Exploration of Spin-Dependent Thermoelectricity in the Chiral Double-Stranded DNA Molecule Coupled to Ferromagnetic Leads

2019 ◽  
Vol 12 (2) ◽  
Author(s):  
Lei-Lei Nian ◽  
Long Bai ◽  
Wenting Yu ◽  
Jun Tang ◽  
Huichao Li ◽  
...  
Keyword(s):  
Dna Molecule ◽  
Double Stranded Dna

scholarly journals High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast

2017 ◽  
Author(s):  
Yi Yin ◽  
Margaret Dominska ◽  
Eunice Yim ◽  
Thomas D. Petes
Keyword(s):  
Type Strain ◽  
Wild Type Strain ◽  
Mitotic Recombination ◽  
Template Switching ◽  
Wild Type ◽  
Dna Breaks ◽  
Repair Synthesis ◽  
Heteroduplex Dna ◽  
Dna Molecule ◽  
Double Stranded Dna

AbstractDouble-stranded DNA breaks (DSBs) can be generated by both endogenous and exogenous agents. In diploid yeast strains, such breaks are usually repaired by homologous recombination (HR), and a number of different HR pathways have been described. An early step for all HR pathways is formation of a heteroduplex, in which a single-strand from the broken DNA molecule pairs with a strand derived from an intact DNA molecule. If the two strands of DNA are not identical, within the heteroduplex DNA (hetDNA), there will be mismatches. In a wild-type strain, these mismatches are removed by the mismatch repair (MMR) system. In strains lacking MMR, the mismatches persist and can be detected by a variety of genetic and physical techniques. Most previous studies involving hetDNA formed during mitotic recombination have been restricted to a single locus with DSBs induced at a defined position by a site-specific endonuclease. In addition, in most of these studies, recombination between repeated genes was examined; in such studies, the sequence homologies were usually less than 5 kb. In the present study, we present a global mapping of hetDNA formed in a UV-treated MMR-defective mlh1 strain. Although about two-thirds of the recombination events were associated with hetDNA with a continuous array of unrepaired mismatches, in about one-third of the events, we found regions of unrepaired mismatches flanking regions without mismatches. We suggest that these discontinuous hetDNAs involve template switching during repair synthesis, repair of a double-stranded DNA gap, and/or Mlh1-independent MMR. Many of our observed events are not explicable by the simplest form of the double-strand break repair (DSBR) model of recombination. We also studied hetDNA associated with spontaneous recombination events selected on chromosomes IV and V in a wild-type strain. The interval on chromosome IV contained a hotspot for spontaneous crossovers generated by an inverted pair of transposable elements (HS4). We showed that HS4-induced recombination events are associated with the formation of very large (>30 kb) double-stranded DNA gaps.

Stabilization of double-stranded DNA molecule by nonhistone peptidic effector from calf thymus

1976 ◽  
Vol 3 (1) ◽  
pp. 55-64 ◽  
Author(s):  
G. L. Gianfranceschi ◽  
D. Amici ◽  
L. Guglielmi
Keyword(s):  
Dna Molecule ◽  
Double Stranded Dna ◽  
Calf Thymus

scholarly journals Light-scattering studies on deoxyribonucleic acid flexibility. The solution properties of a small circular deoxyribonucleic acid molecule

1972 ◽  
Vol 130 (4) ◽  
pp. 1019-1028 ◽  
Author(s):  
Douglas J. Jolly ◽  
Ailsa M. Campbell
Keyword(s):  
Light Scattering ◽  
Deoxyribonucleic Acid ◽  
Persistence Length ◽  
Resolving Power ◽  
Experimental Investigations ◽  
Volume Factor ◽  
Circular Dna ◽  
Dna Molecule ◽  
Double Stranded Dna ◽  
Infected Cells

Previous investigations on the persistence length of DNA in solution have revealed large discrepancies between hydrodynamic results and those from light-scattering techniques which have potentially a greater resolving power. The information obtained from experiments on a small circular DNA molecule has resolved these discrepancies. The non-superhelical circular double-stranded DNA molecule from bacteriophage [unk]X174-infected cells is small enough to permit accurate light-scattering extrapolations, and its solutions have negligible anisotropy. The persistence length obtained from experimental investigations on this molecule is comparable with that obtained by hydrodynamic techniques, even with variation of the excluded-volume factor.

scholarly journals Complete genome sequence of the newly discovered temperate Clostridioides difficile bacteriophage phiCDKH01 of the family Siphoviridae

2021 ◽  
Author(s):  
Krzysztof Hinc ◽  
Monika Kabała ◽  
Adam Iwanicki ◽  
Gajane Martirosian ◽  
Alessandro Negri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Phage Genome ◽  
Putative Orfs ◽  
Dna Molecule ◽  
Clostridioides Difficile ◽  
Double Stranded Dna ◽  
The Family

AbstractA temperate siphovirus, phiCDKH01, was obtained from a clinical isolate of Clostridioides difficile. The phage genome is a 45,089-bp linear double-stranded DNA molecule with an average G+C content of 28.7%. It shows low similarity to known phage genomes, except for phiCD24-1. Genomic and phylogenetic analysis revealed that phiCDKH01 is a newly discovered phage. Sixty-six putative ORFs were predicted in the genome, 37 of which code for proteins with predicted functions. The phiCDKH01 prophage was localized in the host genome. The results of this study increase our knowledge about the genetic diversity of tailed phages.

