Premium
Synthesis, Molecular Recognition, and Enzymology of Oligonucleotides Containing the Non‐standard Base Pair between 5‐Aza‐7‐deazaisoguanine and 6‐Amino‐3‐methylpyrazin‐2(1 H )‐one, a Donor‐Acceptor‐Acceptor Purine Analog and an Acceptor‐Donor‐Donor Pyrimidine Analog
Author(s) -
Voegel Johannes J.,
Benner Steven A.
Publication year - 1996
Publication title -
helvetica chimica acta
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.74
H-Index - 82
eISSN - 1522-2675
pISSN - 0018-019X
DOI - 10.1002/hlca.19960790711
Subject(s) - chemistry , oligonucleotide , nucleobase , phosphoramidite , base pair , stereochemistry , nucleotide , dna , combinatorial chemistry , biochemistry , gene
Abstract A 6‐aminopyrazin‐2(1 H )‐one (pyADD), when incorporated as a pyrimidine‐base analog into an oligonucleotide chain, presents a H‐bond acceptor‐donor‐donor pattern to 5‐aza‐7‐deazaisoguanine (puDAA), the complementrary donor‐acceptor‐acceptor purine analog. Reported here are the syntheses of the phosphoramidite of the 2′‐deoxyribonucleoside bearing the puDAA base, oligonucleotides containing this nucleoside unit, the enzyme‐assisted synthesis of oligoribonucleotides containing the pyADD ribonucleoside, and the molecular‐recognition properties of this non‐standard base pair in an oligonucleotide context. A series of melting experiments suggests that the pyADD · puDAA base pair contributes to the relative stability of a duplex structure approximately the same as an A · T base pair, and significantly more than mismatches between these non‐standard bases and certain standard nucleobases. The pyADD nucleoside bisphosphate is accepted by T4 RNA ligase, but the triphosphate of the pyADD nucleoside was not incorported by T7 RNA polymerase opposite the puDAA nucleobase in a template. Oligonucleotides containing the pyADD base slowly undergo a reversible first‐order reaction, presumably an epimerization process to give the α‐ D ‐anomer. These experiments provide the tools for laboratory‐based use of the pyADD · puDAA base pair as a component of an oligonucleotide‐like molecular‐recognition system based on an expanded genetic alphabet.