2-Phenanthrenyl-DNA: Synthesis, pairing, and fluorescence properties

Article abstract of DOI:10.1002/chem.200801135

Three 2′-phenanthrenyl-C-deoxyribonucleosides with donor (phenNH ₂), acceptor (phenNO₂), or no (phenH) substitution on the phenanthrenyl core were synthesized and incorporated into oligodeoxyribonucleotides. Duplexes containing eithe

Full text of DOI:10.1002/chem.200801135

FULL PAPER
DOI: 10.1002/chem.200801135
2-Phenanthrenyl–DNA: Synthesis, Pairing, and Fluorescence Properties
Nikolay A. Grigorenko and Christian J. Leumann*[a]
Abstract: Three 2’-phenanthrenyl-C-
deoxyribonucleosides with donor
cence spectroscopy. Depending on the
nature of the substituent, the thermal
stability of single-modified duplexes
can vary between ꢀ2.7 to +11.38C in
Tm and that of triple-modified duplexes
from +7.8 to +11.18C. Van’t Hoff
analysis suggested that the observed
higher thermodynamic stability in
phenH- and phenNO2-containing du-
plexes is of enthalpic origin. A single
phenH or phenNO2 residue in a bulge
position also stabilizes a corresponding
duplex. If a phenNO2 residue is placed
in a bulge position next to a base mis-
match this can lead, in a sequence-de-
pendent manner, to duplex destabiliza-
tion. The phenNO2 residue was found
to be a highly efficient (10–100-fold)
quencher of phenH and phenNH2 fluo-
rescence if placed in the opposite posi-
tion to the fluorophores. When phenH
and phenNH2 residues were placed op-
posite each other, efficient quenching
of phenH and enhancement of
phenNH2 fluorescence was found,
which is an indicator for electron- or
energy-transfer processes between the
aromatic units.
(phenNH2), acceptor (phenNO2), or no
(phenH) substitution on the phenan-
threnyl core were synthesized and in-
corporated into oligodeoxyribonucleo-
tides. Duplexes containing either one
or three consecutive phenR residues,
which were located opposite each
other, were formed. Within these resi-
dues, the phenR residues are expected
to recognize each other through inter-
strand stacking interactions, in much
the same way as described previously
for biphenyl DNA. The thermal, ther-
modynamic, and fluorescence proper-
ties of such duplexes were determined
by UV melting analysis and fluores-
Keywords: DNA recognition · hy-
drophobic bases · oligonucleotides ·
phenanthrene
tions
· stacking interac-
Introduction
phobic or stacking interactions. Interesting examples are
shape mimics of the natural base pairs as in the case of, for
example, the difluorotoluene/methylbenzimidazole pair,[18]
or aromatic units that recognize each other and stabilize du-
plexes through interstrand stacking interactions as, for ex-
ample, the propynylcarbostyryl pair.[3,19]
Considerable effort has recently been invested in the design
and development of novel DNA base pairs that are orthogo-
nal in their recognition properties when compared with the
natural base pairs. Most of these investigations were driven
by the search for additional base pairs to be used for the ex-
tension of the genetic alphabet,[1–8] as tools in biotech-
nology,[9–11] for probing recognition, fidelity, and nucleotide
processing by DNA polymerases,[12–15] or for designing novel
genetic systems.[16,17] Of special interest amongst these artifi-
cial constructs are aromatic base replacements that interact
with each other, specifically without the formation of hydro-
gen bonds, merely on the basis of edge-on or face-on hydro-
Growing interest for artificial base pairs also comes from
the side of materials research and nanosciences. The long-
range charge transport through the p stack of the double
helix makes DNA an interesting candidate for biosensor ap-
plications.[20,21] Moreover, the introduction of metallo base
pairs into DNA greatly expands its electronic and magnetic
functionality, which is of interest for molecular storage devi-
ces and applications as molecular wires and semiconduc-
tors.[22–24] The latter field has also recently been reviewed.[25]
Thus, there is clear evidence that novel molecular architec-
tures with enhanced functionality based on the DNA double
helix can dramatically expand the field of DNA materials.
In a related context, we recently synthesized bipyridyl-
and biphenyl–DNA and studied their pairing and spectro-
scopic properties. We found that multiple consecutive bi-
phenyl pairs can recognize each other through interstrand
[a] Dr. N. A. Grigorenko, Prof. C. J. Leumann
Department of Chemistry & Biochemistry
University of Bern
Freiestrasse 3, 3012 Bern (Switzerland)
Fax : (+41)31-631-3422
E-mail: leumann@ioc.unibe.ch
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/chem.200801135.
