optical rotations and the structures unambiguously confirmed by X-
ray crystal data of both enantiomers (Fig. 1). The absolute
configurations were derived from a knowledge of the configuration
of the starting materials. The torsional angles b in both the cases
complex was less stable by 13° due to mismatch while the
destabilisation of cpPNA : DNA 20 complexes was larger by
18–30°. Thus the cpPNAs have a better selectivity (lower mismatch
tolerence) and a higher binding to cDNA sequences than the
unmodified PNA.
2
were around 25°, much less than those in reported PNA : DNA or
PNA : RNA complexes as well as in cyclohexane analogues.7
4
–6
The present results on cis-SR/RS cpPNAs viewed in relation to
9
The monomers 9a and 9b were incorporated into aeg-PNA-T
8
the limited data reported on trans-SS cpPNA clearly suggest a
oligomer 10 at defined positions by standard solid phase synthesis
followed by cleavage with TFA–TFMSA and purification by
reverse phase HPLC. All PNA oligomers (10–18) were charac-
stereochemical dependence of the stability and selectivity in DNA/
RNA binding. The dihedral angle b in 1,2-disubstituted cis-
cyclopentyl system is less than that in chPNA but the relative ease
of conformational adjustments in a cyclopentyl ring seems to have
significant consequences for the hybridization ability of cpPNA
oligomers. In addition to the unprecendented stabilization observed
for homooligomeric, homochiral SR- and RS-cpPNA oligomers
m
terised by MALDI-TOF. The T values of various PNAs
hybridized with complementary DNA 19, mismatched DNA 20 and
poly rA were determined from temperature-dependent UV ab-
sorbance plots and are shown in Table 1. A Job plot generated from
CD data indicated a binding stoichiometry of 2 : 1 for all DNA
m
with cDNA (DT +21–27°, RS > SR), the binding of these cpPNA
complexes indicating the formation of PNA
The data in Table 1 suggest that the T
except PNA 12) of both stereochemistry with complementary
2
: DNA triplexes.
to poly rA was also highly improved. These results suggest that in
cyclopentyl PNAs, the favourable conformational features of the
monomer are co-operatively transmitted to the oligomer level and
such effects are useful from an application perspective. Overall, the
results presented here reinforce the idea of improving stability and
DNA/RNA binding selectivity via rational structural modifications
of PNA. Further studies on sequence dependent and RNA/DNA
discriminatory effects of cpPNA are in progress.
m
of cpPNA complexes
(
DNA 19 and poly rA were significantly higher than the correspond-
ing complexes of control PNA 10. Among the cpPNA : DNA
complexes, RS isomers (PNA 14–16) gave a higher T compared to
m
SR isomers (PNA 11–13). The C-terminal substitution stabilized
the DNA and RNA complexes better than N-terminal substitution.
In case of cpPNA : poly rA complexes (barring cpPNA 15), the
presence of either SR/RS isomers at the C/N terminus or internally,
stabilized the complexes. Importantly, the RS and SR homo-
oligomeric PNAs 17 and 18 exhibited enormous stabilization of
both DNA and RNA complexes as compared to that of control PNA
TG thanks CSIR, New Delhi for the award of a fellowship. We
thank Dr. M. Bhadbhade and Mr. R. Gonnade for X-ray data. VAK
acknowledges DST, New Delhi for a research grant.
Notes and references
1
0. The stronger binding of cpPNA with DNA is achieved without
losing binding selectivity as substantiated by the T values of
mismatched cpPNA : DNA 20 complexes. The control PNA 10
‡
32 4 7
Crystal data: (1S,2R)-9. C21H N O , M = 452.51, crystal system:
m
rectangular, crystal dimensions 0.63 3 0.60 3 0.24 mm, a = 10.6505(7),
3
3 1 1
b = 10.6505(7), c = 43.402(4) Å, space group P4 2 2 , V = 4923.3(6) Å ,
2
3
21
Z = 8, D = 1.221 g cm , m(Mo-Ka) = 0.092 mm , T = 293(2) K,
c
F(000) = 1936, max. and min. transmission 0.9786 and 0.9438, 34716
reflections collected, 4339 unique [I > 2s(I)], S = 1.370, R = 0.0733, wR2
=
=
0.1537 (all data R = 0.0746, wR2 = 0.1543). (1R,2S)-9: C21
452.51, crystal system: tetragonal, crystal dimensions 0.66 3 0.33 3
, a = 10.6483(4), b = 10.6483(4), c =
32 4 7
H N O , M
0
.11 mm, space group P4
1 1 1
2 2
3
23
4
0
0
3.318(3) Å, V = 4911.7(4) Å , Z = 8, D = 1.224 g cm , m(Mo-Ka) =
c
21
.092 mm , T = 293(2) K, F(000) = 1936, max. and min. transmission
.9903 and 0.9416, 24647 reflections collected, 4333 unique [I > 2s(I)], S
=
1.123, R = 0.0537, wR2 = 0.1164 (all data R = 0.0693, wR2 = 0.1224).
