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Stable Oligonucleotide‐Directed Triplex Formation at Target Sites with CG Interruptions: Strong Sequence‐Specific Recognition by 2′,4′‐Bridged Nucleic‐Acid‐Containing 2‐Pyridones under Physiological Conditions
Author(s) -
Obika Satoshi,
Hari Yoshiyuki,
Sekiguchi Mitsuaki,
Imanishi Takeshi
Publication year - 2002
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/1521-3765(20021018)8:20<4796::aid-chem4796>3.0.co;2-o
Subject(s) - oligonucleotide , pyrimidine , chemistry , dna , nucleic acid , stereochemistry , nucleobase , sequence (biology) , ap site , thymine , nucleoside , biochemistry , dna damage
A sequence of double‐stranded DNA (dsDNA) which can be recognized by a triplex‐forming oligonucleotide (TFO) is limited to a homopurine–homopyrimidine sequence. To develop novel nucleoside analogues which recognize CG interruption in homopurine–homopyrimidine dsDNA, we synthesized a novel 2′‐ O ,4′‐ C ‐methyleneribonucleic acid (2′‐ O ,4′‐ C ‐methylene b ridged n ucleic a cid; 2′,4′‐BNA) that bears the unnatural nucleobases, 2‐pyridone (P B ) or its 5‐methyl congener ( m P B ); these analogues were introduced into pyrimidine TFOs using a DNA synthesizer. A TFO with a 2′‐deoxy‐ β ‐ D ‐ribofuranosyl‐2‐pyridone (P) or 2′,4′‐BNA abasic monomer (H B ) was also synthesized. The triplex‐forming ability of various synthesized 15‐mer TFOs and the corresponding homopurine–homopyrimidine dsDNA, which contained a single pyrimidine–purine (PyPu) interruption, was examined in UV melting experiments. It was found that P B and m P B in the TFOs successfully recognized CG interruption under physiological conditions (7 m M sodium phosphate, 140 m M KCl, 5 m M spermine, pH 7.0). Furthermore, triplex formation between the dsDNA target which contained three CG interruptions and the TFO with three P B units was also confirmed. Additional four‐point 2′,4′‐BNA modifications of the TFO containing three P B units significantly enhanced its triplex‐forming ability towards the dsDNA and had a T m value of 43 °C under physiological conditions. These results indicate that a critical inherent problem of TFOs, namely, the sequence limitation of the dsDNA target, may be overcome to a large extent and this should promote antigene applications of TFOs in vitro and in vivo.