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639

stacking interactions in the center of a DNA double helix
with a continuing increase in duplex stability.[26–28] A recent
NMR structure confirmed the interstrand stacking motif for
a system with one biphenyl pair.[29] In addition we could
show that the remote biphenyl rings can be equipped with
acceptor or donor substituents without alteration of the
overall duplex architecture. Such substitutions change the
redox potentials of the aromatic systems and lead to re-
markable differences in relative affinities, and in some cases
to interesting fluorescent properties.[30,31] In a more biologi-
cal context, biphenyl–DNA has also been investigated by
others, for example, as a tool to study the base-flipping
mechanism of DNA-alkylating enzymes.[32–34]
However, biphenyl units are not ideally suited for extend-
ed stacking interactions owing to the intrinsic non-coplanari-
ty of the phenyl rings. An evident way to overcome this lim-
itation with minimal overall structural changes is by substi-
tuting the 4-biphenyl units with 2-phenanthrenyl units. As
an additional advantage, phenanthrene shows a slightly
larger aromatic surface area compared with biphenyl, which
is expected to contribute positively to duplex stability and
has more advantageous fluorescence properties. Non-nucle-
osidic phenanthrene units were previously investigated in
the context of DNA architectures as intercalating strand-
linking elements[35,36] and have recently been used as stabil-
izers for triple-helical DNA structures.[37]
genated aromatic substrates,[38] or addition of metalated aro-
matic substrates with differently activated glycosyl
donors.[39–42] Among the available methods, we have chosen
a direct approach that consists of a reaction of the metalated
species with TBS-protected 2’-deoxyribolactone followed by
reduction of the resulting hemiacetal.[43] Although typically
resulting in poorer yields, it is the shortest synthesis and it
proceeds stereospecifically. Experimental procedures and
analytical characterization of all products and intermediates
are contained in the Supporting Information.
2,7-Dibromophenanthrene[44] was monolithiated and re-
acted with lactone 1[43] (Scheme 1). Subsequent reduction of
the resulting hemiacetal with Et3SiH in the presence of
BF3·Et2O afforded the mixture of the C-nucleosides 2 and 3
in a 16% combined yield and in a 10:1 ratio, both possessing
1
the desired 1’-b-configuration as verified by H NOE experi-
ments. No traces of a-anomers were detected by NMR spec-
troscopy, thus giving evidence for a greater than 98% selec-
Herein we report on the synthesis of three 7-functional-
ized 2-phenanthrenyl-C-nucleosides (Figure 1) their incorpo-
ration into oligodeoxyribonucleotides and the investigation
of their pairing and fluorescence properties.
Scheme 1. Reagents and conditions: a) 2,7-dibromophenanthrene, nBuLi
(1.1 equiv), THF, ꢀ788C, 1 h, then 1 (1 equiv) in THF, ꢀ788C, 4 h;
b) Et3SiH (3 equiv), BF3·OEt2 (3 equiv), CH2Cl2, ꢀ788C, 6 h. Yields: 2
(15%), 3 (1.5%); c) nBuLi (1.1 equiv), THF, ꢀ788C, 1 h, then H2O.
Yield: quantitative; d) nBuLi (1 equiv), THF, ꢀ788C, 40 min, TsN3
(1.2 equiv), THF, ꢀ708C, 5 h, Na2HPO4 (2 equiv), H2O, Et2O, THF,
+58C, 12 h. Yield: 91%; e) SnCl2, MeOH, THF, 08C!RT, 1.5 h. Yield:
85%; f) FmocCl (2 equiv), iPr2NEt (2 equiv), CH2Cl2, RT, 5 h. Yield:
77%; g) dimethyl dioxirane (0.075m, 4.1 equiv), acetone, MeCN, ꢀ808C,
2 h. Yield: 75%; h) TBAF (1.4 equiv), THF, RT or (HF)3·NEt3 (8 equiv),
THF, RT, 24 h. Yield: 75–95%; i) 4,4’-dimethoxytrityl (DMT) chloride
Figure 1. a) Structure of the phenanthrenyl-C-nucleoside units; b) cartoon
representation of the expected zipper-like duplex structure; c) sequence
information of the mono- and triple-modified duplexes. A and B refer to
strand A and B, respectively, whereas 1 and 3 designates single or triple
modification, respectively. phenR denotes the ensemble of phenH,
phenNH2, or phenNO2 residues.
