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T. Tedeschi et al. / Tetrahedron Letters 46 (2005) 8395–8399
monitored by standard Kaiser and Chloranil qualitative
tests. All the PNA oligomers were cleaved from the solid
support by treatment with a TFA/TFMSA/m-cresol/
thioanisole = 6:2:1:1 mixture and obtained, usually
quantitatively, after precipitation with diethyl ether.
All PNAs (7a–h) were purified by a semi-preparative
RP-HPLC (average yield after purification: 20–30%)22
and characterized by ESI-MS.23
are simultaneously oligonucleotide and peptide mimics
therefore potentially able to show both protein-like
and DNA-like recognition properties.
Acknowledgements
Financial support from The Italian Ministry of
Education, University and Research (MIUR) through
Projects of Relevant National Interest (PRIN 2003)
CIB (Consorzio Interuniversitario Di Biotecnologie) is
gratefully acknowledged. The NMR facilities were made
available by The Centro Interfacolta Misure-Universita
Di Parma.
4. Thermal stability of antiparallel PNA–DNA duplexes
As a preliminary study on the effect of the configura-
tions of the stereogenic centres on the DNA binding
abilities, all PNA decamers 7a–h were hybridized to
the complementary antiparallel DNA sequence (50-
AGTGATCTAC-30) and the duplex melting tempera-
tures (Tm) were determined by circular dichroism (CD)
by measuring at 260 nm the ellipticity variation with
the temperature of the solutions containing the duplexes
(5 lm) (Table 1).14 For comparison, also the Tm of the
PNA–DNA duplex formed by the corresponding achiral
PNA and by the two lysine-Ôchiral boxÕ PNAs are
reported.
References and notes
1. Nielsen, P. E.; Egholm, M.; Berg, R. H.; Buchardt, O.
Science 1991, 254, 1497.
2. Egholm, M.; Buchardt, O.; Christensen, L.; Behrens, C.;
Freier, S. M.; Driver, D. A.; Berg, R. H.; Kim, S. K.;
Norden, B.; Nielsen, P. E. Nature 1993, 365, 566.
3. Nielsen, P. E. Lett. Pep. Sci. 2003, 10, 135.
4. Uhlmann, E.; Peyman, A.; Breipohl, G.; Will, D. W.
Angew. Chem., Int. Ed. 1998, 37, 2797.
5. Koppelhus, U.; Nielsen, P. E. Adv. Drug Delivery Rev.
2003, 55, 267.
6. Kumar, V. A.; Ganesh, K. N. Acc. Chem. Res. 2005, 38,
404–412.
From these preliminary experiments it clearly appears
that the configuration of the stereogenic centres has a
profound influence upon the DNA binding abilities of
the PNAs. As it is well known in the literature,13 when
the stereogenic centre is in position 2 (type I) the
DNA binding is slightly favoured by the D configura-
tion (7b better than 7a).
7. Haaima, G.; Lohse, A.; Buchardt, O.; Nielsen, P. E.
Angew. Chem., Int. Ed. 1996, 35, 1939.
8. Puschl, A.; Sforza, S.; Haaima, G.; Dahl, O.; Nielsen,
P. E. Tetrahedron Lett. 1998, 39, 4707.
9. Sforza, S.; Galaverna, G.; Dossena, A.; Corradini, R.;
Marchelli, R. Chirality 2002, 14, 591.
10. Corradini, R.; Di Silvestro, G.; Sforza, S.; Palla, G.;
Dossena, A.; Nielsen, P. E.; Marchelli, R. Tetrahedron:
Asymmetry 1999, 10, 2063.
11. Tedeschi, T.; Corradini, R.; Marchelli, R.; Puschl, A.;
Nielsen, P. E. Tetrahedron: Asymmetry 2002, 13, 1629.
12. Sforza, S.; Tedeschi, T.; Ciavardelli, D.; Corradini, R.;
Dossena, A.; Marchelli, R. Eur. J. Org. Chem. 2003,
1056.
13. Sforza, S.; Haaima, G.; Marchelli, R.; Nielsen, P. E. Eur.
J. Org. Chem. 1999, 197.
14. Sforza, S.; Corradini, R.; Ghirardi, S.; Dossena, A.;
Marchelli, R. Eur. J . Org. Chem. 2000, 2905.
15. Corradini, R.; Feriotto, G.; Sforza, S.; Marchelli, R.;
Gambari, R. J. Mol. Recognit. 2004, 17, 76.
16. Menchise, V.; De Simone, G.; Tedeschi, T.; Corradini, R.;
Sforza, S.; Marchelli, R.; Capasso, D.; Saviano, M.;
Pedone, C. P. Natl. Acad. Sci. U.S.A. 2003, 100, 12021.
17. Tedeschi, T.; Sforza, S.; Corradini, R.; Dossena, A.;
Marchelli, R. Chirality 2005, 17, S196–S204.
It is very interesting to notice that when the stereogenic
centre is in position 5(type III) the situation is reversed
and the DNA binding is much more favoured by the L
configuration (7g much better than 7h). When the two
stereogenic centres are simultaneously present (type
II), it is therefore not surprising that the best DNA bind-
ing takes place when the stereogenic centre in position 2
has the D configuration and the stereogenic centre in
position 5has the L configuration (7e). In this case,
the thermal stability of the PNA–DNA duplex is quite
outstanding, being 7 ꢁC higher than that achieved by
the homologous achiral PNA and 14 ꢁC higher than
the D-Lys Ôchiral boxÕ PNA. According to our previous
results, it seems obvious to speculate that in this case
the side chains are very well placed to fit in a right-
handed helix. Also the configuration 2L, 5L (7c) rather
favours DNA binding, suggesting that the influence of
the stereogenic centre in position 5is stronger than that
exerted by the stereogenic centre in position 2.
18. Kosynkina, L.; Wang, W.; Liang, T. C. Tetrahedron Lett.
1994, 35, 5173.
19. Falkiewicz, B.; Kolodziejczyk, A. S.; Liberek, B.; Wis-
niewki, K. Tetrahedron 2001, 57, 7909.
Studies are now in progress in order to define the pref-
erential handedness of the new PNAs bearing two stereo-
genic centres in the same residue and to confirm
whether the stability of the PNA–DNA duplexes can
be explained by this preference. Work is in progress to
study cases in which the two stereogenic centres induce
the same handedness (chiral sinergy) or the opposite
handedness (chiral conflict), both for antiparallel and
parallel mode of binding. The chiral monomers here
reported can be used for the synthesis of PNA, which
20. Compounds 6c–d: 1H NMR (300 MHZ, DMSO-d6): d
7.9–7.8 (m, 2H, aromatic Fmoc), 7.7–7.6 (m, 2H, aromatic
Fmoc), 7.4–7.3 (m, 12H, aromatic Fmoc + aromatic 2-Cl-
Z), 5.06 (m, 4H, CH2 2-Cl-Z), 4.3–4.2 (m, 3H, CH + CH2
Fmoc), 4 (br s, 1H, C(2)-H), 3.7–3.6 (m, 2H, C(4)-H2),
3.16 (br s, 1H, C(5)-H), 3–2.9 (m, 4H, CH2 Lys side chain),
1.3–1.1 (m, 12H, CH2 Lys side chain), 1.33 (s, 9H CH3
Boc); 13C NMR (75MHz, DMSO- d6): d 175.6, 156.8,