Highly Efficient Fluorescent Interstrand Photo‐crosslinking of DNA Duplexes Labeled with 5‐Fluoro‐4‐thio‐2′‐O‐methyluridine |
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| Authors: | Dr Joanna Nowak‐Karnowska Ziad Chebib Prof Jan Milecki Prof Stefan Franzen Prof Bohdan Skalski |
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| Affiliation: | 1. Centre of Advanced Technology, Adam Mickiewicz University, Grunwaldzka 6, 60‐780 Poznań (Poland);2. Departament of Chemistry, Adam Mickiewicz University, Umultowska 89B, 61‐614 Poznań (Poland);3. Department of Chemistry, North Carolina State University, Raleigh, NC 27695 (USA) |
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| Abstract: | The formation of a fluorescent photoadduct between 5‐fluoro‐4‐thiouridine ( FS U ), in the sequence context 5′‐A FS U A‐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. |
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| Keywords: | enzymatic digestion fluorescence fluorothiouridine interstrand photo‐crosslinking oligonucleotides |
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