm
9
10
11
12
2510 | Org. Biomol. Chem., 2008, 6, 2507–2515
This journal is
The Royal Society of Chemistry 2008
©

Fig. 4 Spectrophotometric titrations of H2TMPyP (left) and 2 (right) with various DNAs; (a) with CT-DNA; (b) with poly(dGdC)2; (c) with poly(dAdT)2.
absence of duplex DNA, but characteristic spectra in the Soret
region were induced with addition of DNA in buffer (Tris·HCl
10 mM, NaCl 50 mM, EDTA 1 mM, pH 7.0). Fig. 5 shows
the ICD spectra of the monoporphyrin H2TMPyP and peptide
2 bound to CT-DNA, poly(dAdT)2 and poly(dGdC)2 at 1/R = 6.
In the presence of poly(dAdT)2, the ICD spectrum for compound
2 comprised a small negative peak at 428 nm and a large positive
peak at 444 nm corresponding to groove binding. In the presence
of poly(dGdC)2 and CT-DNA, a negative peak was induced at 447
and 442 nm, respectively, corresponding to intercalative binding.
ICD spectra of compounds 6–12 bound to various DNAs showed
similar profiles. The obtained results showed only one mode of
interaction for peptides 2, 6–12 in the presence of CT-DNA and
do not support the groove binding mode theory for the second
porphyrin. The data suggest instead an interaction by outside
binding for some of the second porphyrins, since no spectral
changes are observed for this mode of interaction compared to
a positive peak for groove binding.
The binding studies with various DNAs clearly showed that
intercalative binding occurs at GC-rich regions and groove binding
at AT-rich regions.18,29–32 The observed DNA binding properties for
peptides 2, 6–12 were all similar and suggest that the length and
structural properties of the peptidic framework do not seem to
play an important role for the mode of interaction with various
DNA.
Conclusions
We have described a new class of bis-intercalating compounds
composed of two cationic porphyrins attached to engineerable
peptidic nanostructures. The design of the a-helical framework
allows us to easily modify the orientation of the intercalating units
and the distance between them. The solid-phase synthesis of the
bis-porphyrin peptides allows a certain flexibility in the design,
structure and intercalating units simply by replacing one or
This journal is
The Royal Society of Chemistry 2008
Org. Biomol. Chem., 2008, 6, 2507–2515 | 2511
©

Fig. 5 Induced CD with CT-DNA, poly(dGdC)2 and poly(dAdT)2 at 1/R = 6. (a) H2TMPyP; (b) peptide 2.
more amino acids in the sequence. The a-helical structure of the
5-p-Aminophenyl-10-15-20-(tripyridin-4-yl)porphyrin (3). The
nitro-porphyrine (4 mmol) was dissolved in a solution of 6 N HCl
(400 mL) followed by addition of SnCl2 (20 mmol) and the mixture
was stirred at room temperature for 24 h. The reaction mixture was
neutralized with a solution of 1 N NaOH and NaOH on ice. The
aqueous basic solution was extracted with DCM and the resulting
organic phase was washed with water (3×). The organic phase was
dried over MgSO4 and the solvent was evaporated under reduced
designed peptidic frameworks, observed by CD, shows that a-
helical hydrosoluble peptides can be used as frameworks for the
development of functional supramolecular devices. Using UV–
visible titrations and induced CD for DNA binding studies with
various DNA, we found that intercalative binding occurs at GC-
rich regions and groove binding at AT-rich regions and that a
collaboration effect (cooperativity) takes place. DNAse I foot-
printing to determine the sequence specificity of the bis-porphyrin
compounds and kinetic studies are currently in progress in our
laboratory. Binding of the synthesized peptides to quadruplex
DNA and inhibition of the telomerase are also being studied.
Photonuclease activity of the compounds and their metal complex
(Zn, Cu) derivatives will also be analyzed.
1
pressure affording 2.5 g (3.96 mmol, 98%) of purple solid. H
NMR (300 MHz; CDCl3), d = −2.7 (s, 2H, NH pyrrole), 7.05–
7.10 (d, 2H, J = 5 Hz, Hortho NH2), 7.95–8.00 (d, 2H, J = 5 Hz,
Hmeta NH2), 8.16–8.20 (m, 6H, 2,6 pyridine), 8.80–8.88 (m, 6H, 3,5
pyridine), 9.05–9.12 (m, 8H, H pyrrole); EI-MS (70 eV): 632 (M+);
UV–visible (CHCl3), k/nm (e/10−3 M−1 cm−1): 420 (255), 514 (15),
548 (7.7), 588 (5), 644 (6.4).