Results and Discussion
(1.2–1.9 equiv),
pyridine,
08C,
5 h.
Yield:
73–87%;
Synthesis of building blocks: Several methods are known for
the selective synthesis of b-configured C-nucleosides. These
include Heck coupling of glycals with appropriately halo-
j) (iPr2N)(NCCH2CH2O)PCl (1.5 equiv), iPr2NEt (3 equiv), THF, RT,
1.5 h. Yield: 70–83%. Fmoc=9-fluorenylmethoxycarbonyl, TBAF=
tetra-n-butylammonium fluoride, TBS=tert-butyldimethylsilyl.
640
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Investigation of 2-Phenanthrenyl–DNA
FULL PAPER
tivity in the reduction step. Chromatographic separation of
2 and 3 was unsuccessful at this stage but could be per-
formed after reduction of the azide 4. Alternatively, the
mixture of 2 and 3 could be lithiated and quenched with
H2O to obtain pure 3.
For the introduction of the functional groups, a conver-
gent approach based on a nitrogen electrophile was chosen.
Consequently, bromide 2 was treated with nBuLi and react-
ed with p-tosyl azide[45] to give azide 4, which was subse-
quently reduced to the amine 5 with SnCl2. The oxidation of
amine 5 to the nitro compound 7 was performed with dime-
thyldioxirane[46] at low temperature (ꢀ858C) to suppress
concomitant hydroxylation as a side reaction and proceeded
in 75% yield. The remaining steps in the synthesis to the
phosphoramidites 14–16 were classical functional-group
transformations and proceeded as expected.
data (Table 1), it is clear that there are remarkable differen-
ces depending on the nature of the substituents on the
phen-core. Insertion of one phenNO2 pair stabilizes the
Table 1. Tm data (8C) from UV melting curves at 260 nm of duplexes of
the mono-series.[a]
5’-d(GATGAC-phenR-GCTAG) (1A)
3’-d(CTACTG-phenR-CGATC) (1B)
1A/1B
phenH
phenNO2
phenNH2
dG[b]
del[c]
phenH
phenNO2
phenNH2
dC[b]
45.8
51.7
44.8
41.9
50.2
52.4
57.5
51.7
46.7
53.4
45.0
50.8
43.5
40.3
44.2
47.3
49.7
46.3
51.9
–
51.0
53.9
46.0
–
del[c]
46.2[d]
[a] c=1.2 mM in 10 mm NaH2PO4, 0.15m NaCl, pH 7.0. Estimated error
in Tm =ꢁ0.58C. [b] Natural deoxyribonucleotide instead of phenR unit.
[c] del=phenR deletion; opposing phenR residue in bulge position.
[d] Tm of the phenR-deletion mutant duplex.
Design and synthesis of oligonucleotides (ONs): For deter-
mination of the recognition properties, two standard se-
quence contexts were chosen. One sequence (mono-series)
contained a single incorporation of a phenR pair and the
other (triple-series) contained three contiguous phenR pairs
in the center of the duplex (Figure 1). Sequences were de-
signed to contain only one type of phenR-C-nucleoside per
strand. Owing to the fact that the sequences are not self-
complementary, permutational arrangements of donor- and
acceptor-substituted phenR residues in the duplex were pos-
sible and there was no interference from hairpin formation
that had to be taken care of. All ONs were synthesized on a
1.2-mmol scale by using standard protocols for automated
DNA synthesis on solid supports except for an extended
coupling time (6 min) for the non-natural phosphoramidites.
An overview of all synthesized oligonucleotides with mass
analytical data is given in Table S1 in the Supporting Infor-
mation.
duplex by +11.38C relative to a deletion mutant duplex,
which lacks the phenR pair (Tm =46.28C). This is twice the
stability as is brought about by one G–C base pair in the
same position (+5.78C). The unsubstituted phenH pair does
not alter the stability significantly and the phenNH2 pair
leads to a slight destabilization when compared with the
parent deletion mutant duplex. The stability of duplexes
with hetero-phenR pairs is in all cases intermediate to the
corresponding homo phenR pairs.
Replacement of the phenR units in strand A with natural
dC residue (mismatch with natural base) leads to considera-
ble destabilization (up to ꢀ10.88C in the case of phenNO2)
when compared with the duplexes with phenR units in both
strands. This is, however, different when the natural base is
a purine base. Thus replacement of phenR by G in strand B
results in stabilization in the case of phenH and phenNH2,
but is still destabilizing for phenNO2. In general, duplexes
with phenR residues located opposite to the G residue are
more stable than those opposite to the C residue. This is
most likely due to the higher hydrophobicity and enhanced
stacking interactions of guanine with the opposing phenR
unit. When phenR residues were inserted into the bulge po-
sitions, phenNO2 is the most stabilizing (+7.78C/+7.28C),
whereas phenNH2 slightly destabilizes the duplex. PhenH
shows intermediate stability in relation to phenNO2 and
phenNH2.
