[Transcription of the SV40 genome in Saccharomyces cerevisiae yeasts].
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Cloning, Molecular↗
Biomedical subjects
E I Golovanov
Publications and source records attributed to E I Golovanov.
Transcription of colicin E1 plasmid: electron-microscopic mapping of promoters.
The promoters of ColE1 plasmid DNA have been localized. Their position has been determined relative to the functional map of the plasmid. The direction of transcription from each promoter has been established. Superhelical ColE1 DNA was transcribed in vitro by Escherichia coli RNA polymerase. The resulting complexes of DNA with nascent RNA were treated with restriction endonucleases EcoR1 and SmaI and observed in an electron microscope. Statistical analysis of RNA distribution on DNA made it possible to localize the promoters and determine the direction of transcription from them. The analysis was based on a specially prepared computer program.
Bacteriocin Plasmids↗
Equilibrium melting of plasmid ColE1 DNA: electron-microscopic visualization.
The fine structure of the melting curve for the linear colE1 DNA has been obtained. To find the ColE1 DNA regions corresponding to peaks in the melting curve's fine structure, we fixed the melted DNA regions with glyoxal /12/. Electron-microscopic denaturation maps were obtained for nine temperature points within the melting range. Thereby the whole process of colE1 DNA melting was reconstructed in detail. Spectrophotometric and electron microscopic data were used for mapping the distribution of Gc-pairs over the DNA molecule. The most AT-rich DNA regions (28 and 37% of GC-pairs), 380 and 660 bp long resp., are located on both sides of the site of ColE1 DNA's cleavage by EcoR1 endonuclease. The equilibrium denaturation maps are compared with maps obtained by the method of Inman /20/ for eight points of the kinetic curve of ColE1 DNA unwinding by formaldehyde.
DNA Restriction Enzymes↗
[Statistical characteristics in primary structures of functional regions of Escherichia coli genome. I. Frequency characteristics].
Analysis of the frequencies of occurrence of mono- and dinucleotides in sequenced E. coli DNA fragments was performed. The DNA sequences of total length 135 000 nucleotides were considered. It was demonstrated that the fragments of DNA which have different functional properties also have different parameters of neighbour nucleotides correlation. Moreover, periodical positional dependence of correlation parameters in coding regions was found. The evolution significance of stated observation is discussed, so as the opportunity of using them in the special model of nucleotide's sequences, which is needed for development of the computer recognition algorithms for genomic functional units.
Base Sequence↗
[Statistical characteristics in primary structures of functional regions of Escherichia coli genome. II. Non-stationary Markov chains].
We introduced non-stationary Marcov chains for statistical description of the DNA E. coli structural domains. The values of all needed parameters for those chains was determined by the preliminary statistical processing of a wide set of the E. coli coding regions. It was shown that non-stationary models predict frequencies of occurrences of various combinations of nucleotides within the coding fragments of DNA, better than stationary ones. In particular non-stationary models give good approximation for short and long distance arrangement of nucleotides in the coding regions. The correlation parameters for neighbour codons and for neighbour amino acid residuals in E. coli protein's primary structure was determined from the non-stationary model of the second order. With the aid of the statistical criteria it was found that neighbour residuals in polypeptide chains can't be considered as independent. The new model of the DNA structural domain may be used in computer algorithms for recognition and classification of DNA functional regions.
Base Sequence↗
[Statistical characteristics of primary structures of the functional regions of the Escherichia coli genome. III. Computer recognition of coding regions].
We have presented the method for recognition of structural domains of DNA. This method uses statistical description of coding and non-coding regions in the form of stationary or nonstationary Marcov chain, which was introduced in our previous papers. Calculation of the probability that the given fragment of the DNA appears part of the coding region, is the main operation of this algorithm. The results, obtained for the number of E. coli DNA sequences showed the ability of the method to find the structural domains and correct reading frame, so as to give the estimation of the extent of protein expressivity. Provided necessary statistical data are available, the proposed method may be used for the analysis of DNA of other organisms.
Base Sequence↗
[Possible role of tRNA1Lys in recognition of pre-mRNA sequences involved in the control of splicing].
Previously we presented some evidence for involvement of the imported tRNA1Lys in splicing the mitochondrial mosaic genes transcripts in yeast. The new data provided here together with our previous results show that tRNA1Lys/transcripts complementarity permits accurate prediction of intron-exon donor boundaries for at least 7 (probably all 9) Dujonian 1st class introns. A computer-assisted search for homologies between mosaic genes transcripts and sequences complementary to tRNA1Lys reveals most of the control sequences previously determined as the sites of 1) cis-acting splicing blocks, 2) conserved RNA sequences and 3) conserved features of transcripts secondary structure. The sequences revealed in our study are as follows: sequences GGGGG and GGCTC in 2nd class introns and less convincing cases are R + E', E + P and IG in 1st class introns. The results obtained here together with the results of other authors suggest a series of (often weak) alternative RNA-RNA interactions needed to regulate and(or) provide a sufficiently error-free mechanism of splicing for the mosaic genes transcripts. A comparison was made of: 1) sequences near the sites of 2 different autocatalytic Tetrahymena pre-rRNA cleavage-ligation events (splicing and cyclization of the intron RNA) and 2) sequences of tRNA1Lys probably contacting donor boundaries of 1st class mitochondrial introns. The comparison reveals an obvious conservation of some basic structure regardless of the different chemical directions of the strands involved. The result suggests a possible catalytic function for the tRNA1Lys probably involved also in recognition and control processes of mitochondrial transcripts splicing.
Base Sequence↗
[Plan for finding homologies in nucleotide sequence databases using preliminarily calculated sequence samples].
A scheme of fast similarity search of nucleotide sequences is suggested based on sequence imaging, which results in chunks of information much less than original sequence but more specialized for comparison. Three methods were developed using three different imaging functions. The first is based on identity of local sites of up to twelve nucleotides, the second is based on statistical homology of local 42 nucleotide fragments, and the third is based on the homology of 100-150 nucleotide fragments and models the comparison of restriction maps. Each of them requires the library of sequence images. The total size of such a library is less than the size of sequences stored in compressed form. The sequences are aligned allowing local homology searches. The method reduces total time for a similarity search about 100-fold. The programs can be easily included in any software, which allows user to define his own set of sequences. One of the programs is implemented within DNA-SUN software and is used in Institute of Molecular Genetics and Institute of Molecular Biology.
Amino Acid Sequence↗