We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo....

Abbreviations: CPD: Cyclobutane Pyrimidine Diner; DLR: German Aerospace Center; ds-break: Double Strand Break; EST: Experiment Sequence Test; EVT: Experiment Verification Test; ISS: International Space Station; IWF: Institut für Weltraumforschung; LEO: Low Earth’s Orbit; OD: Optical density [log(I0/I)]; PCR: Polymerase Chain Reaction; PLC: Payload Computer; RGB: Research Group for Biophysics; s...

Homing endonucleases are site-specific DNA endonucleases that function as mobile genetic elements by introducing double-strand breaks or nicks at defined locations. Of the major families of homing endonucleases, the modular GIY-YIG endonucleases are least understood in terms of mechanism. The GIY-YIG homing endonuclease I-BmoI generates a double-strand break by sequential nicking reactions duri...

The RecA protein of Escherichia coli, and all filament-forming homologues identified to date, promote DNA strand exchange by a common, ordered pathway. A filament is first formed on single-stranded DNA, followed by uptake of the duplex substrate. These proteins are thereby targeted to single-strand gaps and tails where recombinational DNA repair is required. The observed course of DNA strand ex...

calpastatin (cast) is a specific inhibiter of calpains, playing a role in meat tenderization and myogenesis. in the present study, the polymorphism of the cast gene of makoei sheep was investigated by polymerase chain reaction and single strand conformation polymorphism technique (pcr–sscp). genomic dna was extracted from whole blood samples collected from 100 sheep. a 622 bp cast exon 1 segmen...

Site-specific nicking occurs on the l-strand, but not on the r-strand, of the adenovirus left inverted terminal repeat. Nicks are presumably introduced into double- or single-stranded DNA by a cellular endonuclease in an ATP-independent reaction. The consensus nick site has the sequence: (sequence in text).

Single-stranded viral DNA of bacteriophage f1 is cleaved into specific fragments by endo R-HaeIII, a restriction endonuclease isolated from Hemophilus aegyptius. The sites of the single strand cleavage correspond to those of the double strand cleavage. A single-stranded DNA fragment containing only one HaeIII site is also cleaved by this enzyme. This observation suggests that the reaction of si...

DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule f...

b ackground: the main goal of present study was to detect polymorphism in msp-1 gene which is a major blood stage candidate for vaccine in plasmodium vivax by single strand conformational poly- morphism-polymerase chain reaction (sscp-pcr). m ethods: during 2008 to 2010 fifty samples were collected from iranian patients with p. vivax in hormozgan province, southern iran. all of the samples were...

We have previously reported that poly(l-lysine)-graft-dextran cationic comb-type copolymers accelerate strand exchange reaction between duplex DNA and its complementary single strand by >4 orders of magnitude, while stabilizing duplex. However, the stabilization of the duplex is considered principally unfavourable for the accelerating activity since the strand exchange reaction requires, at lea...