Thermal stability of duplexes of the mono series: The ther-
mal stabilities were determined by UV melting curve analy-
sis. A selection of curves is shown in Figure 2. From the Tm
Thermal stability of the triple-series: The Tm data of duplex-
es containing three phenR pairs are summarized in Table 2.
The consecutive incorporation of three phenNO2 units did
not lead to a further increase in Tm, but caused some desta-
bilization as compared to the mono-modified duplex. In
fact, the phenNO2 duplex was found to be the least stable
among all the triple-modified duplexes. The opposite effect
was observed with the phenH and the phenNH2 modifica-
tions. In these cases, the additional two nucleotides resulted
in a stabilization of 8.78C in the case of phenH and 11.68C
for phenNH2, which is translated into 4.38C and 5.88C per
Figure 2. UV melting curves (260 nm) of selected phenR-containing du-
plexes of the mono series. c=1.2 mm in 10 mm NaH2PO4, 0.15m NaCl,
pH 7.0.
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C. J. Leumann and N. A. Grigorenko
Table 2. Tm-data (8C) from UV melting curves at 260 nm of duplexes of
Table 3. Thermodynamic data of duplex formation.[a]
the triple series.[a]
5’-GATGAC-(phenR)n-GCTAG-3’
3’-CTACTG-(phenR)n-CGATC-5’
5’-d
3’-d
G
E
(3A)
(3B)
N
U
n
DG298 K
DH
DS
3A/3B
phenH
phenNO2
phenNH2
[kcalmolꢀ1
]
[kcalmolꢀ1
]
[cal Kꢀ1 molꢀ1
]
phenH
phenNO2
phenNH2
54.5
56.0
54.0
55.4
53.3
56.8
54.1
57.3
55.1
phenH
phenH
PhenNO2
PhenNO2
1
3
1
3
ꢀ13.3
ꢀ15.2
ꢀ15.7
ꢀ14.9
ꢀ67.4
ꢀ69.6
ꢀ69.3
ꢀ68.5
ꢀ181
ꢀ182
ꢀ180
ꢀ180
[a] c=1.2 mm in 10 mm NaH2PO4, 0.15m NaCl, pH 7.0. Estimated error in
Tm =ꢁ0.58C.
[a] Data from 1/Tm versus ln(c) plots; concentration range: 0.5–15 mm in
10 mm NaH2PO4, 0.15m NaCl, pH 7.0. Quality of linear fit (R2)>0.995.
modification, respectively (Figure 3). Moreover, the stability
of the mixed phenNH2/phenNO2 triple-modified duplex was
higher than that of both corresponding homo-modified du-
plexes, suggesting an additional gain in energy owing to
electrostatic donor–acceptor interactions.
ic molecules by various synthetic and natural receptor sys-
tems is well established and is described by a nonclassical
hydrophobic effect.[47] The data support our model in which
the differences between the mono and the triple series,
which reflect interactions of the phenR units solely, are
mostly due to changes in solvation in the phenH case and to
electrostatic or dispersive effects in the phenNO2 case. Both
these cases are in line with earlier results on biphenyl–
DNA.[30]
Mismatch discrimination: For biotechnological applications,
for example, for single nucleotide polymorphism detection,
it is desirable to have probes with increased sensitivity for
base mismatches. In this context we were interested to de-
termine whether a phenR unit in a bulge position next to a
mismatch can modulate its effect on Tm. We thus compared
the alteration of duplex stability caused by a single mis-
match in presence and absence of a phenR nucleotide in a
bulge position on both the 5’- and 3’-side of the mismatch
on either strand (Figure 4).
Figure 3. Comparison of Tm data for homo mono- and triple-modified du-
plexes.
