Shigeo Matsuda

New synthetic method of 5-formyluracil-containing oligonucleotides and their melting behavior

Abstract A new method for the synthesis of 5-foU-containing oligonuleotides by phosphoramidite chemistry and subsequent post-oxidation with sodium periodate was developed. 5-(1,2-Dihydroxyethyl)uracil-containing oligomers, which are readily converted to 5-foU-containing oligomers by sodium periodate oxidation, were synthesized according to the standard β-cyanoethyl phosphoramidite chemistry. The phosphoramidite of a protected 5-(1,2-dihydroxyethyl)-2′-deoxyuridine derivative was prepared from 5-iodo-2′-deoxyuridine in 7 steps. UV melting behavior of these three oligomers demonstrated that the 5-foU-A base pair are less stable than the T-A base pair.

Template directed photochemical synthesis of branched oligodeoxynucleotides via 5-carboxyvinyldeoxyuridine

Abstract An efficient template directed DNA photoligation using 5-carboxyvinyldeoxyuridine ( CV U) is described. By the use of this photoligation, a new efficient method for the synthesis of branched oligonucleotides is reported.

Template-directed reversible photocircularization of DNA via 5-vinyldeoxycytidine

Abstract An efficient and reversible template-directed photoligation of oligodeoxynucleotides (ODNs) using 5-vinyldeoxycytidine (VC) was described. When ODN containing VC at the 5′ end was photoirradiated with ODN containing thymine at the 3′ end in the presence of a template ODN, an efficient photoligation was observed. Reversible photopadlocking of a circular DNA by the photocircularization using VC was demonstrated.

Replication in vitro and cleavage by restriction endonuclease of 5-formyluracil- and 5-hydroxymethyluracil-containing oligonucleotides

PURPOSEnTo investigate the biological consequences of 5-formyluracil (5-foU) and 5-hydroxymethyluracil (5-hmU).nnnMATERIALS AND METHODnThe authors constructed 22-mer oligonucleotides containing a 5-foU or 5-hmU residue at the same sites. The effects of such modifications on the ability to serve as a template for DNA polymerase and on the cleavage by sequence-specific restriction endonuclease were examined.nnnRESULTSnThe Klenow fragment of DNA polymerase I and Thermus thermophilus DNA polymerase read through the sites of 5-foU and 5-hmU in the templates. 5-FoU directed the incorporation of dCMP in addition to dAMP opposite the lesion during DNA synthesis. The DNA polymerases incorporated only dAMP opposite the 5-hmU. The substitution of thymine by 5-foU within the recognition site of the restriction endonucleases HincII and SalI inhibited or prevented the cleavage by the enzymes, whereas the enzymes cleaved the 5-hmU-containing oligonucleotides at the same rate as the T-containing oligonucleotides.nnnCONCLUSIONSnThese results indicated that the 5-foU-A base pair is less stable than the T-A base pair and that 5-foU can form a base pair with C in addition to A. It was also demonstrated that the oxidation of thymine to 5-hmU does not result in substantial deterioration.

Reversible DNA photocircularization on triple helix: effect of vinyl substituent on base stacking

Abstract An efficient method for the synthesis of circular oligodeoxyribonucleotides (ODNs) using reversible template-directed photoligation via 5-vinyldeoxycytidine (VC) is described. It is shown that the 5′-end VC of ODN reversibly reacts by photoirraditation with thymine at its own 3′-end in the presence of a single-stranded template via triple helix formation to produce circular DNA. Thermodynamic analysis indicated that the stability of triple helix is remarkably enhanced by the vinyl substituent of VC.

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.