ArticleBiophysical journal2011
Sequence-specific ultrasonic cleavage of DNA.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 57 citations in OpenAlex.
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- Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs.International journal of molecular sciences · 2023Article
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- Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters.International journal of molecular sciences · 2022Article
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- Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis.PloS one · 2021Article
- A Method for Identification of the Methylation Level of CpG Islands From NGS Data.Scientific reports · 2020Article
- Monitoring Dehydration and Clearing in Tissue Processing for High-Quality Clinical Pathology.Biopreservation and biobanking · 2019Article
- The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach.Frontiers in microbiology · 2019Review
- Fragmentation Through Polymerization (FTP): A new method to fragment DNA for next-generation sequencing.PloS one · 2019Article
- Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells.Biochimica et biophysica acta. Gene regulatory mechanisms · 2018Article
- Ultrasound-enhanced gene delivery to alfalfa cells by hPAMAM dendrimer nanoparticles.Turkish journal of biology = Turk biyoloji dergisi · 2018Article
- Structural features of DNA that determine RNA polymerase II core promoter.BMC genomics · 2016Article
- Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters.The EMBO journal · 2016Article
- Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo.Genome biology · 2015Article
- Non-random DNA fragmentation in next-generation sequencing.Scientific reports · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We investigated the phenomenon of ultrasonic cleavage of DNA by analyzing a large set of cleavage patterns of DNA restriction fragments using polyacrylamide gel electrophoresis. The cleavage intensity of individual phosphodiester bonds was found to depend on the nucleotide sequence and the position of the bond with respect to the ends of the fragment. The relative intensities of cleavage of the central phosphodiester bond in 16 dinucleotides and 256 tetranucleotides were determined by multivariate statistical analysis. We observed a remarkable enhancement of the mean values of the relative intensities of cleavage (cleavage rates) in phosphodiester bonds following deoxycytidine, which diminished in the row of dinucleotides: d(CpG) > d(CpA) > d(CpT) >> d(CpC). The cleavage rates for all pairs of complementary dinucleotides were significantly different from each other. The effect of flanking nucleotides in tetranucleotides on cleavage rates of all 16 types of central dinucleotides was also statistically significant. The sequence-dependent ultrasonic cleavage rates of dinucleotides are consistent with reported data on the intensity of the conformational motion of their 5'-deoxyribose. As a measure of local conformational dynamics, cleavage rates may be useful for characterizing functional regions of the genome.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.