Experimental
Na-t-Butyloxycarbonyl-c-(5-p-amidophenyl-10,15,20-(tripyridin-
4-yl)porphyrin)-L-glutamic acid methyl ester (4). Boc-Glu-OMe
3 (3.8 mmol) was dissolved in dry DCM at 0 ◦C followed by
addition of triethylamine (4.6 mmol) and ethyl chloroformate
(3.8 mmol). The reaction mixture was stirred for 30 min under N2
atmosphere and evaporated to dryness under reduced pressure.
The resulting solid was redissolved in dry DCM at 0 ◦C followed
by the addition of a solution of porphyrine 1 (1.3 mmol) in
dry DCM and triethylamine (4.6 mmol). The reaction mixture
was stirred for 1 h at 0 ◦C and 1 h at room temperature
under N2 atmosphere. The reaction mixture was washed with
a solution of 5% NaHCO3 (m/v) (3×) and water (3×). The
organic phase was dried over Na2SO4 and the solvent evaporated
under reduced pressure. The resulting solid was purified by silica
gel chromatography (2.5% to 10% ethanol–DCM) to afford
0.91 g (1.04 mmol, 80.3%) of purple solid.1H NMR (300 MHz,
DMSO-d6), d = −2.98 (s, 2H, NH pyrrole), 1.45 (s, 9H, t-butyl),
1.95–2.05 (m, 1H, Hb2), 2.15–2.25 (m, 1H, Hb1), 2.59–2.68 (m,
2H, Hc), 3.75 (s, 3H, OCH3), 4.14–4.21 (m, 1H, Ha), 7.41–7.45 (d,
1H, J = 6 Hz, NH), 8.05–8.12 (d, 2H, J = 8 Hz, Hortho NHCO),
8.14–8.18 (d, 2H, J = 8 Hz, Hmeta NHCO), 8.22–8.30 (m, 6H, 2,6
pyridine), 8.87–8.98 (m, 8H, H pyrrole), 9.05–9.10 (m, 6H, 3,5
pyridine), 10.44 (s, 1H, NHd); ESI-MS: m/z 876 = (M + H)+;
Synthesis
5-p-Nitrophenyl-10-15-20-(tripyridin-4-yl)porphyrin. p-Nitro-
benzaldehyde (85 mmol) and 4-pyridine carboxaldehyde
(157 mmol) were added to a 1 L round bottom flask containing
propionic acid (750 mL) and acetic anhydride (75 mL) at
110 ◦C. Pyrrole (208 mmol) was then added portionwise and the
reaction mixture was refluxed for 1.5 h. The propionic acid and
the acetic anhydride were removed by distillation until 75–100 mL
was left in the flask. The remaining mixture was neutralized
with a solution of 1 N NaOH on ice, filtered and washed with
a solution of 1 N NaOH (3×) and with water (3×). The solid
was dried overnight, dissolved in DCM and filtered. The DCM
was removed under reduced pressure and the resulting purple
solid was purified by silica gel chromatography (gradient of
2.5% to 10% ethanol–DCM) affording 2.8 g (4.22 mmol, 8%)
of purple solid.1H NMR (300 MHz; CDCl3), d = −2.7 (s, 2H,
NH pyrrole), 8.16–8.18 (m, 6H, 2,6 pyridine), 8.38–8.41 (d, 2H,
Hortho NO2), 8.66–8.68 (d, 2H, Hmeta NO2), 8.77–8.92 (m, 8H, H
pyrrole), 9.05–9.15 (m, 6H, 3,5 pyridine); EI-MS (70 eV): 662
(M+); UV–visible (CHCl3), k/nm (e/10−3 M−1 cm−1): 418 (353),
514 (18.2), 548 (6.3), 588 (5.8), 644 (1.9).
2512 | Org. Biomol. Chem., 2008, 6, 2507–2515
This journal is
The Royal Society of Chemistry 2008
©

UV–visible (CHCl3), k/nm (e/10−3 M−1 cm−1): 420 (344), 516
(16.9), 552 (8.2), 590 (6.0), 642 (3.7).
resin (0.7 mmol g−1).25 Coupling of Fmoc-protected amino acids
(5 eq.) was achieved with DIC (5 eq.), HOBt (5 eq.) and DIEA
(6 eq.) in DMF during 30 min at 0 C. Fmoc-Glu(TPyP)-OH 5
◦
Na-t-Butyloxycarbonyl-c-(5-p-amidophenyl-10,15,20-(tripyridin-
(1.5 eq.) was coupled using HATU (1.5 eq.) and DIEA (2 eq.)
