ABSTRACT
In this paper, the nonenzymatic detection of 5-methylcytosine with high selectivity is described. We present a new methylation detection method by using template-directed photoligation through 5-cyanovinyl-2'-deoxyuridine ((C)U). Significantly, the photoligation yield of the 5-methylcytosine case was approximately 9.1-fold higher than that in the case of cytosine.
Subject(s)
5-Methylcytosine/analysis , 5-Methylcytosine/chemistry , Deoxyuridine/analogs & derivatives , Deoxyuridine/chemistry , Hydrophobic and Hydrophilic Interactions , Oligodeoxyribonucleotides/chemistry , Photochemical Processes , Photochemistry/methodsABSTRACT
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.
ABSTRACT
We report a new photosensitive probe, that takes advantage of the electronic structural changes associated with the triazole ring formed in the Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition. We succeeded in performing photoligation on the second time scale. Huisgen cycloaddition are employed to various labeling. As an example, we report a procedure for preparing the DNA probe for quick SNP typing.
Subject(s)
DNA Probes/chemistry , Oligodeoxyribonucleotides/chemistry , Polymorphism, Single Nucleotide , DNA Probes/chemical synthesis , Oligonucleotide Array Sequence Analysis , PhotochemistryABSTRACT
We report the construction of a one-pot autonomous DNA computing machine based on photochemical gate transition (photocleavage, hybridization, and photoligation), and we performed binary digit additions using this machine. In our method, both photochemical DNA manipulations previously reported, photoligation via 5-carboxyvinyldeoxyuridene (cvU) containing ODN and photocleavage via carbazole-modified ODN, were employed. The binary digit additions were autonomously carried out by one-time irradiation at 366 nm in the single test tube. The fluorescence readout by the DNA chip was in good agreement with the correct answer of binary digit additions. We believe that this system is easily applicable to correlation analysis between SNPs as well as other binary digit processing, such as subtraction.
Subject(s)
Computers, Molecular , DNA , Photochemistry , Mathematical ComputingABSTRACT
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.
Subject(s)
Carbazoles/chemistry , DNA/radiation effects , Oligodeoxyribonucleotides/radiation effects , Uracil/analogs & derivatives , Uracil/chemistry , Base Sequence , Light , Molecular StructureABSTRACT
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.
Subject(s)
Cross-Linking Reagents/chemistry , DNA/chemistry , Polymorphism, Single Nucleotide , Sequence Analysis, DNA/methods , Base Sequence , Cross-Linking Reagents/radiation effects , DNA/radiation effects , Nucleic Acid Conformation , Nucleosides/chemistry , Nucleosides/radiation effects , Oligodeoxyribonucleotides/chemistry , Oligonucleotide Array Sequence Analysis/methods , Phenols/chemistry , Phenols/radiation effects , Photochemistry , Polymorphism, Single Nucleotide/radiation effects , Substrate Specificity , Ultraviolet RaysABSTRACT
We report a method for the rapid differentiation of nucleic acid sequences with 5-carboxyvinyl-2'-deoxyuridine that allows the simultaneous observation of two colors and facilitates the SNP typing of a heterozygous sample.
Subject(s)
DNA Mutational Analysis/methods , Deoxyuridine/analogs & derivatives , Fluorescent Dyes/chemistry , Point Mutation , Polymorphism, Single Nucleotide , Base Pair Mismatch , Carbocyanines/chemistry , Deoxyuridine/chemistry , Oligonucleotide Array Sequence Analysis , Oligonucleotide Probes/chemistry , PhotochemistryABSTRACT
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.
