scholarly journals DNA unwinding upon strand-displacement binding of a thymine-substituted polyamide to double-stranded DNA.

1993 ◽  
Vol 90 (5) ◽  
pp. 1667-1670 ◽  
Author(s):  
D. Y. Cherny ◽  
B. P. Belotserkovskii ◽  
M. D. Frank-Kamenetskii ◽  
M. Egholm ◽  
O. Buchardt ◽  
...  
Keyword(s):  
Dna Unwinding ◽  
Strand Displacement ◽  
Double Stranded Dna

Specific defects in double-stranded DNA unwinding and homologous pairing of a mutant RecA protein

FEBS Letters ◽  
2000 ◽  
Vol 477 (1-2) ◽  
pp. 129-134 ◽  
Author(s):  
Hitoshi Kurumizaka ◽  
Hideki Aihara ◽  
Shukuko Ikawa ◽  
Takehiko Shibata
Keyword(s):  
Reca Protein ◽  
Dna Unwinding ◽  
Homologous Pairing ◽  
Double Stranded Dna

scholarly journals Single-molecule visualization of RecQ helicase reveals DNA melting, nucleation, and assembly are required for processive DNA unwinding

2015 ◽  
Vol 112 (50) ◽  
pp. E6852-E6861 ◽  
Author(s):  
Behzad Rad ◽  
Anthony L. Forget ◽  
Ronald J. Baskin ◽  
Stephen C. Kowalczykowski
Keyword(s):  
Single Molecule ◽  
Fluorescent Sensor ◽  
Holliday Junctions ◽  
Dna Unwinding ◽  
Recq Helicase ◽  
Dna Breaks ◽  
Dna Helicases ◽  
Double Stranded Dna ◽  
Functional Forms ◽  
And Migration

DNA helicases are motor proteins that unwind double-stranded DNA (dsDNA) to reveal single-stranded DNA (ssDNA) needed for many biological processes. The RecQ helicase is involved in repairing damage caused by DNA breaks and stalled replication forks via homologous recombination. Here, the helicase activity of RecQ was visualized on single molecules of DNA using a fluorescent sensor that directly detects ssDNA. By monitoring the formation and progression of individual unwinding forks, we observed that both the frequency of initiation and the rate of unwinding are highly dependent on RecQ concentration. We establish that unwinding forks can initiate internally by melting dsDNA and can proceed in both directions at up to 40–60 bp/s. The findings suggest that initiation requires a RecQ dimer, and that continued processive unwinding of several kilobases involves multiple monomers at the DNA unwinding fork. We propose a distinctive model wherein RecQ melts dsDNA internally to initiate unwinding and subsequently assembles at the fork into a distribution of multimeric species, each encompassing a broad distribution of rates, to unwind DNA. These studies define the species that promote resection of DNA, proofreading of homologous pairing, and migration of Holliday junctions, and they suggest that various functional forms of RecQ can be assembled that unwind at rates tailored to the diverse biological functions of RecQ helicase.

scholarly journals Reversible Control of Gelatin Hydrogel Stiffness Using DNA Crosslinkers

2020 ◽  
Author(s):  
Alex Buchberger ◽  
Harpinder Saini ◽  
Kiarash Rahmani Eliato ◽  
Ryan Merkley ◽  
Yang Xu ◽  
...  
Keyword(s):  
Elastic Modulus ◽  
Regenerative Medicine ◽  
Crosslink Density ◽  
Strand Displacement ◽  
Encapsulated Cells ◽  
Gelatin Hydrogel ◽  
Double Stranded Dna ◽  
Spatiotemporal Behavior ◽  
Basic Biology ◽  
Dna Strand