in DMF for 3 h. Fmoc protecting groups were removed with
20% piperidine in DMF (2 × 15 min). After each coupling and
deprotection, the resin was washed thoroughly with DMF (3×),
MeOH (3×) and DMF (3×). N-Methylation of the porphyrin
side chains on a solid support was achieved with a mixture of
iodomethane and DMF (6 : 94) for 24 h followed by washing
with DMF (5×). The peptides were cleaved from the resin with
a mixture of trifluoroacetic acid (TFA), triisopropylsilane (TIS)
and water (95 : 2.5 : 2.5) for 4 h at room temperature. The resin
was filtered and washed with DCM (2×) and MeOH (3×). The
filtrate was evaporated under reduced pressure and the resulting
mixture precipitated with diethyl ether. The solid was washed with
diethyl ether (3×) and purified by exclusion chromatography using
4-yl)porphyrin)-L-glutamic
acid. Boc-Glu(TPyP)-OMe
4
(0.8 mmol) was dissolved in THF at 0 ◦C followed by the addition
of a solution of 1 N NaOH (3.2 mmol). The reaction mixture
was stirred at room temperature until complete conversion was
observed and the THF was evaporated under reduced pressure.
The remaining aqueous phase was extracted with DCM (2×)
combined with the addition of acetic acid. The acetic acid
breaks the emulsion and pushes the Na-protected amino acid
in the organic phase. The colored organic phase was dried over
Na2SO4 and the solvent evaporated under reduced pressure.
The remaining acetic acid was co-evaporated with toluene (4×)
under reduced pressure or lyophilized. The resulting purple solid
was purified by short column silica gel chromatography (DCM,
10% ethanol–DCM and finally MeOH–DCM (1 : 1)) to afford
R
Sephadexꢀ LH-20 in MeOH or semi-preparative RP-HPLC (C-
1
620 mg (0.72 mmol, 90%) of purple solid. H NMR (300 MHz,
18, MeCN 10–50% in 30 min).
DMSO-d6), d = −2.98 (s, 2H, NH pyrrole), 1.45 (s, 9H, t-butyl),
2.01–2.19 (m, 2H, Hb), 2.52–2.58 (m, 2H, Hc), 3.85–3.91 (m, 1H,
Ha), 6.38–6.42 (d, 1H, J = 6 Hz, NH Glu), 8.05–8.18 (m, 4H,
Hortho NH + Hmeta NH), 8.22–8.30 (m, 6H, 2,6 pyridine), 8.87–8.98
(m, 8H, H pyrrole), 9.05–9.10 (m, 6H, 3,5 pyridine), 10.44 (s, 1H,
NHd Glu); ESI-MS: m/z 862 = (M + H)+; UV–visible (MeOH),
k/nm (e/10−3 M−1 cm−1): 416 (265), 512 (12.9), 546 (5.9), 588
(4.0), 650 (4.9)
H-Ala-Lys-Glu(TMPyP)-Ala-Ala-Glu-Lys-Ala-Ala-Ala-Glu-
Lys-Ala-Ala-Glu(TMPyP)-Glu-Ala-OH (2). ESI-MS, m/z: calc.
3008.4 (M + H)+, found 3008.5. UV–visible (buffer TE 10 mM,
NaCl 50 mM, EDTA 1 mM, pH 7.0), kmax/nm (e/10−3 M−1 cm−1):
422 (172). RP-HPLC tR = 9.6 min (10–50%).
H-Ala-Glu(TMPyP)-Lys-Ala-Ala-Ala-Glu-Lys-Ala-Ala-Ala-
Glu-Lys-Ala-Ala-Glu(TMPyP)-Glu-Ala-OH (6). ESI-MS, m/z:
calc. 3079.5 (M + H)+, found 3078.8. UV–visible (buffer TE
10 mM, NaCl 50 mM, EDTA 1 mM, pH 7.0), kmax/nm
(e/10−3 M−1 cm−1): 424 (121). RP-HPLC tR = 9.6 min (10–50%).
H-Ala-Lys-Ala-Glu(TMPyP)-Ala-Glu-Lys-Ala-Ala-Glu(TMPyP)-
Glu-Ala-OH (7). ESI-MS, m/z: calc. 2537.9 (M + H)+, found
2537.6. UV–visible (buffer TE 10 mM, NaCl 50 mM, EDTA
1 mM, pH 7.0), kmax/nm (e/10−3 M−1 cm−1): 424 (100). RP-HPLC
tR = 9.5 min (10–50%).
