Specific and reversible photochemical labeling of plasmid DNA using photoresponsive oligonucleotides containing 3-cyanovinylcarbazole

Abstract

To develop a covalent and specific labeling method for single- and double-stranded plasmid DNA, photoresponsive oligonucleotide containing 3-cyanovinylcarbazole nucleoside was adopted. Single- and double-stranded plasmid DNA was successfully labeled/de-labeled with Cy3 and/or biotin by photoirradiation.

Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand

“…On the other hand, we previously reported that ODNs having 3-cyanovinylcarbazole nucleoside ( CNV K) can photocrosslink to complementary DNA strand via [2 + 2] photocycloaddition between CNV K and pyrimidine base in complementary strand with 1 s of 366 nm irradiation [14–18]. If the rapid photocrosslinking reaction of CNV K had the selectivity for m C like V U derivatives having hydrophobic group, rapid and selective detection of m C in the target DNA sequence will be possible.…”

Photochemical modifications for DNA/RNA oligonucleotides

“…8 Biological applications. Vinylcarbazole-based photocrosslinkers have been used for applications such as targeted site plasmid labeling, 113 transient transgene silencing, 114 and identifying targets of endogenous small RNAs. 115 CNV K and PC X have been used for detecting locations of RNA, 7,116 and methylcytosines in DNA in cells by uorescence in situ hybridization (FISH).…”

Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties

“…38 Furthermore, 3-cyanovinylcarbazole-modified ONs with threoninol linker showed promising DNA photo-cross-linking reactivity, 39 and specific and reversible photochemical labeling of single-and double-stranded plasmid DNA. 40 Taking into account the general sensitivity of carbazole-functionalized probes toward hybridization, [36][37][38] and the high-affinity hybridization of LNA-T, 14,[41][42][43][44][45] we present here a new ON design that combine the interesting fluorescence properties of the thiophenyl-substituted carbazole (absorbs around 310 nm and emits around 400 nm) together with the known stabilization properties of the LNA-T monomer. We choose to incorporate one LNA-T monomer into the middle of the 9mer DNA ON due to the known positive effect of LNA on duplex thermostability, favorable mismatch discrimination and improved resistance toward nucleolytic digestion.…”