scholarly journals Can a double stranded DNA be unzipped by pulling a single strand?: Phases of adsorbed DNA

2009 ◽  
Vol 130 (14) ◽  
pp. 145105 ◽  
Author(s):  
Rajeev Kapri
Keyword(s):  
Single Strand ◽  
Double Stranded Dna

Promotion of Single-Strand Invasion of PNA to Double-Stranded DNA by Pseudo-Complementary Base Pairing

2019 ◽  
Vol 92 (2) ◽  
pp. 330-335 ◽  
Author(s):  
Narumi Shigi ◽  
Yuki Mizuno ◽  
Hiroko Kunifuda ◽  
Kazunari Matsumura ◽  
Makoto Komiyama
Keyword(s):  
Single Strand ◽  
Base Pairing ◽  
Double Stranded Dna ◽  
Strand Invasion

scholarly journals Single-strand specific nuclease enhances accuracy of error-corrected sequencing and improves rare mutation-detection sensitivity

2021 ◽  
Author(s):  
Yuki Otsubo ◽  
Shoji Matsumura ◽  
Naohiro Ikeda ◽  
Masayuki Yamane
Keyword(s):  
Dna Sequences ◽  
Mutation Detection ◽  
Single Strand ◽  
Detection Sensitivity ◽  
Induced Mutations ◽  
Mung Bean Nuclease ◽  
S1 Nuclease ◽  
Rare Mutation ◽  
Rare Mutations ◽  
Double Stranded Dna

AbstractError-corrected sequences (ECSs) that utilize double-stranded DNA sequences are useful in detecting mutagen-induced mutations. However, relatively higher frequencies of G:C > T:A (1 × 10−7 bp) and G:C > C:G (2 × 10−7 bp) errors decrease the accuracy of detection of rare G:C mutations (approximately 10−7 bp). Oxidized guanines in single-strand (SS) overhangs generated after shearing could serve as the source of these errors. To remove these errors, we first computationally discarded up to 20 read bases corresponding to the ends of the DNA fragments. Error frequencies decreased proportionately with trimming length; however, the results indicated that they were not sufficiently removed. To efficiently remove SS overhangs, we evaluated three mechanistically distinct SS-specific nucleases (S1 Nuclease, mung bean nuclease, and RecJf exonuclease) and found that they were more efficient than computational trimming. Consequently, we established Jade-Seq™, an ECS protocol with S1 Nuclease treatment, which reduced G:C > T:A and G:C > C:G errors to 0.50 × 10−7 bp and 0.12 × 10−7 bp, respectively. This was probably because S1 Nuclease removed SS regions, such as gaps and nicks, depending on its wide substrate specificity. Subsequently, we evaluated the mutation-detection sensitivity of Jade-Seq™ using DNA samples from TA100 cells exposed to 3-methylcholanthrene and 7,12-dimethylbenz[a]anthracene, which contained the rare G:C > T:A mutation (i.e., 2 × 10−7 bp). Fold changes of G:C > T:A compared to the vehicle control were 1.2- and 1.3-times higher than those of samples without S1 Nuclease treatment, respectively. These findings indicate the potential of Jade-Seq™ for detecting rare mutations and determining the mutagenicity of environmental mutagens.

scholarly journals Processivity, velocity and universal characteristics of nucleic acid unwinding by helicases

2018 ◽  
Author(s):  
Shaon Chakrabarti ◽  
Christopher Jarzynski ◽  
D. Thirumalai
Keyword(s):  
Quantitative Analysis ◽  
Single Molecule ◽  
Physical Principle ◽  
Single Strand ◽  
Mathematical Framework ◽  
Double Stranded Dna ◽  
Analytic Expressions ◽  
Xpd Helicase ◽  
Partner Proteins ◽  
Magnitude Increase

AbstractHelicases that act as motors and unwind double stranded nucleic acids are broadly classified as either active or passive, depending on whether or not they directly destabilize the double strand. By using this description in a mathematical framework, we derive analytic expressions for the velocity and run-length of a general model of finitely processive helicases. We show that, in contrast to the helicase unwinding velocity, the processivity exhibits a universal increase in response to external force. We use our results to analyze velocity and processivity data from single molecule experiments on the superfamily-4 ring helicase T7, and establish quantitatively that T7 is a weakly active helicase. We predict that compared to single-strand translocation, there is almost a two orders-of-magnitude increase in the back-stepping probability of T7 while unwinding double-stranded DNA. Our quantitative analysis of T7 suggests that the tendency of helicases to take frequent back-steps may be more common than previously anticipated, as was recently shown for the XPD helicase. Finally, our results suggest the intriguing possibility of a single underlying physical principle governing the experimentally observed increase in unwinding efficiencies of helicases in the presence of force, oligomerization or partner proteins like single strand binding proteins. The clear implication is that helicases may have evolved to maximize processivity rather than speed.