H-Ala-Glu(TMPyP)-Lys-Ala-Ala-Glu(TMPyP)-Glu-Ala-OH
(8). ESI-MS, m/z: calc. 2138.4 (M + H)+, found 2138.6. UV–
visible (buffer TE 10 mM, NaCl 50 mM, EDTA 1 mM, pH 7.0),
kmax/nm (e/10−3 M−1 cm−1): 424 (121). RP-HPLC tR = 9.4 min
(10–50%).
Na-9-Fluorenylmethoxycarbonyl-c-(5-p-amidophenyl-10,15,20-
(tripyridin-4-yl)porphyrin)-L-glutamic acid (5). Boc-Glu(TPyP)-
OH (0.7 mmol) was dissolved in a solution of 4 M HCl–dioxane
◦
(1.4 mmol) at 0 C and stirred for 30 min at room temperature.
The reaction mixture was evaporated to dryness and the resulting
solid dried under vacuum. The Na-deprotected amino acid was
dissolved in H2O–MeCN (1 : 9) at 0 ◦C followed by addition
of DIEA (4.2 mmol) and Fmoc-OSu (0.77 mmol). The reaction
mixture was stirred for 3 h at room temperature and the MeCN
evaporated under reduced pressure. The resulting solution was
extracted with DCM (2×) combined with the addition of acetic
acid as described previously. The colored organic phase was dried
over Na2SO4 and the solvent evaporated under reduced pressure.
The remaining acetic acid was co-evaporated with toluene (4×)
under reduced pressure or lyophilized. The resulting purple solid
was purified by short column silica gel chromatography (10%
ethanol–DCM and MeOH–DCM (1 : 1)) to afford 550 mg
H-Ala-Glu(TMPyP)-Gly-Glu(TMPyP)-Ala-OH
(9). ESI-
MS, m/z: calc. 1796.1 (M + H)+, found 1797.0. UV–visible
(buffer TE 10 mM, NaCl 50 mM, EDTA 1 mM, pH 7.0), kmax/nm
(e/10−3 M−1 cm−1): 422 (187). RP-HPLC tR = 6.6 min (10–50%).
1
(0.56 mmol, 80%) of purple solid. H NMR (300 MHz, DMSO-
d6) d = −2.98 (s, 2H, NH pyrrole), 2.05–2.35 (m, 2H, Hb), 2.54–
2.60 (m, 2H, Hc), 3.97–4.01 (m, 1H, Ha), 4.20–4.41 (m, 3H, H9
fluorenyl + OCH2-fluorenyl), 6.90–6.95 (d, 1H, J = 6 Hz, NH
Glu), 7.32–7.41 (m, 4H, Harom fluorenyl), 7.70–7.78 (d, 2H, Harom
fluorenyl), 7.80–7.88 (d, 2H, Harom fluorenyl), 8.05–8.26 (m, 10H,
Hortho NH + Hmeta NH + 6H, 2,6 pyridine), 8.71–8.95 (m, 8H,
H pyrrole), 9.00–9.10 (m, 6H, 3,5 pyridine), 10.44 (s, 1H, NHd);
ESI-MS: m/z 985 = (M + H)+; UV–visible (MeOH), k/nm
(e/10−3 M−1 cm−1): 416 (181), 514 (10.7), 548 (6.7), 590 (5.3), 650
(5.0).
H-Ala-Glu(TMPyP)-Gly-Gly-Gly-Glu(TMPyP)-Ala-OH (10).
ESI-MS, m/z: calc. 1910.2 (M + H)+, found 1910.8. UV–visible
(buffer TE 10 mM, NaCl 50 mM, EDTA 1 mM, pH 7.0), kmax/nm
(e/10−3 M−1 cm−1): 424 (124). RP-HPLC tR = 7.4 min (10–50%).
H-Ala-Glu(TMPyP)-Gly-Gly-Gly-Gly-Gly-Glu(TMPyP)-Ala-
OH (11). ESI-MS, m/z: calc. 2024.3 (M + H)+, found 2023.1.
UV–visible (buffer TE 10 mM, NaCl 50 mM, EDTA 1 mM,
pH 7.0), kmax/nm (e/10−3 M−1 cm−1): 422 (151). RP-HPLC tR
9.8 min (10–50%).