CCDC 227530 and 227531. See http://www.rsc.org/suppdata/cc/b3/
b317000d/ for crystallographic data in CIF or other electronic format.
Fig. 1 ORTEP diagrams of crystal structures of 9. a (1S,2R); b (1R,2S).‡
1 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,
1
993, 365, 566–568.
Table 1 UV-T
m
of cpPNA : DNA/RNA triplexesa
DNA 19 DNA 20 Poly rA
2 D. A. Braasch and D. R. Corey, Biochemistry, 2002, 41, 4503–4510.
3
4
(a) K. N. Ganesh and P. E. Nielsen, Curr. Org. Chem., 2000, 4,
1931–1943; (b) V. A. Kumar, Eur. J. Org. Chem., 2002, 2021–2032.
S. C. Brown, S. A. Thomson, J. M. Veal and D. J. Davis, Science, 1994,
265, 777–780.
5 M. Ericksson and P. E. Nielsen, Nat. Struct. Biol., 1996, 3, 410–413.
6 L. Betts, J. A. Josey, M. Veal and S. R. Jordan, Science, 1995, 270,
1838–1841.
7 T. Govindaraju, R. G. Gonnade, M. M. Bhadbhade, V. A. Kumar and K.
N. Ganesh, Org. Lett., 2003, 5, 3013–3016.
8 J. B. Lambert, J. J. Papay, S. A. Khan, K. A. Kappauf and E. S. Magyar,
J. Am. Chem. Soc., 1974, 96, 6112–6118.
Entry PNA
1
2
3
4
5
6
7
8
9
a
PNA 10, H-TTTTTTTTT-LysNH
2
45.0
51.0
22.0
44.5
55.0
62.0
48.7
66.6
72.0
34.5
27.8
11.0
26.4
28.0
32.0
27.8
nd
62.0
73.5
76.0
66.0
> 85.0
61.0
69.0
> 85.0
> 85.0
PNA 11, H-TTTTTTTTtSR-LysNH
PNA 12, H-TTTTtSRTTTT-LysNH
PNA 13, H-tSRTTTTTTTT-LysNH
PNA 14, H-TTTTTTTTtRS-LysNH
PNA 15, H-TTTTtRSTTTT-LysNH
PNA 16, H-tRSTTTTTTTT-LysNH
2
2
2
2
2
2
PNA 17, H-(tSR
PNA 18, H-(tRS
)
8
-LysNH
-LysNH
2
)
8
2
nd
9 M. C. Myers, M. A. Witschi, N. V. Larionova, J. M. Franck, R. D.
Haynes, T. Hara, A. Grakowski and D. H. Appella, Org. Lett., 2003, 5,
All values are an average of at least 3 experiments and accurate to within
2
695–2698.
0 (a) K. Faber, H. Honig and P. Seufer-Wasserthal, Tetrahedron Lett.,
988, 29, 1903–1904; (b) H. Honig and P. Seufer-Wasserthal, J. Chem.,
Soc., Perkin Trans. 1, 1989, 2341–2345.
±
0.5°. DNA 19, d(CGCAAAAAAAACGC); DNA 20, d(CGCAAAA-
1
CAAACGC). Buffer. Sodium phosphate (10 mM), pH 7.2 with 100 mM
NaCl and 0.1 mM EDTA; nd, not determined.
1
C h e m . C o m m u n . , 2 0 0 4 , 8 6 0 – 8 6 1
861