Details of the ultrafast DNA photo-cross-linking reaction of 3-cyanovinylcarbazole nucleoside: cis-trans isomeric effect and the application for SNP-based genotyping.

To clarify the cis-trans isomeric effect on the ultrafast DNA photo-cross-linking reaction of 3-cyanovinylcarbazole nucleoside ((CNV)K) in the DNA duplex, which gives a single photodimer on the reversed-phase HPLC chromatogram, the kinetics of the cis-trans photoisomerization of (CNV)K in double-stranded DNA was evaluated. Since the photoisomerization rate constant for cis to trans isomerization in double-stranded DNA was significantly larger than that for trans to cis isomerization, and the thermodynamic stability of the trans isomer was higher than that of the cis isomer, it was strongly suggested that the trans isomer of (CNV)K is a reactive species of the photo-cross-linking reaction. (1)H-(1)H NOESY analysis of the photoadduct consisting of (CNV)K and T also supported the trans-mediated photo-cross-linking reaction of (CNV)K.

Quick regulation of mRNA functions by a few seconds of photoirradiation.

3-Cyanovinylcarbazole nucleoside, which effectively photocrosslinks to the pyrimidine base in complementary RNA strands, was incorporated into antisense oligonucleotides, and we evaluated the photoreactivity and the sequence selectivity to mutated K-ras oligoRNAs, as well as the regulation of the function of K-ras mRNA. We demonstrated that the reverse transcription and the translation activity of K-ras mRNA were quickly suppressed by a few seconds of photoirradiation with the addition of the photoresponsive antisense ODN.

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

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.

Site-specific photochemical RNA editing.

Photo-induced artificial RNA editing was demonstrated using photo-reactive oligonucleotides containing 3-cyanovinylcarbazole nucleoside. This non-enzymatic and sequence-specific methodology will make a major contribution to the elucidation of RNA functions including non-coding RNAs and to the development of drugs based on sequence-specific RNA editing.

Photoreversible DNA end capping for the formation of hairpin structures.

We describe a photoreversible DNA end capping via 3-cyanovinylcarbazole nucleoside. Doubly end-capped oligodeoxynucleotide (ODN) exhibits increased stability against snake venom phosphodiesterase and shows high thermal stability.

Surface-enhanced Raman spectroscopy for facile DNA detection using gold nanoparticle aggregates formed via photoligation.

We present a new type of nanoparticle-based DNA sensor using surface-enhanced Raman scattering (SERS) on gold nanoparticle (Au NP) aggregates formed by DNA photoligation. The DNA sensor exploits the photoligation reaction between oligodeoxynucleotides (ODNs) attached to the surfaces of Au NPs in the presence of target DNA (T-DNA). When hybridization takes place between the ODNs and T-DNA, Au NPs are covalently crosslinked to form aggregates via photoligation.

A selective and sensitive detection of SNP between rice cultivars by using DNA photoligation.

We describe a selective and sensitive single-nucleotide polymorphism (SNP) typing of genes from rice cultivars by using DNA photoligation. This SNP typing method facilitates qualitative determination of genes from indica and japonica rice, and showed a high degree of single nucleotide specificity.

Development of a rapid and reversible photocrosslinking of RNA.

We describe a novel reversible interstrand photocrosslinking reaction of RNA. In this system, a modified oligodeoxynucleotide (ODN) containing 3-cyanovinylcarbazole nucleoside ((CNV)K) reacts by photoirradiation at 366 nm for 1 s with pyrimidine residue of a complementary template RNA to yield a crosslinked product in 94% yield.

SNP genotyping by DNA photoligation: application to SNP detection of genes from food crops.

We describe a simple and inexpensive single-nucleotide polymorphism (SNP) typing method, using DNA photoligation with 5-carboxyvinyl-2'-deoxyuridine and two fluorophores. This SNP-typing method facilitates qualitative determination of genes from indica and japonica rice, and showed a high degree of single nucleotide specificity up to 10 000. This method can be used in the SNP typing of actual genomic DNA samples from food crops.

Development of template-directed reversible DNA photocrosslinking.

We describe a novel reversible DNA interstrand photocrosslinking reaction via the artificial nucleoside (X). Oligodeoxynucleotide (ODN) containing X can be photocrosslinked by irradiation at 366 nm for 1 s, and the photocrosslinked ODN can be split by irradiation at 312 nm for 60 s.

Synthesis of a photoresponsive alpha-dideoxyuridine triphosphate derivative.

The synthesis of a photoresponsive alpha-5-cyanovinyl- 2',3'-dideoxyuridine-5'-triphosphate (alpha dd(C)UTP) is described. A one-pot enzymatic synthesis of photoresponsive alpha-5-cyanovinyl-2',3'-dideoxyuridine (alpha dd(C)U) labeled ODNs with terminal deoxynucleotideyl transferase (TdT) would be a powerful tool for the development of modified long-chain DNA and branched DNA unable to be prepared by DNA synthesizer or enzymatic ligation.

