Differential effect of supercoiling on bacterial transcription in topological domains. [PDF]
PLoS Computational BiologyDNA supercoiling (SC), the over- and under-winding of DNA, is generated by transcription as described in the twin-domain model. Conversely, SC also impacts transcription through torsional stress.
Boaz Goldberg +3 more
doaj +2 more sources
Susceptibility to superhelically driven DNA duplex destabilization: a highly conserved property of yeast replication origins. [PDF]
PLoS Computational Biology, 2005 Strand separation is obligatory for several DNA functions, including replication. However, local DNA properties such as A+T content or thermodynamic stability alone do not determine the susceptibility to this transition in vivo.
Prashanth Ak, Craig J Benham
doaj +2 more sources
Theoretical analysis of competing conformational transitions in superhelical DNA. [PDF]
PLoS Computational Biology, 2012 We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence.
Dina Zhabinskaya, Craig J Benham
doaj +1 more source
Theoretical analysis of the stress induced B-Z transition in superhelical DNA. [PDF]
PLoS Computational Biology, 2011 We present a method to calculate the propensities of regions within a DNA molecule to transition from B-form to Z-form under negative superhelical stresses.
Dina Zhabinskaya, Craig J Benham
doaj +1 more source
Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling. [PDF]
, 2020 The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of ...
Aris, Kevin D Palacio +5 more
core +3 more sources
Supercoiling Effects on Short-Range DNA Looping in E. coli. [PDF]
PLoS ONE, 2016 DNA-protein loops can be essential for gene regulation. The Escherichia coli lactose (lac) operon is controlled by DNA-protein loops that have been studied for decades.
Lauren S Mogil +2 more
doaj +1 more source
Superhelical duplex destabilization and the recombination position effect. [PDF]
PLoS ONE, 2011 The susceptibility to recombination of a plasmid inserted into a chromosome varies with its genomic position. This recombination position effect is known to correlate with the average G+C content of the flanking sequences.
Cheryl L Sershen +3 more
doaj +1 more source
S1-Type Endonuclease 2 in Dedifferentiating Arabidopsis Protoplasts: Translocation to the Nucleus in Senescing Protoplasts Is Associated with De-Glycosylation. [PDF]
PLoS ONE, 2017 Cell dedifferentiation characterizes the transition of leaf cells to protoplasts and is accompanied by global chromatin decondensation. Here we show that in Arabidopsis, chromocentric chromatin undergoes prompt and gradual decondensation upon ...
Yemima Givaty-Rapp +3 more
doaj +1 more source
Fluctuations in superhelical DNA
Nucleic Acids Research, 1979 The effect of superhelicity on the base-pair opening probability and on the probability of occurrence of cruciform states in palindromic regions is theoretically treated. The calculations show that below the superhelix density value of -sigma=0.05 superhelicity does not appreciably affect the characteristics of DNA secondary structure fluctuations.
A V, Vologodskii +3 more
openaire +3 more sources
Nature Communications, 2019 Amphihelical antimicrobial peptides (AMPs) are bactericidal host defense factors, but their function as immunomodulators is emerging. Here the authors show that several AMPs organize DNA into periodic nanocrystals by self-assembling into superhelical ...
Ernest Y. Lee +10 more
doaj +1 more source