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Pyrenemethyl ara ‐Uridine‐2′‐carbamate: A Strong Interstrand Excimer in the Major Groove of a DNA Duplex
Author(s) -
Dioubankova Natalia N.,
Malakhov Andrei D.,
Stetsenko Dmitry A.,
Gait Michael J.,
Volynsky Pavel E.,
Efremov Roman G.,
Korshun Vladimir A.
Publication year - 2003
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/cbic.200300678
Subject(s) - duplex (building) , dna , chemistry , oligonucleotide , stereochemistry , uridine , nucleotide , nucleoside , derivatization , biophysics , biochemistry , rna , organic chemistry , biology , high performance liquid chromatography , gene
The synthesis of new nucleoside derivatives , ara ‐uridine‐2′‐carbamates, and their incorporation into synthetic DNA oligomers is described. The modification directs ligands into the major groove of duplex DNA and somewhat destabilizes the duplexes of modified oligonucleotides with complementary DNA or RNA. In the case of pyrenemethyl carbamate modification in DNA–DNA duplexes, the destabilization is considerably reduced. The pyrenemethyl derivative also shows remarkable spectral properties: a 'reversed' absorbance change for pyrene at 350 nm in the course of denaturation of the DNA duplex, as compared to the change seen in the nucleotide absorbance at 260 nm. This derivatization also causes pronounced sequence‐dependent excimer formation in the major groove.