Biomedical subjects

B R Amirikyan

Publications and source records attributed to B R Amirikyan.

4 recordsLinked to original sources

PubMed1989

Neural network models for promoter recognition.

The problem of recognition of promoter sites in the DNA sequence has been treated with models of learning neural networks. The maximum network capacity admissible for this problem has been estimated on the basis of the total of experimental data available on the determined promoter sequences. The model of a block neural network has been constructed to satisfy this estimate and rules have been elaborated for its learning and testing. The learning process involves a small (of the order of 10%) part of the total set of promoter sequences. During this procedure the neural network develops a system of distinctive features (key words) to be used as a reference in identifying promoters against the background of random sequences. The learning quality is then tested with the whole set. The efficiency of promoter recognition has been found to amount to 94 to 99%. The probability of an arbitrary sequence being identified as a promoter is 2 to 6%.

Base Sequence↗

PubMed1987

The ionic strength dependence of the cooperativity factor for DNA melting.

The melting temperature for the d(AT)24.d(AT)24 stretch, located inside the DNA helix and terminally, have been determined in a wide range of ionic strength values (0.01 - 1 M Na+). The cooperativity factor was calculated from the shifts in the melting temperature of the stretch due to its different boundary conditions. With the sodium concentration decreasing from 1 M to 0.01 M the cooperativity factor dropped by three orders of magnitude, its change being less marked at high than at low ionic strength.

DNA↗

PubMed1984

Allowance for heterogeneous stacking in the DNA helix-coil transition theory.

Melting profiles of eight DNA molecules with lengths ranging from 849 to 4362 bp have been measured in an SSC buffer where the melting is an equilibrium process up to complete strand separation. A theoretical analysis shows that the melting profiles depend on only eight invariants that are linear combinations of 10 original stacking parameters. As a result it is impossible to determine the 10 parameters from the melting profiles. The 8 variants have been determined by fitting theoretical profiles to experimental ones for two fragments. Then theoretical and experimental profiles are compared for those 6 fragments that were not used in the fitting procedure. This comparison demonstrates that allowance for heterogeneous stacking considerably improves the agreement between theory and experiment. The values of invariants have proved to be small. This confirms the previous conclusion that heterogeneous stacking interactions produce only small corrections to the major effect of the difference in the mean stabilities of AT and GC pairs. Some discrepancy between theory and experiment that remains after the allowance for heterogeneous stacking is probably due to even finer effects of long-range interactions.

Base Composition↗

PubMed1981

Determination of DNA cooperativity factor.

The paper presents measurements of the difference in the melting temperature of a colE1 DNA region when it is located inside the DNA helix and at its end. A direct comparison of calculations based on the rigorous theory of helix-coil transition with experimental data for .2 M Na+ (the conditions for fully reversible melting) yielded the value of 2.5-5x10(-5) for the cooperatively factor sigma. We discuss the reversibility of DNA melting and the possibility of applying the "all-or-nothing" concept to the melting of DNA regions.

DNA, Bacterial↗