Sequence- and Temperature-Dependent Intrastrand Photocrosslinking of 5-Fluoro-2’-O-methyl- 4-thiouridine Modified Oligonucleotides

Abstract

Abstract DNA photocrosslinking reactions occur widely in biological systems and are often used as a valuable tool in molecular biology. With regard to the latter, highly efficient and selective photoactive DNA crosslinking agents are of particular interest. 4-Thiouridine is one of the most frequently used photoactivatable DNA crosslinking agents. Our previous studies revealed that it’s 5-halogeno derivatives, namely 5-fluoro- and 5-chloro-4-thiouridines (FSU and ClSU, respectively), incorporated into double stranded DNA oligonucleotide form highly fluorescent interstrand crosslink with thymidine in nearly quantitative yield. Here we reported the sequence- and temperature dependent formation of intrastrand crosslink products from the irradiation of single stranded oligodeoxynucleotides bearing FSU. Our results showed that two types of intrastrand crosslink products could be formed, namely the fluorescent one with T and nonfluorescent with C. Moreover, partial photooxidation of FSU residue to 5-fluorouridine was also observed. Our studies confirm the possibility of intrastrand photocrosslinking of nonadjacent bases in short oligodeoxynucleotides. The results were supported by molecular dynamics simulations and are valuable for the future designing of FSU-labeled probes for fluorescence-based detection of specific DNA sequences.