Highly efficient fluorescent interstrand photo-crosslinking of DNA duplexes labeled with 5-fluoro-4-thio-2'-o-methyluridine.
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.
['Nowak-Karnowska|Joanna|J|', 'Chebib|Ziad|Z|', 'Milecki|Jan|J|', 'Franzen|Stefan|S|', 'Skalski|Bohdan|B|']
D001483:Base Sequence D003432:Cross-Linking Reagents D004247:DNA D018076:DNA, Complementary D005456:Fluorescent Dyes D056004:Molecular Dynamics Simulation D009841:Oligonucleotides D010777:Photochemistry D013891:Thiouridine D014529:Uridine
fluorescence interstrand photo-crosslinking oligonucleotides enzymatic digestion fluorothiouridine