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5‐Aza‐7‐deaza‐2′‐deoxyguanosine: Oligonucleotide Duplexes with Novel Base Pairs, Parallel Chain Orientation and Protonation Sites in the Core of a Double Helix
Author(s) -
Seela Frank,
Melenewski Alexander
Publication year - 1999
Publication title -
european journal of organic chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.825
H-Index - 155
eISSN - 1099-0690
pISSN - 1434-193X
DOI - 10.1002/(sici)1099-0690(199902)1999:2<485::aid-ejoc485>3.0.co;2-j
Subject(s) - chemistry , oligonucleotide , phosphoramidite , antiparallel (mathematics) , base pair , stereochemistry , hydrogen bond , guanine , protonation , crystallography , guanosine , cytosine , nucleotide , dna , molecule , biochemistry , organic chemistry , ion , physics , quantum mechanics , magnetic field , gene
Oligonucleotides containing 5‐aza‐7‐deaza‐2′‐deoxyguanosine ( 1 ) were synthesized. Solid‐phase synthesis was performed with the phosphonate 15 or the phosphoramidite 5 . The amino‐unprotected phosphonate 4 was also employed. Hybridization studies of oligonucleotides containing 1 resulted in new base pairs leading to duplexes with parallel (ps) or antiparallel (aps) chain orientation. Among those with parallel chains a stable “purine‐purine” base pair was observed between 5‐aza‐7‐deazaguanine and guanine or 7‐deazaguanine. Antiparallel stranded duplexes are formed when 5‐aza‐7‐deazaguanine pairs with cytosine. This base pair has only two hydrogen bonds under neutral conditions but is stabilized by a third one in acidic medium. A new base pair is also detected between the base of 1 and isoguanine (neutral medium).