Thionucleoside disulfides as covalent constraints of DNA conformation

Reversible diselenide cross-links are formed between oligonucleotides containing 2′-deoxy-6-selenoinosine

“…Thio-nucleobase-modified oligonucleotides have been shown to form disulfide bridges in complementary sequences where the bridging atoms are in proximity to one another after hybridization. 16,17 In order to observe the timescale of dimerization after cleavage from the solid-support, time trials were performed by analysing the crude dI-Se-ODN oligonucleotide by SAX HPLC after deprotection in the absence of DTT. Dimerization was however, too fast under these experimental conditions.…”

Interstrand disulfide crosslinking of DNA bases supports a double nucleotide unpairing mechanism for flap endonucleases

“…To investigate a requirement for nucleotide unpairing in FEN reactions, we prepared DF substrates containing disulfide crosslinks at "base pairs" either side of the scissile phosphate diester bond (Figure 2a-b and Supplemental Figure S1). Dynamic simulations show that such crosslinks are tolerated in B-DNA 10 . To facilitate crosslinking, but mimic the preferred conformer of a biological hFEN1 substrate, the single nt 3'-flap and the 5 nt 5'flap were not complementary to the template strand.…”

“…In contrast, in model duplexes not supplied within the context of the DF structure, we did observe some spontaneous oxidation 9 . However, disulfide was formed within the DFs upon addition of I 2 (10-20 equivalents with respect to concentration of annealed substrate) 10 . No side reactions of the unmodified nucleic acid occurred during iodine treatment, but desulfurisation of the thionucleosides occurred in the absence of crosslinking partner and iodination (mainly di-) of the FAM moiety of flap strands also occurred under these conditions (Supplemental Table S1).…”

Unnatural Nucleosides with Unusual Base Pairing Properties

“…Current Protocols in Nucleic Acid Chemistry linkage is formed by oxidation of thiols to yield a cross-linking disulfide. Hatano and coworkers studied the reversible linkage of S.88 to yield base pair S.89 (Hatano et al, 2005), while an earlier study from Coleman and coworkers used 4-thiouracil deoxyribonucleoside (S.90) and 6-thiohypoxanthine (S.91) to obtain the cross-link S.92 (Coleman et al, 1999).…”