Phase Transition and Phase Segregation in a Single Double-Stranded DNA Molecule

1996 ◽  
Vol 77 (10) ◽  
pp. 2133-2136 ◽  
Author(s):  
Masanori Ueda ◽  
Kenichi Yoshikawa
Keyword(s):  
Phase Transition ◽  
Phase Segregation ◽  
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.

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

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.

NMR STUDY OF THE ANTIFERROMAGNETIC TO SUPERCONDUCTOR PHASE TRANSITION IN (TMTSF)2PF6

2002 ◽  
Vol 16 (20n22) ◽  
pp. 3090-3095 ◽  
Author(s):  
W. YU ◽  
S. E. BROWN ◽  
F. ZAMBORSZKY ◽  
I. J. LEE ◽  
P. M. CHAIKIN
Keyword(s):  
Phase Transition ◽  
Tricritical Point ◽  
Density Wave ◽  
Spin Density Wave ◽  
Nmr Relaxation ◽  
Phase Segregation ◽  
Lattice Relaxation ◽  
Spin Lattice Relaxation ◽  
Hyperfine Fields ◽  
Nmr Study

The pressure-tuned quantum phase transition from spin-density wave (SDW) to Fermi Liquid (FL) ground states is studied in (TMTSF) 2 PF 6 by NMR relaxation and spectroscopy. As for recent transport measurements, we find evidence in the distribution of local hyperfine fields for phase segregation, from which we conclude the transition between normal and SDW phases is discontinuous. A tricritical point (TCP) is identified. A crossover to FL behavior identified by spin-lattice relaxation measurements intersects the normal to SDW phase boundary very close to the TCP.

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