A second form of the single-strand specific endonuclease of Neurospora crassa which is associated with a double-strand exonuclease

1976 ◽  
Vol 54 (11) ◽  
pp. 971-980 ◽  
Author(s):  
M. J. Fraser ◽  
R. Tjeerde ◽  
K. Matsumoto
Keyword(s):  
Neurospora Crassa ◽  
Heat Stability ◽  
Single Strand ◽  
Dna Unwinding ◽  
Endonuclease Activity ◽  
Wild Type ◽  
Double Stranded Rna ◽  
Heat Stable ◽  
Double Stranded Dna ◽  
Heating Up

A second form of single-strand specific endonuclease, which is stable to heating up to 74 °C and does not bind strongly to phosphocellulose, has been partially purified from extracts of mycelia of wild-type Neurospora crassa. The endonuclease is associated with an equally heat-stable exonuclease which degrades linear but not circular double-stranded DNA and does not attack double-stranded RNA. The exonuclease probably also degrades single-stranded DNA. Both endonuclease and exonuclease activities are inhibited by 0.1–0.5 mM ATP. The exonuclease is preferentially inhibited by a variety of agents and preferentially inactivated by trypsin. A DNA-unwinding activity has also been detected in the nuclease preparation. Protease(s) present in the nuclease preparation destroy the DNA-unwinding and exonuclease activities on incubation at 37 °C, but do not affect the endonuclease activity. However, the heat-stability and chromatographic properties of the endonuclease are affected by this treatment. The altered properties of the endonuclease are very similar to those of the single-strand specific endonuclease which has been previously described. The combined nuclease activities of the unaltered preparation make up a putative recombination nuclease of N. crassa.

Functionally diverse type V CRISPR-Cas systems

Science ◽  
2018 ◽  
Vol 363 (6422) ◽  
pp. 88-91 ◽  
Author(s):  
Winston X. Yan ◽  
Pratyusha Hunnewell ◽  
Lauren E. Alfonse ◽  
Jason M. Carte ◽  
Elise Keston-Smith ◽  
...  
Keyword(s):  
Functional Diversity ◽  
Single Strand ◽  
Double Stranded Dna ◽  
Type V ◽  
Functionally Diverse

Type V CRISPR-Cas systems are distinguished by a single RNA-guided RuvC domain-containing effector, Cas12. Although effectors of subtypes V-A (Cas12a) and V-B (Cas12b) have been studied in detail, the distinct domain architectures and diverged RuvC sequences of uncharacterized Cas12 proteins suggest unexplored functional diversity. Here, we identify and characterize Cas12c, -g, -h, and -i. Cas12c, -h, and -i demonstrate RNA-guided double-stranded DNA (dsDNA) interference activity. Cas12i exhibits markedly different efficiencies of CRISPR RNA spacer complementary and noncomplementary strand cleavage resulting in predominant dsDNA nicking. Cas12g is an RNA-guided ribonuclease (RNase) with collateral RNase and single-strand DNase activities. Our study reveals the functional diversity emerging along different routes of type V CRISPR-Cas evolution and expands the CRISPR toolbox.

Discrimination of monomer from multimer DNA disk-shaped toruses by freezeetch TEM

1984 ◽  
Vol 42 ◽  
pp. 210-211
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Biochemical Data ◽  
Dna Structures ◽  
Ice Surface ◽  
Double Stranded Dna ◽  
Data Support ◽  
Dna Organization ◽  
Trivalent Cations

In vitro collapse of DNA by trivalent cations like spermidine produces torus (donut) shaped DNA structures thought to have a DNA organization similar to certain double stranded DNA bacteriophage and viruses. This has prompted our studies of these structures using freeze-etch low Pt-C metal (9Å) replica TEM. With a variety of DNAs the TEM and biochemical data support a circumferential DNA winding model for hydrated DNA torus organization. Since toruses are almost invariably oriented nearly horizontal to the ice surface one of the most accessible parameters of a torus population is annulus (ring) thickness. We have tabulated this parameter for populations of both nicked, circular (Fig. 1: n=63) and linear (n=40: data not shown) ϕX-174 DNA toruses. In both cases, as can be noted in Fig. 1, there appears to be a compact grouping of toruses possessing smaller dimensions separated from a dispersed population possessing considerably larger dimensions.

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