Results 11 to 20 of about 11,225 (206)
Bubble statistics and positioning in superhelically stressed DNA [PDF]
Physical Review E, 2011 We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our results are obtained
B. Alberts +4 more
core +4 more sources
Structures of pentatricopeptide repeat proteins. [PDF]
Acta Crystallogr F Struct Biol CommunA number of crystal, cryo‐EM and solution structures of pentatricopeptide repeat proteins have been solved, revealing details of how they interact with single‐stranded RNA and other proteins, as well as their conformational repertoire.Pentatricopeptide repeat (PPR) proteins constitute the largest family of RNA‐binding proteins in land plants, playing ...
Pullakhandam A +3 more
europepmc +2 more sources
PCR-Free Site-Directed Mutagenesis on Repetitive Sequences Using Single-Stranded DNA-Assisted Double-Stranded DNA Nicking by DNAzymes. [PDF]
Angew Chem Int Ed EnglWe describe single‐stranded DNA‐assisted double‐stranded DNA nicking by DNAzymes (DANDA), in which DNAzymes are used to sequence‐specifically nick or cleave superhelical plasmids, with help from assisting single‐stranded DNAs. The DANDA system can be used for PCR‐free site‐directed mutagenesis on plasmids to create mutations on difficult targets such ...
Lyu M, Kong L, Shao X, Lu Y.
europepmc +3 more sources
Nucleic Acids Res, 2023 Abstract Closing each strand of a DNA duplex upon itself fixes its linking number L. This topological condition couples together the secondary and tertiary structures of the resulting ccDNA topoisomer, a constraint that is not present in otherwise identical nicked or linear DNAs.
Benham CJ.
europepmc +3 more sources
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
Polymer induced condensation of dna supercoils [PDF]
, 2008 Macromolecular crowding is thought to be a significant factor driving DNA condensation in prokaryotic cells. Whereas DNA in prokaryotes is supercoiled, studies on crowding-induced DNA condensation have so far focused on linear DNA.
Bessa Ramos Jr., J.E. +2 more
core +2 more sources
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