=
General procedure for the synthesis of peptides 2 and 6–12. All
peptides were synthesized manually using standard solid-phase
peptide chemistry with Fmoc-protected amino acids on Wang
H-Ala-Glu(TMPyP)-Gly-Gly-Gly-Gly-Gly-Gly-Gly-Glu(TMPyP)-
Ala-OH (12). ESI-MS, m/z: calc. 2138.4 (M + H)+, found
2137.9. UV–visible (buffer TE 10 mM, NaCl 50 mM, EDTA
This journal is
The Royal Society of Chemistry 2008
Org. Biomol. Chem., 2008, 6, 2507–2515 | 2513
©

1 mM, pH 7.0), kmax/nm (e/10−3 M−1 cm−1): 424 (259). RP-HPLC
tR = 9.7 min (10–50%).
3 V. C. Pierre, J. T. Kaiser and J. K. Barton, Proc. Natl. Acad. Sci. USA,
2007, 104, 429; I. Ghosh, C. I. Cliff, D. A. T. Ooi and D. J. Segal,
Mol. BioSyst., 2006, 2, 551–560; M. Gearhart, L. Dickinson, J. Ehley,
C. Melander, P. Dervan, P. Wright and J. Gottesfeld, Biochemistry,
2005, 44, 4196; J. Pindur, M. Jansen and T. Lemster, Curr. Med. Chem.,
2005, 12, 2805; P. Kohli, C. C. Harrell, Z. Cao, R. Gasparac, W. Tan
and C. R. Martin, Science, 2004, 305, 984; M. Thompson and N. W.
Woodbury, Biochemistry, 2000, 39, 4327; D. E. Thurston, Br. J. Cancer,
1999, 80(S1), 65.
4 P. B. Dervan and B. S. Edelson, Curr. Opin. Struct. Biol., 2003, 13, 283;
P. B. Dervan, Bioorg. Med. Chem., 2001, 9, 2215; J. W. Trauger, E. E.
Baird and P. B. Dervan, J. Am. Chem. Soc., 1998, 120, 3534; S. White,
J. W. Szewczyk, J. M. Turner, E. E. Baird and P. B. Dervan, Nature,
1998, 391, 468; S. E. Swalley, E. E. Baird and P. B. Dervan, J. Am.
Chem. Soc., 1997, 119, 6953; P. B. Dervan, Science, 1986, 232, 464.
5 J. Hu and D. R. Corey, Biochemistry, 2007, 46, 7581; S. Shakeel, S.
Karim and A. Ali, J. Chem. Technol. Biotechnol., 2006, 81, 892; P. E.
Nielsen, Chem.–Eur. J., 1997, 3, 505; M. Egholm, O. Buchardt, L.
Christensen, C. Behrens, S. M. Freier, D. A. Driver, R. H. Berg, S. K.
Kim, B. Norden and P. E. Nielsen, Nature, 1993, 365, 566.
6 M. Tanada, S. Tsujita, T. Kataoka and S. Sasaki, Org. Lett., 2006, 8,
2475; M. Tanada, S. Tsujita and S. Sasaki, J. Org. Chem., 2006, 71, 125.
7 D. M. Gowers and K. R. Fox, Nucleic Acids Res., 1999, 27, 1569; S.
Neidle, Anti-Cancer Drug Des., 1997, 12, 433.
8 J. R. Desjarlais and J. M. Berg, Proc. Natl. Acad. Sci. USA, 1992, 89,
7345.
9 J. B. Chaires, Curr. Opin. Struct. Biol., 1998, 8, 314; C. Bailly and J. B.
Chaires, Bioconjugate Chem., 1998, 9, 513; F. Leng, W. Priebe and J. B.
Chaires, Biochemistry, 1998, 37, 1743.
10 L. P. G. Wakelin, Med. Rev. Res., 1986, 6, 275; L. P. G. Wakelin, T. S.
Creasy and M. J. Waring, FEBS Lett., 1979, 104, 261.
Conformational studies by circular dichroism
Samples were prepared in a buffer Tris·HCl 10 mM, NaCl 50 mM,
EDTA 1 mM, pH 7.0 with a peptide concentration of 50 lM. CD
spectra were recorded at 25 ◦C on a Jasco J-710 spectropolarimeter
with at least 20 scans from 250 to 190 nm. Spectra are expressed
in mean residue molar ellipticity [h] (mdeg·cm2/dmol) and are
corrected for the background. The molecular weight used was
113 g mol−1. The pathlength of the quartz cell was 0.05 cm.
DNA binding studies
Sample preparation. The concentrations of polynucleic acids
for measurements were determined spectrophotometrically with
e260 = 1.31 × 104 M−1 cm−1 (as base pair) for CT-DNA, e262
=
6.6 × 103 M−1 cm−1 (as base pair) for poly(dAdT)2 and e256
=
8.4 × 103 M−1 cm−1 (as base pair) for poly(dGdC)2.31 Bis-porphyrin
peptide concentrations for measurements were also determined
spectrophotometrically using the e determined during compound
characterization. All measurements were carried out in a buffer
Tris·HCl 10 mM, NaCl 50 mM, EDTA 1 mM, pH 7.0.
