Biomedical subjects

A Ubasawa

Publications and source records attributed to A Ubasawa.

5 recordsLinked to original sources

PubMed1991

A variant database.

Variant biomacromolecules, either natural or artificially created, are proving to be useful in determining structure-function relationships. Research in this field would be facilitated by the compilation of data of variants into a central and widely available repository. The Variant Database acts as a repository for data concerning variant molecules. It complements the Biological Activity and the Physicochemical Property Databases as well as provides variant sequences.

Amino Acid Sequence↗

PubMed1986

Oligonucleotide duplexes containing inosine, 7-deazainosine, tubercidin, nebularine and 7-deazanebularine as substrates for restriction endonucleases HindII, SalI and TaqI.

Synthetic hexadecanucleotide duplexes containing a single purine nucleotide analogue in the recognition sites of the restriction endonucleases HindII, SalI and TaqI were used to investigate the restriction site determinants required by these enzymes for sequence recognition and phosphodiester bond cleavage. The enzymes were, in general, unaffected by changes introduced into the minor groove of the helix. SalI was found to be inhibited by the major groove modifications introduced into the fourth position of its recognition sequence GTCGAC. HindII and TaqI were, by contrast, able to cleave the sites containing the analogues at this position. TaqI and, to a lesser extent, HindII could also be shown to tolerate "mismatch analogues" at this site.

Base Sequence↗

PubMed1986

Guanine and adenine analogues as tools in the investigation of the mechanisms of mismatch repair in E. coli.

The efficiency of in vivo correction of five "mismatch analogues", incorporated into M13mp9 DNA, was studied in an attempt to elucidate the structural determinants required for mismatch recognition by the repair machinery of E. coli. Inosine was efficiently removed from an I/T mismatch, presumably by the action of hypoxanthine glycosylase. The mismatch analogues DI/T (DI = 7-deazainosine), Tu/C (Tu = tubercidin), N/C (N = nebularine) and DN/C (DN = 7-deazanebularine) were left largely unrepaired, giving rise to high yields of mutant phenotype. The efficiency of correction of these mismatch analogues could be correlated with their structure within the base-pair.

Adenine↗

PubMed1984

Nucleotide sequence of the insertion sequence found in the T-DNA region of mutant Ti plasmid pTiA66 and distribution of its homologues in octopine Ti plasmid.

The octopine tumor-inducing (Ti) plasmid pTiA66 has an insertion mutation in its T region (the DNA region incorporated into the plant genome) that results in the slow growth of crown gall tumors. These tumors exhibit hormonal autonomy different from that of the crown gall tumors caused by wild-type Ti plasmids. In the present study, the nucleotide sequences of both the DNA segment inserted into pTiA66 and its target site have been determined. The inserted segment is 2548 base pairs long and has 20-base-pair terminal inverted repeats. An 8-base-pair sequence at the target site is duplicated at both integration junctions. These structural features of the insert suggest that it is a bacterial insertion sequence (IS) element, which we have named IS66. Blot-hybridization analyses using IS66 probes revealed that genomes of octopine Ti plasmids contain at least three sequences homologous to IS66: two homologues are located in the virulence region and one is located between the left-hand (TL-DNA) and right-hand (TR-DNA) portions of T-DNA. The chromosome of Agrobacterium tumefaciens A66 also contains two sequences highly homologous to IS66. These results suggest that the mutant pTiA66 plasmid was generated by translocation of one of the sequences showing homology with IS66 into the T region. The fact that a sequence homologous to IS66 is present between TL-DNA and TR-DNA also suggests that the octopine T region was split into two portions, TL-DNA and TR-DNA, by translocation of IS66 or its relatives. Thus, IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids.

Arginine↗

PubMed1980

Nature of side-reactions in oligonucleotide synthesis involving arenesulphonyl derivatives of 3-nitro-1,2,4-triazole and related condensing agents.

The protected guanosine and uridine derivatives (10a, 10b and 11) react with MSNT (2a) to give the nitrotriazole derivatives (12a, 12b and 14, respectively); the 2'-deoxyguanosine derivative (16) is converted into 17 in the same way. All of these reactions proceed more rapidly in the presence of diphenyl phosphate (8). The starting materials (10b and 11, respectively) may easily be regenerated from 12b and 14 by treatment with N1,N1,N3,N3-tetramethylguanidinium syn-4-nitrobenzaldoximate in dioxan solution, when 14 is treated with ammonia in aqueous dioxan, cytidine is obtained. N-Acyl-2',3',5'-tri-O-acyl derivatives of adenosine and cytidine and 3',5'-di-O-acetylthymidine are unaffected by MSNT (2a) even in the presence of diphenyl phosphate (8). TPSNT (2b) reacts with 2-N-benzoylguanine and uracil residues in the same way as does MSNT (2a), but somewhat more slowly. MSTe (1; R = Me) reacts with 11 to give 19; however, its reaction with 10b is complete.

Adenosine↗