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Hoogsteen ‐Duplex DNA: Synthesis and base pairing of oligonucleotides containing 1‐deaza‐2′‐deoxyadenosine
Author(s) -
Seela Frank,
Wenzel Thomas
Publication year - 1994
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.19940770604
Subject(s) - chemistry , phosphoramidite , oligonucleotide , stereochemistry , duplex (building) , deoxyribonucleotide , deoxyadenosine , base pair , nucleoside , pyrimidine , dna , oligonucleotide synthesis , biochemistry
Oligodeoxyribonucleotides containing 1‐deaza‐2′‐deoxyadenosine ( = 7‐amino‐3‐(2‐deoxy‐β‐ D ‐ erythro ‐pentofuranosyl)‐3 H ‐imidazo[4, 5‐ b ]pyridine; 1b ) form Hoogsteen duplexes. Watson ‐ Crick base pairs cannot be built up due to the absence of N(1). For these studies, oligonucleotide building blocks – the phosphonate 3a and the phosphoramidite 3b – were prepared from 1b via 4a and 5 , as well as the Fractosil ‐linked 6b , and used in solid‐phase synthesis. The applicability of various N ‐protecting groups (see 4a – c ) was also studied. The Hoogsteen duplex d[(c 1 A) 20 ] · d(T 20 ) ( 11 · 13 ; T m 15°) is less stable than d(A 20 ) · d(T 20 ) ( 12 · 13 ; T m 60°). The block oligomers d([c 1 A) 10 –;T 10 ] ( 14 ) and d[T 10 –(c 1 A) 10 ] ( 15 ) containing purine and pyrimidine bases in the same strand are also able to form duplexes with each other. The chain polarity was found to be parallel.