UV–visible titration. Spectroscopic measurements were car-
ried out on a Hewlett Packard HP 8452-A spectrophotometer.
Absorbances were measured in a 1 mL, 10 mm pathlength quartz
cuvette, using 0.5 mL of a 5 lM solution of porphyrin (2.5 lM of
bis-porphyrin peptide) and adding successive aliquots of a solution
containing the same concentration of porphyrin and a 100 fold
excess of DNA (500 lM, 1/R = 100).
11 W. D. Wilson and R. L. Jones, Adv. Pharmacol. Chemother., 1981, 18,
177; L. S. Lerman, Proc. Natl. Acad. Sci. USA, 1963, 49, 94; L. S.
Lerman, J. Mol. Biol., 1961, 3, 18.
12 L. H. Hurley, Nat. Rev. Cancer, 2002, 2, 188; M. F. Bran˜a, M. Cacho, A.
Gradillas, B. Pascual-Teresa and A. Ramos, Curr. Pharm. Des., 2001, 7,
1745; D. E. Graves and L. M. Velea, Curr. Org. Chem., 2000, 4, 915; I.
Haq and J. Ladbury, J. Mol. Recognit., 2000, 13, 188; D. E. Thurston,
Br. J. Cancer, 1999, 80, 65.
13 J. B. Chaires, F. Leng, T. Przewloka, I. Fogt, Y. H. Ling, R. Perez-Soler
and W. Priebe, J. Med. Chem., 1997, 40, 261; C. Bailly, M. F. Bran˜a
and M. J. Waring, Eur. J. Biochem., 1996, 240, 195; P. F. Bosquet,
M. F. Bran˜a, D. Conlon, K. M. Fitzgerald, D. Perron, C. Cocchiaro,
R. Miller, M. Moran, J. Georges, X.-D. Quian, G. Keilhauer and C. A.
Romerdahl, Cancer Res., 1995, 55, 1176; R. J. McRipley, P. E. Burns-
Horwitz, P. M. Czerniak, R. J. Diamond, M. A. Diamond, J. L. D.
Miller, R. J. Page, D. L. Dexter, S.-F. Chen, J.-H. Behrens, S. P. Seitz
and J. L. Gross, Cancer Res., 1994, 54, 159; M. Delepiene, C. Milhe,
A. Namane, T. H. Dinh and B. P. Roques, Biopolymers, 1991, 31, 331;
M. J. Waring and K. R. Fox, Molecular Aspects of Anticancer Drug
Action, Macmillan, London, 1983.
Induced circular dichroism. CD measurements were performed
with a 1.5 mL, 0.5 cm cylindrical quartz cuvette, using the same
general procedure as above to analyse the mixture with different
1/R values. Aliquots of a 250 lM DNA solution were added
successively to 0.75 mL of a 25 lM solution of porphyrin (12.5 lM
of bis-porphyrin peptide). All the spectra were obtained by an
average of 20 accumulations from 500 to 400 nm.
14 Y. Chu, V. Lynch and B. L. Iverson, Tetrahedron, 2006, 62, 5536; R. S.
Lokey, Y. Kwok, V. Guelev, C. J. Pursell, L. H. Hurley and B. L. Iverson,
J. Am. Chem. Soc., 1997, 119, 7202; S. Takenaka, S. Nishira, K. Tahara,
H. Kondo and M. Takagi, Supramol. Chem., 1993, 2, 41; M. Wirth, B.
Ole, K. Torben, P. E. Nielsen and B. J. Norden, J. Am. Chem. Soc.,
1988, 110, 932; W. A. Denny, G. J. Atwell, G. A. Willmott and L. P. G.
Wakelin, Biophys. Chem., 1985, 22, 17; G. J. Atwell, W. Leupin, S. J.
Twigden and W. F. Denny, J. Am. Chem. Soc., 1983, 105, 2913; J. B.
Hansen, T. Koch, O. Buchard, P. E. Nielsen, M. Wirth and B. J. Norden,
Biochemistry, 1983, 22, 4878.
Acknowledgements
This research was supported by the NSERC of Canada and the
FQRNT of Quebec. E.B. thanks the NSERC of Canada and the
FQRNT of Quebec for postgraduate scholarships.
