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The Base‐Pairing Properties of 7‐Deaza‐2′‐deoxyisoguanosine and 2′‐Deoxyisoguanosine in Oligonucleotide Duplexes with Parallel and Antiparallel Chain Orientation
Author(s) -
Seela Frank,
Wei Changfu
Publication year - 1999
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/(sici)1522-2675(19990505)82:5<726::aid-hlca726>3.0.co;2-k
Subject(s) - chemistry , antiparallel (mathematics) , oligonucleotide , phosphoramidite , cytosine , duplex (building) , base pair , stereochemistry , thymine , crystallography , dna , guanine , nucleic acid , nucleotide , biochemistry , physics , quantum mechanics , magnetic field , gene
Oligonucleotides with parallel (ps) or antiparallel (aps) chain orientation containing 7‐deaza‐2′‐deoxyisoguanosine ( 1 ) or 2′‐deoxyisoguanosine ( 2 ) were prepared. The phosphoramidite and phosphonate building blocks 3 – 6 were synthesized and used in solid‐phase synthesis. The diphenylcarbamoyl (dpc) residue was used for the 2‐oxo group protection and the isobutyryl (iBu=ib) residue for the amino function. Hybridization experiments were performed with oligonucleotides containing 7‐deazaisoguanine or isoguanine. Regarding 7‐deazapurine‐containing oligonucleotides, the 7‐deazaisoguanine⋅cytosine base pair was the strongest in ps‐duplexes, while that of 7‐deazaisoguanine⋅5‐methylisocytosine was the most stable one in aps‐DNA. Ambiguous base pairing of 7‐deazaisoguanine with cytosine, 5‐methylisocytosine, thymine, and guanine was observed in the case of aps‐duplexes, whereas in ps‐duplexes, the ambiguity was extended to adenine. The 7‐deazaisoguanine‐containing duplexes showed almost identical base‐pair stabilities as those containing isoguanine. According to this, various base‐pair motifs are proposed. The 7‐deaza‐2′‐deoxyisoguanosine was found to be an effective substitute of 2′‐deoxyisoguanosine.