Ultrafast reversible photo-cross-linking reaction: toward in situ DNA manipulation.

We describe a novel ultrafast reversible DNA interstrand photo-cross-linking reaction via 3-cyanovinylcarbazole nucleoside ( (CNV)K). Oligodeoxynucleotide (ODN) containing (CNV)K can be photo-cross-linked by irradiation at 366 nm for 1 s, and the photo-cross-linked ODN can be split by irradiation at 312 nm for 60 s.

A light-controlled reversible DNA photoligation via carbazole-tethered 5-carboxyvinyluracil.

We describe a light-controlled template-directed reversible DNA photoligation via carbazole-tethered 5-carboxyvinyluracil. Carbazole-tethered 5-carboxyvinyl-2'-deoxyuridine-containing oligodeoxynucleotide (ODN) can be ligated by irradiation at 366 nm in the presence of template ODN, and the ligated ODN can be split by irradiation at 366 nm in the absence of template ODN.

Cy3-3-acylcholine: a fluorescent analogue of acetylcholine for single molecule detection.

We synthesized a novel fluorescent analogue of acetylcholine, Cy3-3-acylcholine. The molecular weight of the products agreed with structural predictions. Discrete intensity changes of fluorescent spots due to a single ligand binding/unbinding to nAChR were visualized by TIRF microscopy.

Photochemical transition of 5-methylcytosine to thymine by DNA photoligation.

We report that deamination coupled with 5-carboxyvinyl-2'-deoxyuridine-mediated photoligation causes the heat-induced transition of 5-methylcytosine to thymine with high selectivity and efficiency without any side reaction. The difference of deamination rate between 5-methylcytosine and cytosine is useful for evaluation of DNA methylation status and the study of gene expression and stability.

Sequence specific interstrand photocrosslinking for effective SNP typing.

We describe a simple and inexpensive SNP typing method by using sequence specific interstrand photocrosslinking via p-carbamoylvinyl phenol nucleosides. Interstrand photocrosslinking showed a high degree of single nucleotide specificity as high as 10(3)-fold and more, and can be used in the diagnostic detection of DNA sequences.

Reversible photopadlocking on double-stranded DNA.

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.

Highly sequence specific RNA terminal labeling by DNA photoligation.

We report the nonenzymatic terminal labeling of oligoribonucleotide (ORN) by using template-directed photoligation through 5-carboxyvinyl-2'-deoxyuridine ((CV)U) with high selectivity.

Photoinduced repair of a thymine dimer in DNA via carbazole nucleoside.

We report the photoinduced repair of a thymine dimer incorporated in a DNA duplex via oligodeoxynucleotide (ODN) containing carbazole nucleoside (K). The occurrence of an electron transfer between K and thymine dimer is evidenced by fluorescence quenching measurements. K acts as a good electron donor for the photoinduced repair of a thymine dimer.

Nucleotide insertion opposite a cyclobutane pyrimidine dimer analogue caused from photoligation by a replicative DNA polymerase.

We previously reported an efficient and reversible template-directed photoligation using 5-carboxyvinyl-2'-deoxyuridine ((CV)U)-containing ODN at the 5'-terminal. This method forms d(T-(CV)U) as a cyclobutane pyrimidine dimer (CPD) analogue between 3'-terminal thymidine and 5'-terminal (CV)U of two oligodeoxynucleotides (ODNs). In this study, we performed PCR using a DNA template containing d(T-(CV)U).

RNA template-directed photoligation via 5-carboxyvinyl-2'-deoxyuridine.

An efficient RNA template-directed photoligation of oligodeoxynucleotides (ODNs) via 5-carboxyvinyl-2'-deoxyuridine ((CV)U) was described. When ODN containing (CV)U at the 5' end was photoirradiated with ODN containing a pyrimidine base at the 3' end in the presence of template RNA, an efficient photoligation was observed. RNA template-directed photoligation of ODNs should provide a useful technique for sensitive and accurate RNA detection.

Interstrand DNA photocrosslinking by photoresponsive artificial nucleic acid.

We report a novel interstrand photocrosslink of oligodeoxynucleotides (ODNs). In this system, a modified ODN containing 3-carbonylvinyl phenol nucleoside reacts by photoirradiation at 366 nm with adenine residue of a complementary template ODN to yield a crosslinked ODN.

Reversible DNA photoligation via alpha-5-cyanovinyldeoxyuridine.

An efficient and reversible Template-directed Photoligation of oligodeoxynucleotides (ODNs) using alpha-5-cyanovinyldeoxyuridine (alpha-(CNV)U) was described. When ODN containing alpha-(CNV)U at the 3' end was photoirradiated with ODN containing thymidine at the 5' end in the presence of a template ODN, an efficient photoligation was observed. The ligated ODN can be split site-selectively to regenerate parent ODN by photoirradition at the 312 nm.