Ultrasonic cleavage of DNA: Quantitative analysis of sequence specificity

Grokhovsky, S. L.; Il’icheva, I. A.; Nechipurenko, Dmitry; Panchenko, L. A.; Polozov, R. V.; Nechipurenko, Yu. D.

doi:10.1134/s0006350908030159

Cited by 12 publications

(6 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Relative cleavage intensities of each of 16 dinucleotides ( R index) and relative cleavage intensities of each of 256 tetranucleotides ( T index) were obtained from experiments of DNA fragmentation by ultrasound [23]. The products of ultrasound irradiation of plasmid DNA restriction fragments with known sequences were separated by gel electrophoresis technique with subsequent computer digitization of the gel band densities and statistical treatment of more than 20 500 relative cleavage intensities [23, 53, 54]. One can see that the intensities of the cleavage in complementary di- or tetranucleotides are different if their base-paired fragment is asymmetrical.…”

Section: Resultsmentioning

confidence: 99%

Structural features of DNA that determine RNA polymerase II core promoter

et al. 2016

View full text Add to dashboard Cite

BackgroundThe general structure and action of all eukaryotic and archaeal RNA polymerases machinery have an astonishing similarity despite the diversity of core promoter sequences in different species. The goal of our work is to find common characteristics of DNA region that define it as a promoter for the RNA polymerase II (Pol II).ResultsThe profiles of a large number of physical and structural characteristics, averaged over representative sets of the Pol II minimal core promoters of the evolutionary divergent species from animals, plants and unicellular fungi were analysed. In addition to the characteristics defined at the base-pair steps, we, for the first time, use profiles of the ultrasonic cleavage and DNase I cleavage indexes, informative for internal properties of each complementary strand.ConclusionsDNA of the core promoters of metazoans and Schizosaccharomyces pombe has similar structural organization. Its mechanical and 3D structural characteristics have singular properties at the positions of TATA-box. The minor groove is broadened and conformational motion is decreased in that region. Special characteristics of conformational behavior are revealed in metazoans at the region, which connects the end of TATA-box and the transcription start site (TSS). The intensities of conformational motions in the complementary strands are periodically changed in opposite phases. They are noticeable, best of all, in mammals. Such conformational features are lacking in the core promoters of S. pombe. The profiles of Saccharomyces cerevisiae core promoters significantly differ: their singular region is shifted down thus pointing to the uniqueness of their structural organization. Obtained results may be useful in genetic engineering for artificial modulation of the promoter strength.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3292-z) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultsmentioning

confidence: 99%

Structural features of DNA that determine RNA polymerase II core promoter

et al. 2016

View full text Add to dashboard Cite

show abstract

“…The sequence specificity of ultrasonic cleavage of DNA [24][25][26][27][28] as well as the sequence specificity of DNase I cleavage [29][30][31] allow us to study the genomic structures in more details.…”

Section: Local Variations Of Ultrasonic Cleavage and Dnase I Cleavage...mentioning

confidence: 99%

Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs

Savina

Anashkina

2023

IJMS

View full text Add to dashboard Cite

RNA polymerase II (POL II) is responsible for the transcription of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs). Previously, we have shown the evolutionary invariance of the structural features of DNA in the POL II core promoters of the precursors of mRNAs. In this work, we have analyzed the POL II core promoters of the precursors of lncRNAs in Homo sapiens and Mus musculus genomes. Structural analysis of nucleotide sequences in positions −50, +30 bp in relation to the TSS have shown the extremely heterogeneous 3D structure that includes two singular regions - hexanucleotide “INR” around the TSS and octanucleotide “TATA-box” at around ~−28 bp upstream. Thus, the 3D structure of core promoters of lncRNA resembles the architecture of the core promoters of mRNAs; however, textual analysis revealed differences between promoters of lncRNAs and promoters of mRNAs, which lies in their textual characteristics; namely, the informational entropy at each position of the nucleotide text of lncRNA core promoters (by the exception of singular regions) is significantly higher than that of the mRNA core promoters. Another distinguishing feature of lncRNA is the extremely rare occurrence in the TATA box of octanucleotides with the consensus sequence. These textual differences can significantly affect the efficiency of the transcription of lncRNAs.

show abstract

“…This technology has shown immense potential in various fields, including medicine, agriculture, and environmental science, as it provides a non-invasive and precise method for manipulating DNA. Ultrasonic cleavage is a new method for obtaining DNA fragments [13,14]. The library preparation for whole-genome sequencing (WGS) using next-generation sequencing (NGS) begins with DNA fragmentation, and sonication is the most commonly used approach due to its ease and reliability [15,16].…”

Section: Introductionmentioning

confidence: 99%

Identification and Characterization of an Antifungal Gene Mt1 from Bacillus subtilis by Affecting Amino Acid Metabolism in Fusarium graminearum

Song

Dong

2023

IJMS

View full text Add to dashboard Cite

Fusarium head blight is a devastating disease that causes significant economic losses worldwide. Fusarium graminearum is a crucial pathogen that requires close attention when controlling wheat diseases. Here, we aimed to identify genes and proteins that could confer resistance to F. graminearum. By extensively screening recombinants, we identified an antifungal gene, Mt1 (240 bp), from Bacillus subtilis 330-2. We recombinantly expressed Mt1 in F. graminearum and observed a substantial reduction in the production of aerial mycelium, mycelial growth rate, biomass, and pathogenicity. However, recombinant mycelium and spore morphology remained unchanged. Transcriptome analysis of the recombinants revealed significant down-regulation of genes related to amino acid metabolism and degradation pathways. This finding indicated that Mt1 inhibited amino acid metabolism, leading to limited mycelial growth and, thus, reduced pathogenicity. Based on the results of recombinant phenotypes and transcriptome analysis, we hypothesize that the effect of Mt1 on F. graminearum could be related to the metabolism of branched-chain amino acids (BCAAs), the most affected metabolic pathway with significant down-regulation of several genes. Our findings provide new insights into antifungal gene research and offer promising targets for developing novel strategies to control Fusarium head blight in wheat.

show abstract

Ultrasonic cleavage of DNA: Quantitative analysis of sequence specificity

Cited by 12 publications

References 8 publications

Structural features of DNA that determine RNA polymerase II core promoter

Structural features of DNA that determine RNA polymerase II core promoter

Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs

Identification and Characterization of an Antifungal Gene Mt1 from Bacillus subtilis by Affecting Amino Acid Metabolism in Fusarium graminearum

Contact Info

Product

Resources

About