title: Highly efficient fluorescent interstrand photo-crosslinking of DNA duplexes labeled with 5-fluoro-4-thio-2'-o-methyluridine.
abstract: The formation of a fluorescent photoadduct between 5-fluoro-4-thiouridine ((FS) U), in the sequence context 5'-A(FS) UA-3' and incorporated into a synthetic oligonucleotide either at its 3'- or 5'-end, and one of the thymines of the TAT motif in a complementary target DNA strand led to photo-crosslinking of the two strands for several oligonucleotide constructs. Enzymatic digestion, MS, UV, and fluorescence spectral analyses of the interstrand crosslinked oligonucleotides revealed the identity of the thymidine that participates in the photo-crosslinking reaction as well as the diastereomeric structures of the crosslinks. The proposed pathways of interstrand photo-crosslinking are supported by experiments with isotopically labeled oligonucleotide constructs and visualized by means of molecular dynamics simulations.
authors.affiliation: Centre of Advanced Technology, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań (Poland).
authors.forename: Joanna
authors.initials: J
authors.lastname: Nowak-Karnowska
authors.forename: Ziad
authors.initials: Z
authors.lastname: Chebib
authors.forename: Jan
authors.initials: J
authors.lastname: Milecki
authors.forename: Stefan
authors.initials: S
authors.lastname: Franzen
authors.forename: Bohdan
authors.initials: B
authors.lastname: Skalski
mesh_terms: D001483:Base Sequence; D003432:Cross-Linking Reagents / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D018076:DNA, Complementary / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009841:Oligonucleotides / Q000737:chemistry*; D010777:Photochemistry; D013891:Thiouridine / Q000031:analogs & derivatives* / Q000737:chemistry; D014529:Uridine / Q000031:analogs & derivatives* / Q000737:chemistry
chemical_list: C548253:5-fluoro-4-thiouridine; D003432:Cross-Linking Reagents; D018076:DNA, Complementary; D005456:Fluorescent Dyes; D009841:Oligonucleotides; D013891:Thiouridine; C052202:2'-O-methyluridine; D004247:DNA; D014529:Uridine
keywords: enzymatic digestion; fluorescence; fluorothiouridine; interstrand photo-crosslinking; oligonucleotides