It clearly appears that a phenNH2 bulge in strand A
(Figure 4, top) leads to stabilization of all mismatches (4 to
68C), except purine–purine mismatches. Incorporation of a
phenH in the bulge had an effect analogous to that of
PhenNH2, namely considerable stabilization, again with the
exception of purine–purine mismatches. Conversely,
phenNO2 had little, if any, effect on mismatch Tm. The pic-
ture is somewhat different if the bulge is moved to strand B
(Figure 4, bottom). In this case, a phenNO2 bulge decreased
mismatch Tm values in all cases by 2–58C. Only phenNH2 in
the bulge had a significant stabilizing effect on A–C and C–
C mismatches on the 5’ side of the modification. Generally
speaking, phenNO2 in a bulge leads, in most cases, to equal
or substantially stronger discrimination of mismatches on
either the 3’ or 5’ side of the bulge. As a result, this best fits
the profile of a mismatch discrimination enhancer within the
three phenR units investigated here. We note, however, that
there is considerable sequence dependence. The fact that
purine–purine mismatches are more strongly discriminated
by a phenR bulge might be due to their preferred structural
arrangement in the double helix, which is also intercalative
in nature.[48] This prevents the concomitant intercalation of
the bulged phenR residue through steric causes.
The thermal melting behavior of phenR–DNA follows the
same trend as that described earlier for biphenyl–DNA.[30]
However, the Tm values for the phenR-containing duplexes
are typically higher by 3–78C compared with biphenyl-con-
taining duplexes. This is most likely due to the higher stack-
ing surface and the intrinsically flat structure of the phen-
core, increasing the hydrophobic effect upon duplex forma-
tion and adjusting the geometry of the aromatic unit for
easier intercalation.
Thermodynamic data of duplex formation: To obtain more
information about the origin of the differences in thermal
stability as a function of the phenR units, we measured the
thermodynamic parameters of duplex formation by concen-
tration-dependent Tm measurements (van’t Hoff analysis)
for the homo phenH and the homo phenNO2 duplexes
(mono and triple series). The results are summarized in
Table 3.
The free energy changes (DG) upon duplex formation are
in agreement with the order of thermal duplex stabilities. In
all cases, the differences in thermodynamic stability seem to
be enthalpy (DH) based, whereas the entropy terms are sur-
prisingly constant. Enthalpy-driven complexation of aromat-
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Investigation of 2-Phenanthrenyl–DNA
FULL PAPER
Figure 5. Normalized excitation spectra of ONs 1B-H and 3B-H and
duplex 1 A-H/1B-H, monitoring emission intensity at 373 nm (c=1.2 mm
ON in 10 mm NaH2PO4, 0.15m NaCl, pH 7.0, T=208C). If =fluorescence
intensity.
Figure 4. DTm data from UV melting curves (conditions as in Table 2)
from mismatched duplexes with and without a phenR residue (Z) in the
bulge position next to the mismatch. The phenR-containing strands are
from the mono-series strand A (top) and strand B (bottom) that were
paired to their mismatched DNA complement.
Fluorescence properties of phenR containing oligonucleo-
tides: We studied the fluorescence properties of phenR-con-
taining ONs both in the single-strand and the duplex state.
Single-strand ONs containing one or three phenH insertions
show a well-structured emission spectrum with a maximum
at 373 nm that, apart from a slight solvent shift, is analogous
to the emission spectrum of the corresponding monomeric
nucleoside in methanol. The absence of a red-shifted band
in the fluorescence spectra of 3B-H and the duplexes 1A-H/
1B-H and 3A-H/3B-H indicated no excimer or exciplex for-
mation. Excitation spectra, monitoring emission intensity at
373 nm, revealed a rather broad band with maximum excita-
tion around 250 nm for all phenH ONs (Figure 5). This is in
good agreement with the absorption maximum of the
parent, free nucleoside (252 nm). The fluorescence intensity
of single strands is reduced with increasing temperature in a
non-cooperative manner owing to enhanced collisional
quenching.
Pairing with a complementary strand leads to a marked
quenching of the phenH fluorescence in the case of the
mono series (Figure 6a), thus proving the tight positioning
of phenH residues inside the base stack relative to neighbor-
ing G bases, which are known to quench fluorescence. How-
ever, for triple-modified ONs, addition of a complementary
strand slightly increases fluorescence intensity. This leads to
different fluorescence melting profiles for mono- and triple-
Figure 6. a) Fluorescence spectra of phenH-containing ONs and duplexes.
b) Melting curves of the duplexes 1 A-H/1B-H and 3 A-H/3B-H as moni-
tored by the emission intensity at 373 nm. Conditions: excitation wave-
length 252 nm; c=1.2 mm duplex in 10 mm NaH2PO4, 0.15m NaCl,
pH 7.0; T=208C (for a)); heating rate 0.58C per min (for b)). If =fluo-
rescence intensity.
modified duplexes, as illustrated in Figure 6b. The vibration-
al structure in the fluorescence spectrum of the duplexes
was nearly completely preserved. Also, in the triple-modi-
fied duplex, no red-shifted emission bands were observed
below the melting temperature, thus again excluding exci-
mer formation.
