Oligonucleotides Containing Pyrazolo[3,4-d]Pyrimidines: 8-Aza-7-deazaadenines With Bulky Substituents in the 2- or 7-Position

The synthesis of the 2′-deoxyadenosine analogues 1b, 2b, and 3c modified at the 7- and/or 2-position is described. The effect of 7-chloro and 2-methylthio groups on the duplex stability is evaluated. For that, the nucleosides 1b, 2b, and 3c were converted to the corresponding phosphoramidites 15, 19, and 22, which were employed in the solid-phase oligonucleotide synthesis. In oligonucleotide duplexes, compound 1b forms stable base pairs with dT, of which the separated 1b- dT base pairs contribute stronger than that of the consecutive base pairs. Compound 2b shows universal base pairing properties while its N8 isomer 3c forms duplexes with lower stability.

Keywords:

• Nucleosides
• Oligonucleotides
• Pyrazolo[3,4d]pyrimidines
• Bulky susbtituents
• Base pairing
• Duplex stability

In memory to my good friend the late Professor Dr. John A. Montgomery.

We thank Dr. Helmut Rosemeyer for the NMR measurements, Mrs. Elisabeth Michalek for oligonucleotide synthesis, Mrs. Monika Dubiel for her help during the preparation of the manuscript, and Mr. Khalil Shaikh for MALDI-TOF spectra. Financial support by the Roche Diagnostic GmbH, Penzberg, is gratefully acknowledged.

Notes

^a Measured in 100 mM NaCl, 10 mM MgCl₂, and 10 mM Na-cacodylate (pH 7.0) with 5 μM single-strand concentration.

^{a a} Measured in 1 M NaCl, 100 mM MgCl₂, and 60 mM Na-cacodylate (pH 7.0) with 5 μM single-strand concentration.

^a Measured in DMSO-d₆.

^b Systematic numbering.

^c Superimposed by DMSO-d₆.

^a Measured at 260 nm in 1 M NaCl, 100 mM MgCl₂, and 60 mM Na-cacodylate (pH 7.0) with 5 μM single-strand concentration.

^a Measured at 260 nm in 1 M NaCl, 100 mM MgCl₂, and 60 mM Na-cacodylate (pH 7.0) with 5 μM single-strand concentration.