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Berlin YuA

Publications and source records attributed to Berlin YuA.

15 recordsLinked to original sources
PubMed1998

Conjugates of oligonucleotides with polyaromatic fluorophores as promising DNA probes.

Conjugates of pyrene and perylene with oligodeoxynucleotides were synthesized and tested as hybridisation probes. A 13-mer containing a 3-peryleneacetic acid residue attached to the 5' end through a hexamethylenediamine linker showed no response in the fluorescent spectrum upon hybridisation to the complementary sequence. At the same time, pyrene-labelled probes are sensitive to duplex formation. A pyrene pseudonucleotide unit based on 4-(1-pyrenyl)-1,3-butanediol can be introduced into any predetermined position(s) of the oligonucleotide chain. The probes polylabelled in this fashion displayed considerable changes in the excimer-to-monomer fluorescence intensity ratio after duplex formation. The internal location of two pyrene residues in the probe provides a drastic enhancement of excimer fluorescence (approximately 470 nm) upon hybridisation. When two pyrene units were brought into close proximity to two pyrenes in the complementary strand upon duplex formation, strong excimer emission at approximately 450 nm was detected. This effect provides a basis for a sensor construction designed to detect nucleic acid hybridisation.

Animals↗
PubMed1995

Optimization of PCR-based diagnostics for human cytomegalovirus.

Various techniques of DNA template preparation for the PCR-based analysis of human CMV in biological fluids have been compared. Structural polymorphism of a CMV DNA segment (part of the major immediate early gene) in clinical isolates is described; the molecular markers (nucleotide substitutions, deletions, insertions) localized in the analyzed amplicon appear to be suitable for molecular-epidemiological studies. A scheme of spreading of the molecular markers in the population is suggested.

Base Sequence↗
PubMed1994

Identification of the linkage of mutations causing cystic fibrosis to different alleles of a tetranucleotide repeat in intron 6a of the CFTR gene.

The linkage of the intragenic polymorphic (GATT)n repeat to a number of cystic fibrosis transmembrane conductance regulator gene mutations (delta F-508, G542X, G551D, R553X, R1162X, W1282X, N1303K, R334W, and R347P) was studied. The linkage of delta F-508, G542X, and N1303K to a six-copy allele and of R334W to a seven-copy allele of the repeat was found.

Alleles↗
PubMed1991

Method of artificial DNA splicing by directed ligation (SDL).

An approach to directed genetic recombination in vitro has been devised, which allows for joining together, in a predetermined way, a series of DNA segments to give a precisely spliced polynucleotide sequence (DNA splicing by directed ligation, SDL). The approach makes use of amplification, by means of several polymerase chain reactions (PCR), of a chosen set of DNA segments. Primers for the amplifications contain recognition sites of the class IIS restriction endonucleases, which transform blunt ends of the amplification products into protruding ends of unique primary structures, the ends to be used for joining segments together being mutually complementary. Ligation of the mixture of the segments so synthesized gives the desired sequence in an unambiguous way. The suggested approach has been exemplified by the synthesis of a totally processed (intronless) gene encoding human mature interleukin-1 alpha.

Base Sequence↗
PubMed1991

Synthesis and modification of genes through artificial splicing by directed ligation (ASDL).

An approach to the directed genetic recombination in vitro mediated by synthetic oligodeoxynucleotides and polymerase chain reaction (PCR) is devised, which allows the joining, in a predetermined chemical-enzymatic way, of a series of DNA segments to give a precisely spliced polynucleotide sequence (Artificial Splicing by Directed Ligation, ASDL). The approach can thus lead to the totally processed eukaryotic genes using genomic DNA, with no mRNA needed. This approach has been used for the synthesis of artificial genes of interleukin-1 alpha and, in combination with PCR on the mRNA-cDNA duplex as template, of interleukin-1 receptor antagonist and their analogues, as well as for the modified genes.

Base Sequence↗
PubMed1989

Lambda plac10 transducing bacteriophage: DNA primary structure of the region of the abnormal excision.

In studying molecular mechanisms of the formation of transducing bacteriophages, we have elucidated the primary structure of the phage-bacterial DNA junction which resulted from the abnormal excision of the lambda plac10 phage. The process is structurally similar to the excision of the lambda plac5 phage and involves, in both cases, highly homological DNA stretches approximately 20 bp long, one of them being a part of the Z-Y spacer of the lac operon and possessing a developed secondary structure. The conception of regioselective recombination as a type of illegitimate recombinational process with a certain degree of site-specificity is suggested.

Bacteriophages↗
PubMed1988

Structural bases of a long-stretched deletion: completing the lambda plac5 DNA primary structure.

In studying molecular mechanisms of specialised transduction, the lacI (E. coli)-Ea47 (lambda) DNA junction in transducing bacteriophage lambda plac 5 has been structurally elucidated, thus yielding the complete sequence of lambda plac 5 DNA including the lac5 substitution, a well-known segment of lambdoid vectors. The lambda plac5 DNA is shown to consist of 19368 bp (lambda left arm) + 3924 bp (lac5 substitution) + 25353 bp (lambda right arm), totally amounting to 48645 bp. The presence of the phage rho bL promoter near to the right end of the lac5 insert is shown. The lacI gene distal end in lambda plac5 proved to be much longer than it was postulated earlier, coding for 224 C-terminal amino acid residues of lac repressor. Both the recombination studied in this paper and the earlier studied abnormal prophage excision (2, 3) occur near to Chi-like structures (chi*lacI and chi*lom, respectively). On the basis of the data obtained, a key role of the E. coli RecBCD system and Chi-like sequences in the formation of deletions in bacterial cells is suggested.

Bacteriophage lambda↗
PubMed1983

A new site-specific endodeoxyribonuclease from Citrobacter freundii.

Cfr10 I, a site-specific endonuclease from Citrobacter freundii strain RFL10, was isolated. It recognizes and cleaves the family of related sequences: 5'Pu decreases CCGGPy to generate DNA fragments with 5' tetranucleotide extensions. Cfr10 I may be useful in molecular cloning experiments, especially in conjunction with other enzymes which generate the same terminal extensions.

Base Sequence↗
PubMed1982

A new restriction endonuclease from Citrobacter freundii.

CfrI, a new restriction endonuclease of unique substrate specificity, has been isolated from a Citrobacterfreundii strain. The enzyme recognizes a degenerated sequence PyGGCCPu in double-strand DNA and cleaves it between Py and G residues to yield 5' -protruding tetranucleotide ends GGCC.

Base Sequence↗