The absence of excimer formation is no surprise as phen-
anthrene itself does not form an excimer under classical
conditions.[49] Excimers with emission maxima in the range
of 384–432 nm could only be identified when fixed in close
proximity in a face-to-face orientation by means of rigid
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643

C. J. Leumann and N. A. Grigorenko
scaffolds, such as phen-cyclophanes, and also depending on
surface overlap and interplanar distance.[50]
Nitroaromatic compounds are generally known to be non-
fluorescent, even if the parent hydrocarbon is highly emis-
sive. This is also the case for PhenNO2 units incorporated
into ONs that showed no emission upon excitation at
277 nm (maximum of PhenNO2 absorption). Moreover,
when paired to complementary ONs with PhenH or
PhenNH2 units, PhenNO2-containing ONs acted as excellent
quenchers, reducing the fluorescence by 1–2 orders of mag-
nitude in the triple-modified series (Figure 7) and to a
slightly reduced extent also in the mono-modified series.
This observation calls for tight packing of the phenR-pairs
inside the base stack.
Figure 8. a) Fluorescence emission spectra of the triple-modified duplexs-
es with homo and hetero phenH and phenNH2 pairs and the correspond-
ing single strands. Excitation wavelength: 252 nm; b) normalized excita-
tion spectra monitoring emission at 425 nm. Conditions: T=208C, c=
1.2 mm duplex in 10 mm NaH2PO4, 0.15m NaCl, pH 7.0. If =fluorescence
intensity.
Figure 7. Quenching of phenH and and phenNH2 fluorescence in the
triple series upon pairing with a complementary ON containing three
PhenNO2 residues. Excitation wavelength: 252 nm (for phen-H) or
264 nm (for phenNH2), c=1.2 mm duplex in 10 mm NaH2PO4, 0.15m
NaCl, pH 7.0, T=208C. If =fluorescence intensity.
mally occurs at wavelengths higher than that of the emission
of the isolated constituents, we assume again that no exci-
plex is formed in the 3phenH/3phenNH2 duplex, although
we cannot completely rule it out. The mechanistically most-
plausible explanation for the observed fluorescence behav-
ior therefore involves charge transfer. Given that stacking of
the aromatic moieties in a face-to-face manner is a require-
ment for efficient charge or energy transfer, our results sug-
gest efficient interstrand interaction of the phenR residues
in these duplexes.
Duplexes with mixed phenH/phenNH2 pairs feature inter-
esting fluorescence properties compared with the duplexes
with the respective homo-pairs. (Figure 8a). In the mixed ar-
rangement, the phenH emission at 373 nm is completely
quenched and the emission at the phenNH2 band is substan-
tially enhanced when excited at the maximum absorbance of
the phenH residues at 252 nm. The excitation spectra of the
mixed duplex with monitoring of the emission intensity at
425 nm revealed a maximum at 249–250 nm, which corre-
sponds to the maximum absorption of the phenH fragments
and not to the maximum absorption of the phenNH2 units
(262 nm) (Figure 8b). This observation strongly suggests
that emission enhancement at 425 nm is due to electronic
coupling of the two chromophores. A similar effect was also
observed in the mono-modified series (see the Supporting
Information).
Conclusion
We have prepared a set of novel phenanthrene-C-nucleo-
sides that contain donor and acceptor substituents and have
incorporated them into oligonucleotides. As observed previ-
ously for biphenyl–DNA,[30] these residues, when located in
opposite positions in the duplex, most likely organize in a
zipper-like interstrand intercalation motif. We observed re-
markable differences in thermal stability as a function of the
chemical properties of the substituted phenR residues and
their interaction with the nearest natural base pairs, or
phenR neighbors. The fluorescent properties of these phenR
residues in oligonucleotide duplexes range from highly
Quenching of the excited states of aromatic hydrocarbons
by aromatic amines is a well established process and is typi-
cally known to proceed through electron transfer.[51] Fur-
thermore, it has been shown that phenanthrene efficiently
forms exciplexes with aromatic amines, in particular with
N,N-dimethylaniline.[52] Given that exciplex emission nor-
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Investigation of 2-Phenanthrenyl–DNA
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Received: June 10, 2008
Revised: August 27, 2008
Published online: December 3, 2008
Chem. Eur. J. 2009, 15, 639 – 645
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