Reversible photopadlocking on double-stranded DNA

Abstract

We describe a highly efficient method for reversible photocircularization of oligonucleotide (ODN) on a double-stranded DNA template: 5-carboxyvinyl-2'-deoxyuridine-containing ODN was reversibly circularized around the target sequence of the double-stranded plasmid DNA resulting in formation of a catenated plasmid.

Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly

“…These modifications have been extensively explored and optimised for use in complex DNA systems, such as logic circuits, by the Fujimoto group. [107][108][109][110] The inclusion of electron-withdrawing groups (for example, carboxyl and cyanomoieties) further enhances reactivity; 111,112 enabling light manipulation of DNA structures, even for highly complex origami assemblies. 113 The cyanovinyl carbazole nucleoside is a commonly used photo-crosslinking modification in the field of nucleic acid chemistry.…”

“…In addition to the development of the cyanovinyl carbazole, Fujimoto's group evaluated the commercially available 5-carboxyvinyl-2′-deoxyuridine as a photo-crosslinking modification. 108 They demonstrated that 5-carboxyvinyl-2′-deoxyuridine could be used to photo-ligate two ends of an oligonucleotide to form a cyclic oligonucleotide. By irradiating at 366 nm, these artificial nucleotides produced photo-ligated catenated sequences with high efficiency without any side reactions.…”

Oligonucleotide-Templated Reactions for Sensing Nucleic Acids

“…Therefore, these authors succeeded in developing a reversible photoligation method by switching between irradiation at two wavelengths. Furthermore, they improved the photoactivation reagent and reported a photoligation reaction using 5'-carboxyvinyldeoxyuridine [15,16,17,18,19,20,21]. The irradiation of these probes at 366 nm for 1 h in the presence of template resulted in the expected ligation product, with a yield of 93%.…”

“…The irradiation of these probes at 366 nm for 1 h in the presence of template resulted in the expected ligation product, with a yield of 93%. These authors applied these probes to the detection of single-base mismatches [19,22,23,24,25], the formation of various special structures [13,14,15,17,21,26,27], the site-specific transition of cytosine to uracil [16,28,29], and the development of DNA computing [18].…”

Templating Photoreactions in Solution

“…143 -146 Much work in the fi eld is based on the [2 + 2] cycloaddition between uridine derivatives developed by Fujimoto and coworkers. 147 -149 The method relies on a modifi ed uridine in which the chromophore ' s absorption envelope is extended into the visible by conjugation and is applicable to circular DNA 150 and RNA. 151,152 A particularly interesting aspect is that the photoligation can be made reversible under the irradiation conditions by using a tethered carbazole PET sensitizer.…”