Supercoils in human DNA

1975 ◽  
Vol 19 (2) ◽  
pp. 261-279
Author(s):  
P.R. Cook ◽  
I.A. Brazell
Keyword(s):  
Gamma Rays ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Hydrodynamic Properties ◽  
Dna Molecule ◽  
Double Stranded Dna ◽  
Human Dna ◽  
Nuclear Structures ◽  
Intercalating Agents ◽  
Characteristic Manner

The three-dimensional structure of a double-stranded DNA molecule may be described by distinguishing the helical turns of the DNA duplex from any superhelical turns that might be superimposed upon the duplex turns. There are characteristic changes in the hydrodynamic properties of superhelical DNA molecules when they interact with intercalating agents. The hydrodynamic properties of nuclear structures released by gently lysing human cells are changed by intercalating agents in this characteristic manner. The characteristic changes are abolished by irradiating the cells with gamma-rays but may be restored by incubating the cells at 37 degrees C after irradiation. These results are interpreted as showing that human DNA is supercoiled. A model for the structure of the chromosome is suggested.

scholarly journals Pleomorphic archaeal viruses: the family Pleolipoviridae is expanding by seven new species

2020 ◽  
Vol 165 (11) ◽  
pp. 2723-2731 ◽  
Author(s):  
Tatiana A. Demina ◽  
Hanna M. Oksanen
Keyword(s):  
New Species ◽  
Membrane Vesicles ◽  
Virus Species ◽  
Virus Taxonomy ◽  
Dna Viruses ◽  
Dna Molecule ◽  
Double Stranded Dna ◽  
Archaeal Viruses ◽  
The Family ◽  
Globally Distributed

AbstractEstablished in 2016, the family Pleolipoviridae comprises globally distributed archaeal viruses that produce pleomorphic particles. Pseudo-spherical enveloped virions of pleolipoviruses are membrane vesicles carrying a nucleic acid cargo. The cargo can be either a single-stranded or double-stranded DNA molecule, making this group the first family introduced in the 10th Report on Virus Taxonomy including both single-stranded and double-stranded DNA viruses. The length of the genomes is approximately 7–17 kilobase pairs, or kilonucleotides in the case of single-stranded molecules. The genomes are circular single-stranded DNA, circular double-stranded DNA, or linear double-stranded DNA molecules. Currently, eight virus species and seven proposed species are classified in three genera: Alphapleolipovirus (five species), Betapleolipovirus (nine species), and Gammapleolipovirus (one species). Here, we summarize the updated taxonomy of the family Pleolipoviridae to reflect recent advances in this field, with the focus on seven newly proposed species in the genus Betapleolipovirus: Betapleolipovirus HHPV3, HHPV4, HRPV9, HRPV10, HRPV11, HRPV12, and SNJ2.

scholarly journals Intravirion DNA Can Access the Space Occupied by the Bacteriophage P22 Ejection Proteins

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1504
Author(s):  
Justin C. Leavitt ◽  
Eddie B. Gilcrease ◽  
Brianna M. Woodbury ◽  
Carolyn M. Teschke ◽  
Sherwood R. Casjens
Keyword(s):  
Dna Packaging ◽  
Bacteriophage P22 ◽  
Portal Protein ◽  
Dna Molecule ◽  
Double Stranded Dna ◽  
Phage P22

Tailed double-stranded DNA bacteriophages inject some proteins with their dsDNA during infection. Phage P22 injects about 12, 12, and 30 molecules of the proteins encoded by genes 7, 16 and 20, respectively. After their ejection from the virion, they assemble into a trans-periplasmic conduit through which the DNA passes to enter the cytoplasm. The location of these proteins in the virion before injection is not well understood, although we recently showed they reside near the portal protein barrel in DNA-filled heads. In this report we show that when these proteins are missing from the virion, a longer than normal DNA molecule is encapsidated by the P22 headful DNA packaging machinery. Thus, the ejection proteins occupy positions within the virion that can be occupied by packaged DNA when they are absent.

scholarly journals Identification of a microsatellite region composed of a long homopurine/homopyrimidine tract surrounded by AT-rich sequences upstream of the rat stress-inducible hsp 70.1 gene.

1997 ◽  
Vol 44 (1) ◽  
pp. 147-152 ◽  
Author(s):  
K Lisowska ◽  
T Loch ◽  
A Fiszer-Kierzkowska ◽  
D Scieglińska ◽  
Z Krawczyk
Keyword(s):  
Inverted Repeat ◽  
Cleavage Site ◽  
Dna Structure ◽  
Transcription Unit ◽  
Hsp 70 ◽  
Microsatellite Sequence ◽  
Dna Molecule ◽  
Double Stranded Dna ◽  
Dna Fragment ◽  
Susceptibility Assay

A DNA region containing several repetitive motifs has been detected about 1.9 kbp upstream of the transcription unit of the rat stress-inducible hsp 70.1 gene. The most interesting element of this area is a microsatellite sequence (GA)6CAG(TC)24 that consists of an inverted repeat partially overlapping with the long homopurine/homopyrimidine tract (Pu/Py). DNA molecule within the described sequence can theoretically adopt alternate, non-B structures (H-DNA or cruciform) containing single-stranded regions. This microsatellite region is flanked by AT-rich sequences containing several poly(A) tracts. The longest of them with a possible potential to destabilized a double-stranded DNA helix is localized around 160 bp downstream the (GA)6CAG(TC)24. The DNA fragment containing sequences described above was subcloned into the pUC19 vector and the resulting plasmid was subjected to the standard S1 susceptibility assay. Preliminary mapping of the S1 cleavage site indicates for the formation of the non-B-DNA structure within the Pu/Py tract. This is to our knowledge a first report on the existence of a complex microsatellite region on upstream the 5'-end of the hsp 70 gene in mammals.

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