Biomedical subjects

F N Gnuchev

Publications and source records attributed to F N Gnuchev.

5 recordsLinked to original sources

PubMed1996

Efficiency of sequencing by hybridization on oligonucleotide matrix supplemented by measurement of the distance between DNA segments.

DNA sequencing by hybridization on oligonucleotide microchip (SHOM) allows the determination of a spectrum of overlapping oligonucleotides constituting a DNA fragment that hybridizes to form perfect duplexes with an array of immobilized oligonucleotides and, as a result, enables reconstitution of the nucleotide sequence of the fragment. In longer DNA fragments, unambiguous reconstitution of DNA sequence is often impeded by the presence of repetitive regions and simple sequence repeats. Here it is demonstrated that SHOM supplemented by measurement of the distance between certain sites (for example, restriction sites or priming sites for PCR) within the analyzed DNA enables sequencing of much longer DNA fragments, containing repeats of different complexity.

Base Sequence↗

PubMedDate not supplied

[Use of continuous stacking hybridization in sequencing using modified oligonucleotide matrices].

The opportunity of DNA sequencing by hybridization with oligonucleotide matrix (SHOM) with simultaneously use continuous stacking hybridization and gapped-matrices is considered. The analysis of reconstruction efficiency for various combinations matrices and l-oligonucleotides libraries were made. In most cases combine use of continuous stacking hybridization and gapped matrices permits to decrease the number of additional stacking hybridization twice without lost of efficiency.

Nucleic Acid Hybridization↗

PubMedDate not supplied

[Effectiveness of sequencing using stacking hybridization on oligonucleotide matrices with varying length of immobilized oligonucleotides].

The opportunity of enhancing the sequencing efficiency by applying continuous stacking hybridization is considered. The approach is based on the increase of duplex length by continuous stacking hybridization of oligonucleotides added to solution (l-oligonucleotides) to oligonucleotides immobilized on matrix (L-oligonucleotides). An analysis of reconstruction efficiency for sequenced fragments up to length of 30000 nucleotides was made. Various combinations of L- and l-oligonucleotide length were considered. The results obtained enable one to evaluate the potentialities of the proposed method for various nucleotide matrices and the complexity of experiment. Use of continuous stacking hybridization permits a considerable increase of the length of sequenced DNA fragments. We offer the approach for resolving ambiguities in branching points, which occur because of long repeats. It is based on continuous stacking hybridization of several l-oligonucleotides which form a "chain" stabilized by mutual stacking interaction.

DNA↗

PubMedDate not supplied

[Measurement of distances between DNA segments for increasing the effectiveness of sequencing using hybridization on an oligonucleotide matrix].

DNA sequencing by hybridization on oligonucleotide matrix (SHOM) makes use of a matrix of immobilized oligonucleotides. Yet the method is not directly applicable for sequencing of fragments with long monotonous repeats. Measurement of the distances between certain segments within the DNA fragment analyzed provide additional information for sequencing. This information can be obtained by digesting DNA with a set of restriction endonucleases, or by PCR with primers complementary to certain DNA regions, with subsequent measurement of the length of the resulting fragments in gel electrophoresis. Use of this additional information increases the reconstruction efficiency and in many cases solves the problem of repeating and monotonous segments within analyzed DNA fragment. The current work presents the use of this information and the estimated efficiency of its usage.

Algorithms↗

PubMedDate not supplied

[A compressed form for presenting data to banks on the primary and spatial structure of biopolymers. Means for accessing compressed data banks].

Description of open CAN format (Compressed Amino acids and Nucleotides) is presented for storing genetic information in compressed form in data banks (DB). Data compression principles are demonstrated in detail on examples of EMBL DB (sequences of nucleotides), SWISSPROT DB (sequences of amino acids) and PDB DB (3D structures). A unified compressed data format provides a possibility to integrate EMBL, SWISSPROT, and PDB DB in one data bank. We are going to use this approach for integration of GENBANK and other similar DBs. One of the outcomes of the research is a library of data retrieval procedures for access to DB, providing developers of the application software packages with a uniform interface to DBs with biologically related data. The proposed scheme for data representation was recommended by the Expert Commission of the Informatics Section of the RSSIP "Human Genome" as a standard for distribution of data banks in Russia.

Amino Acid Sequence↗