Notes and references
15 J. A. Spicer, S. A. Gamage, G. J. Atwell, G. J. Finlay, B. C. Baguley and
W. A. Denny, Anti-Cancer Drug Des., 1999, 14, 281; W. M. Cholody,
L. Hernandez, L. Hassner, D. A. Scudiero, D. B. Djurickovic and C. J.
Michejda, J. Med. Chem., 1995, 38, 3043; Y. H. Hsiang, J. B. Jiang and
L. F. Liu, Mol. Pharmacol., 1989, 36, 371.
16 L. D. Van Vliet, T. Ellis, P. J. Foley, L. G. Liu, F. M. Pfeffer, R. A. Russell,
R. N. Warrener, F. Hollfelder and M. J. Waring, J. Med. Chem., 2007, 50,
2326; W. M. Cholody, T. Kosakowska-Cholody, M. G. Hollingshead,
H. K. Hariprakasha and C. J. Michejda, J. Med. Chem., 2005, 48, 4474;
M. F. Bran˜a, M. Cacho, M. A. Garcia, T. B. Pascual, A. Ramos, M. T.
Dominguez, J. M. Pozuelo, C. Abradelo, S. M. F. Rey, M. Yuste, C. M.
Banez and J. C. Lacal, J. Med. Chem., 2004, 47, 1391; V. Guelev, J. Lee,
J. Ward, S. Sorey, D. W. Hoffman and B. L. Iverson, Chem. Biol., 2001,
8, 415; V. M. Guelev, M. T. Harting, R. S. Lokey and B. L. Iverson,
1 E. Mateo-Marti, C. Briones, C. M. Pradier and J. A. Martin-
Gago, Biosens. Bioelectron., 2007, 22, 1926; M. Thompson, Biomacro-
molecules, 2007, 8, 3628; E. Y. Chan, N. M. Goncalves, R. A. Haeusler,
A. J. Hatch, J. W. Larson, A. M. Maletta, G. R. Yantz, E. D. Carstea,
M. Fuchs, G. G. Wong, S. R. Sullans and R. Gilmanshin, Genome Res.,
2004, 14, 1137; N. Svanvik, G. Westman, D. Wang and M. Kubista,
Anal. Biochem., 2000, 281, 26; D. Whitecombe, J. Theaker, S. P. Guy,
T. Brown and S. Little, Nat. Biotechnol., 1999, 17, 804; S. Tyagi, D. P.
Bratu and F. R. Kramer, Nat. Biotechnol., 1998, 16, 49; A. S. Piatek, S.
Tyagi, A. C. Pol, A. Telenti, L. P. Miller, F. R. Kramer and D. Alland,
Nat. Biotechnol., 1998, 16, 359.
2 E. J. Fechter, O. Bogdan and P. B. Dervan, J. Am. Chem. Soc., 2005,
127, 16685; J. P. Sluka, S. J. Horvath, M. F. Bruist, M. I. Simon and
P. B. Dervan, Science, 1987, 238, 1129.
2514 | Org. Biomol. Chem., 2008, 6, 2507–2515
This journal is
The Royal Society of Chemistry 2008
©

Chem. Biol., 2000, 7, 1; S. Girault, P. Grellier, A. Berecibar, L. Maes, E.
Mouray, P. Lemiere, M. A. Debreu, C. E. Davidoud and C. Sergheraert,
J. Med. Chem., 2000, 43, 2646.
22 R. Boyer, in Concepts in Biochemistry, John Wiley & Sons, Weinheim,
2nd edn, 2002, ch. 5, pp. 102–103.
23 E. Biron and N. Voyer, Chem. Commun., 2005, 4652.
17 R. F. Pasternack, J. I. Goldsmith, S. Sze´p and E. J. Gibbs, Biophys. J.,
1998, 75, 1024; L. A. Lipscomb, F. X. Zhou, S. R. Presnell, R. J. Woo,
M. E. Peek, R. R. Plaskon and L. D. Williams, Biochemistry, 1996,
35, 2818; G. Dougherty, J. R. Pilbrow, A. Skorobogaty and T. Smith,
J. Chem. Soc., Faraday Trans. 2, 1985, 81, 1739; J. M. Kelly, J. M.
Murphy, D. J. McConnell and C. OhUigin, Nucleic Acids Res., 1985,
13, 167; R. F. Pasternack, E. J. Gibbs and J. J. Villafranca, Biochemistry,
1983, 22, 5409; R. J. Fiel, J. C. Howard, E. H. Mark and N. Datta-
Gupta, Nucleic Acids Res., 1979, 6, 3093.
