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K.-H. Altmann et al. / Bioorg. Med. Chem. Lett. 10 (2000) 929±933
Table 1. Melting temperatures (Tm's) of complexes between oligomer A and complementary RNA and DNAa
RNA/DNA complement
r[(AG)5A5]
r[A5(GA)5]
d[(AG)5A5]
d[A5(GA)5]
r[(AG)4ACA5]
Tm (ꢀC):
TmWT (ꢀC):b
34.0c (33.2d)
52.4
34.5c (34.9d)
53.3
n.c.e
42.8
n.c.e
43.2
23.3
42.9
aTm's were determined in 10 mM phosphate buer, pH7, 100 mM Na+, 0.1 mM EDTA at 4 mM strand concentrations (for details cf. ref 21).
bTm's for the corresponding natural (antiparallel) DNA/RNA and DNA/DNA duplexes.
cTransition-temperature obtained upon slow heating (0.5 ꢀC/min) of a 1/1 mixture of oligomer A and the corresponding RNA complement from
5
to 95ꢀ after initial slow heating and subsequent slow cooling over the same temperature range. In the case of A/r[(AG)5A5] two cooperative transi-
tions were observed at 33.5 and 68.4 ꢀC, respectively, upon immediate slow heating of a freshly prepared 1/1 mixture. The latter transition was not
observed upon subsequent cooling or re-heating of the same sample (cf text).
dTransition-temperature obtained upon slow cooling of a 1/1 mixture of oligomer A and the corresponding RNA complement from 95 to 5 ꢀC
after initial slow heating over the same temperature range.
eNo cooperative transition observed.
signi®cantly more stable than the corresponding com-
plexes incorporating oligonucleotide analogues of types
Acknowledgements
II±IV (cf. Fig. 1).6b On the other hand, Lowe et al.5a
have recently reported that oligonucleotide analogues
We thank A. Garnier, R. Wille, V. von Arx, and M.-L.
Piccolotto for technical assistance.
related to those of type I by the replacement of the
-CH2O- unit with an amide group -C(O)NH- supposedly
bind to natural RNA as well as DNA with similar a-
nities as PNA (and thus more tightly than natural DNA).
References and Notes
The dierence between Lowe's system and our structure I
1. For recent reviews on antisense technology and the
could conceivably be caused by an increase in conforma-
importance of structural modi®cations of oligonucleotides
tional ¯exibility in the latter, which would entropically
for antisense applications cf., e.g.: a Crooke, S. T. Med. Res.
disfavor hybrid formation (cf., however, ref 25).
Rev. 1996, 16, 319. (b) Matteucci, M. D. Persp. Drug Disc.
Des. 1996, 4, 1. (c) Altmann K.-H.; Cuenoud, B.; von Matt,
P. In Applied Antisense Oligonucleotide Technology; Stein, C.
A.; Krieg, A. M., Eds.; Wiley-Lyss: New York, 1997; pp 73±
107.
2. For recent reviews on backbone modi®ed oligonucleotides
cf., e.g.: (a) De Mesmaeker, A.; Haner, R.; Martin, P.; Moser,
H. E. Acc. Chem. Res. 1995, 28, 366. (b) De Mesmaeker, A.;
Altmann, K.-H.; Waldner, A.; Wendeborn, S. Curr. Opinion
Struct. Biol. 1995, 5, 343.
3. For recent reviews on PNA cf., e.g.: (a) Nielsen, P. Curr.
Opin. Struct. Biol. 1999, 9, 353. (b) Hyrup; B.; Nielsen, P. E.
Bioorg. Med. Chem. 1996, 4, 5.
4. Cf., e.g.: (a) Schah, V. J.; Cerpa, R.; Kuntz, I. D.; Kenyon,
G. L. Bioorg. Chem. 1996, 24, 201. (b) Petersen, K. H.;
Buchardt, O.; Nielsen, P. E. Bioorg. Med. Chem. Lett. 1996,
6, 793. (c) Lenzi, A.; Reginato, G.; Taddei, M. Tetrahedron
Lett. 1995, 36, 1713; Lenzi, A.; Reginato, G.; Taddei, M.;
Tri®lie, E. Tetrahedron Lett. 1995, 36, 1717. (d) Garner, P.;
Yoo, J. U. Tetrahedron Lett. 1993, 34, 1275. (e) Lewis, I.
Tetrahedron Lett. 1993, 36, 5697. (f) Hudziak, R. M.; Bar-
ofsky, E.; Douglas, F.; Weller, D. L.; Huang, S.-B.; Weller,
D. D. Antisense Nucleic Acid Drug Dev. 1996, 6, 267. For a
review on earlier attempts to construct polyamide-based
nucleic acid analogues see: Jones, S. A. Int. J. Biol. Macro-
molecules 1979, 1, 194.
Cooperative binding of A to its parallel23 RNA comple-
ment (r[A5(GA)5]) was also observed and occurs with
comparable anity as for complementary RNA with an
antiparallel alignment (Table 1). Most notably, only a
single transition was observed under all experimental
conditions and the binding curve was fully reversible upon
heating and cooling without any indication of hysterisis. It
is not clear, however, whether the interaction between A
and r[A5(GA)5] in fact involves formation of a parallel A/
RNA duplex, as binding of A to r[A5(GA)5] could also
occur through the formation of an 11-base pair anti-
parallel duplex based on Watson±Crick base pairs
between residues 5 to 15 of A and 15 to 5 of r[A5(GA)5].26
In contrast to complementary RNA, cooperative bind-
ing of A to complementary DNA, either in an antiparallel
or parallel fashion, was not observed. This is contrary to
the behaviour of the corresponding oligomers of type II±
IV (Fig. 1), for which complexes with complementary
DNA appear to be of comparable stability as those with
RNA.6b
In summary, we have achieved the synthesis of a new
polyamide based oligonucleotide analogue incorporat-
ing thymine- and cytosine-derived building blocks of
type I. Homo-pyrimidine oligomer A exhibits sequence-
speci®c binding to complementary RNA, but not DNA.
As nucleoamino acids of type I easily lend themselves to
further chemical modi®cation (e.g., through introduction
of additional substituents on the pyrrolidine ring or at
the position a to the carboxy group; cf. also ref 6b),
these building blocks could represent an appropriate
template for the design of DNA analogues exhibiting
further improved RNA-binding properties.
5. (a) Lowe, G.; Vilaivan, T.; Westwell, M. S. Bioorg. Chem.
1997, 25, 321. (b) Jordan, S.; Schwemler, C.; Kosch, W.;
Kretschmer, A.; Stropp, U.; Schwenner, E.; Mielke, B. Bioorg.
Med. Chem. Lett. 1997, 7, 687.
6. (a) Altmann, K.-H.; Schmit Chiesi, C.; Garcõa-Echeverrõa,
C. Bioorg. Med. Chem. Lett. 1997, 7, 1119. (b) Garcõa-Eche-
verrõa, C.; Schmit Chiesi, C.; Husken, D.; Altmann, K.-H.
Bioorg. Med. Chem. Lett. 1997, 7, 1123.
7. Related structures have recently been described (cf. ref. 5).
8. The term nucleoamino acid is meant to signify amino acids
with side chains bearing nucleic acid bases.
9. Baker, G. L.; Fritschel, S. J.; Stille, J. R.; Stille, J. K. J. Org.
Chem. 1981, 46, 2954.