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Geometric Effect on the Photocrosslinking Reaction between 3‐Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex
Author(s) -
Fujimoto Kenzo,
Kishi Satomi,
Sakamoto Takashi
Publication year - 2013
Publication title -
photochemistry and photobiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.818
H-Index - 131
eISSN - 1751-1097
pISSN - 0031-8655
DOI - 10.1111/php.12118
Subject(s) - chemistry , nucleoside , pyrimidine , heteroduplex , stereochemistry , glycosidic bond , uridine , rna , dna , moiety , biochemistry , gene , enzyme
Abstract To clarify the geometric effect of the ultra‐fast photocrosslinking reaction of photoreactive oligodeoxyribonucleotide containing 3‐cyanovinylcarbazole nucleoside ( CNV K ) on uridine in complementary RNA strands, pseudouridine (Ψ), which is an isomer of uridine with a C5–C1′ glycosidic bond, was introduced to the photocrosslink site of CNV K in complementary RNA instead of U. The photoreactivity of CNV K toward Ψ was two‐fold lower than that of U, suggesting that the geometry between the vinyl moiety on CNV K and the reactive double bond in the pyrimidine base has a large affect on the photoreactivity of CNV K . Contrary to the case of U, the reactivity of the CNV K toward Ψ was decreased by the decrease of reaction temperature below the Tm of heteroduplex, suggesting that the flexible structure of the duplex is advantageous for the photocrosslinking reaction with Ψ, whose reactive double bond possesses unfavorable geometry for the photocrosslinking reaction with CNV K . These basic findings might contribute to the development of a geometry selective photocrosslinking reaction. This is the first example of a sequence specific photocrosslinking reaction toward Ψ, which is the most abundant posttranscriptionally modified nucleoside.