24 A. D. Adler, F. R. Longo, J. D. Finarelli, J. Goldmacher, J. Asour
and L. Korsakoff, J. Org. Chem., 1967, 32, 476; L. Ding, C. Casas, G.
Eternad-Moghadam and B. Meunier, New J. Chem., 1990, 14, 421.
25 G. B. Fields and R. L. Noble, Int. J. Pept. Protein Res., 1990, 35, 161.
26 M. Carvlin and R. J. Fiel, Nucleic Acids Res., 1983, 11, 6121; M.
Carvlin, E. Mark, R. J. Fiel and J. C. Howard, Nucleic Acids Res.,
1983, 11, 6141; D. R. McMillin and K. M. McNett, Chem. Rev., 1998,
98, 1201; S. Mohammadi, M. Perree-Fauvet, N. Gresh, K. Hillairet and
E. Taillandier, Biochemistry, 1998, 37, 6165.
18 R. F. Pasternack, E. J. Gibbs and J. J. Villafranca, Biochemistry, 1983,
22, 2406.
19 S. Marqusee and R. L. Baldwin, Proc. Natl. Acad. Sci. USA, 1987, 84,
8898; G. Merutka and E. Stellwagen, Biochemistry, 1990, 29, 894.
20 E. Biron, F. Otis, J.-C. Meillon, M. Robitaille, J. Lamothe, P. Van Hove,
M.-E. Cormier and N. Voyer, Bioorg. Med. Chem., 2004, 12, 1279; N.
Voyer, J. Am. Chem. Soc., 1991, 113, 1818.
21 F. Formaggio, S. Oancea, C. Peggion, M. Crisma, C. Toniolo, K.
Wright, M. Wakselman and J.-P. Mazaleyrat, Biopolymers, 2003, 71,
667; M. Crisma, C. Toniolo, S. Royo, A. I. Jimenez and C. Cataviela,
Org. Lett., 2006, 8, 6091; E. Cerasoli, B. K. Sharpe and D. N. Wollfson,
J. Am. Chem. Soc., 2005, 127, 15008; M. J. Pandya, E. Cerasoli, A.
Joseph, R. G. Stoneman, E. Waite and D. N. Wollfson, J. Am. Chem.
Soc., 2004, 126, 1716; D. Papapostolou, A. M. Smith, E. D. T. Atkins,
S. J. Oliver, M. G. Ryadnov, L. C. Serpell and D. N. Wollfson, Proc. Natl.
Acad. Sci. USA, 2007, 104, 10853; P. K. Kienker, W. F. DeGrado and
J. D. Lear, Proc. Natl. Acad. Sci. USA, 1994, 91, 4859; W. F. DeGrado
and J. D. Lear, J. Am. Chem. Soc., 1985, 107, 7684.
27 G. D. Strahan, D. Lu, M. Tsuboi and K. Nakamoto, J. Phys. Chem.,
1992, 96, 6450; J. A. Strickland, L. G. Marzilli and W. D. Wilson,
Biopolymers, 1990, 29, 1307; D. L. Banville, L. G. Marzilli, J. A.
Strickland and W. D. Wilson, Biopolymers, 1986, 25, 1837.
28 R. F. Pasternack, E. J. Gibbs, A. Gaudemer, A. Antebi, S. Bassner,
L. D. Poy, D. H. Turner, A. Williams, F. Laplace, M. H. Lansard, C.
Merienne and M. Perre-Fauvet, J. Am. Chem. Soc., 1985, 107, 8179.
29 H. Okada, H. Imai and Y. Uemori, Bioorg. Med. Chem., 2001, 9, 3301;
N. Yamakawa, Y. Ishikawa and T. Uno, Chem. Pharm. Bull., 2001, 49,
1531; Y. Ishikawa, N. Yamakawa and T. Uno, Bioorg. Med. Chem.,
2002, 10, 1953.
30 N. E. Mukundan, G. Petho, D. W. Dixon and L. G. Marzilli, Inorg.
Chem., 1995, 34, 3677.
31 C. Verche`re-Be´aur, M. Perre´e-Fauvet, E. Tarnaud, G. Anneheim-
Herbelin, N. Boˆne and A. Gaudemer, Tetrahedron, 1996, 52, 13589
and references cited therein.
32 R. J. Fiel, J. Biomol. Struct. Dyn., 1989, 6, 1259; R. F. Pasternack and
E. J. Gibbs, Met. Ions Biol. Syst., 1996, 33, 367.
This journal is
The Royal Society of Chemistry 2008
Org. Biomol. Chem., 2008, 6, 2507–2515 | 2515
©