Site specific photo-crosslinking of single stranded oligonucleotides by a complementary sequence equipped with an internal photoactive probe

Abstract

Fig. 2 Identification of RNA residues involved in crosslinking. Sequencing gel of free and crosslinked OR. Lane 1: partial digestion of free OR with RNase T1; lanes 2 and 4: limited alkaline hydrolysis of OR; lane 3: limited alkaline hydrolysis of the major OR-O4-7 photoadduct. The spots corresponding to G positions are marked. The arrow points to nucleotide C6 involved in the crosslink.

Synthesis and Photochemical Behavior of Peptide Nucleic Acid Dimers and Analogues Containing 4-Thiothymine: Unprecedented (5−4) Photoadduct Reversion

“…As it is well-known that such nucleobases exhibit remarkable photochemical properties which are currently exploited in photolabeling studies of systems containing nucleic acids, the introduction of such modifications in PNA could receive many applications. For example, since oligonucleotides incorporating a 4-thiouridine at its 5‘ end exhibit 100% cross-linking capacity with the residue located at the 3‘ end of its complement, thio-substituted nucleobase containing PNAs could be used to determine unambiguously the binding orientation of a stretch of PNA relative to its target.…”

Photoinduced Fluorescent Cross-Linking of 5-Chloro- and 5-Fluoro-4-thiouridines with Thymidine

“…The 4-thiouracil (4SU) chromophore and its derivatives have attracted considerable interest in recent years as efficient photo-cross-linking agents in the studies of the structure of nucleic acids and their interactions with proteins. − The use of 4-thiouridine and 4-thiothymidine as structural probes , indicates that a range of cross-links is possible, including interstrand cross-links . To identify the covalent bonds that form and to better understand the cross-linking mechanism, a number of experiments involving photoirradiation of thiouridine have been conducted in solution in the presence of common nucleosides or using dinucleotides. − In agreement with the results of 4SU photo-cross-linking experiments with DNA, it has been demonstrated that 4SU forms mixed photoadducts with all nucleobases with thymidine being the best acceptor. , The (5-4) or (6-4) bipyrimidine compounds were identified as major photoproducts of irradiation of 4SU in the presence of pyrimidine nucleosides.…”

“…[1][2][3] The use of 4-thiouridine and 4-thiothymidine as structural probes 2,4 indicates that a range of cross-links is possible, including interstrand cross-links. 5 To identify the covalent bonds that form and to better understand the cross-linking mechanism, a number of experiments involving photoirradiation of thiouridine have been conducted in solution in the presence of common nucleosides or using dinucleotides. [6][7][8][9] In agreement with the results of 4SU photo-cross-linking experiments with DNA, it has been demonstrated that 4SU forms mixed photoadducts with all nucleobases with thymidine being the best acceptor.…”

Highly Efficient Fluorescent Interstrand Photo‐crosslinking of DNA Duplexes Labeled with 5‐Fluoro‐4‐thio‐2′‐O‐methyluridine

“…Notably, the appearance of a red‐shifted, intense absorption band with a maximum at around 330 nm, and high photoreactivity towards pyrimidines are useful properties. Although S U has been extensively used as a photoaffinity probe in studies of the tertiary folding of RNA, its application in ICL of DNA is rather limited, and only few reports are available 11a…”