Biomaterials with dynamically tunable properties are critical for a range of applications in regenerative medicine and basic biology. In this work, we show the reversible control of gelatin methacrylate (GelMA) hydrogel stiffness through the use of DNA crosslinkers. We replaced some of the inter-GelMA crosslinks with double-stranded DNA, allowing for their removal via toehold-mediated strand displacement. The crosslinks could be restored by adding fresh dsDNA with complementary handles to the hydrogel. The elastic modulus (G’) of the hydrogels could be tuned between 500 and 1000 Pa, reversibly, over two cycles without degradation of performance. By functionalizing the gels with a second DNA strand, it was possible to control the crosslink density and a model ligand in an orthogonal fashion with two different displacement strands. Our results demonstrate the potential for DNA to reversibly control both stiffness and ligand presentation in a protein-based hydrogel, and will be useful for teasing apart the spatiotemporal behavior of encapsulated cells.

scholarly journals Mechanism of RPA-Facilitated Processive DNA Unwinding by the Eukaryotic CMG Helicase

2019 ◽  
Author(s):  
Hazal B. Kose ◽  
Sherry Xie ◽  
George Cameron ◽  
Melania S. Strycharska ◽  
Hasan Yardimci
Keyword(s):  
Single Molecule ◽  
Replication Fork ◽  
Double Helix ◽  
Dna Unwinding ◽  
Helicase Activity ◽  
Replicative Helicase ◽  
Double Stranded Dna ◽  
Order Of Magnitude ◽  
Dna Strand ◽  
Dna Double Helix

AbstractThe DNA double helix is unwound by the Cdc45/Mcm2-7/GINS (CMG) complex at the eukaryotic replication fork. While isolated CMG unwinds duplex DNA very slowly, its fork unwinding rate is stimulated by an order of magnitude by single-stranded DNA binding protein, RPA. However, the molecular mechanism by which RPA enhances CMG helicase activity remained elusive. Here, we demonstrate that engagement of CMG with parental double-stranded DNA (dsDNA) at the replication fork impairs its helicase activity, explaining the slow DNA unwinding by isolated CMG. Using single-molecule and ensemble biochemistry, we show that binding of RPA to the excluded DNA strand prevents duplex engagement by the helicase and speeds up CMG-mediated DNA unwinding. When stalled due to dsDNA interaction, DNA rezipping-induced helicase backtracking re-establishes productive helicase-fork engagement underscoring the significance of plasticity in helicase action. Together, our results elucidate the dynamics of CMG at the replication fork and reveal how other replisome components can mediate proper DNA engagement by the replicative helicase to achieve efficient fork progression.

scholarly journals Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Dmitriy A. Khodakov ◽  
Anastasia S. Khodakova ◽  
David M. Huang ◽  
Adrian Linacre ◽  
Amanda V. Ellis
Keyword(s):  
Strand Displacement ◽  
Single Nucleotide ◽  
Double Stranded Dna ◽  
Dna Strand Displacement ◽  
Dna Strand

scholarly journals Synthesis, Crystal Structure and Interaction With DNA of N,N′-(Butane-1,4-Diyl)Bis(Guanidinium) Tetrachloroplatinate (II)

1998 ◽  
Vol 5 (5) ◽  
pp. 279-285 ◽  
Author(s):  
Christian Bailly ◽  
Bernard Viossat ◽  
Xavier Labouze ◽  
Georges Morgant ◽  
Carmella Saturnino ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermal Denaturation ◽  
Dna Unwinding ◽  
Crystal Data ◽  
Gauche Conformation ◽  
Design Synthesis ◽  
Space Group ◽  
Imine Group ◽  
Double Stranded Dna ◽  
Linker Chain

The design, synthesis, crystal structure and interaction with DNA of the N,N′-(butane-1,4-diyl)bis(guanidinium) tetrachloroplatinate(ll) are described. Crystal data: a = 8.152(1), b = 8.889(4), c = 10.700(3) Å , α = 81.59(3), β = 87.99(5), γ = 78.48(6)°, V = 752(1) Å3, Z = 2 , space group P-1. The structure was refined to R = 0.039 and Rw = 0.046 from 1853 reflections (I > 3σ(I)). This compound, named PtC4Gua, does not exhibit a center of symmetry and the center linker chain C(2) - C(3) - C(4) - C(5) is in gauche conformation. The cation is bisprotonated with the H+ attached to the imine group of each terminal guanidinium function. The presence of the platinum moiety reinforces the binding of the butane(bis)guanidinium structure with double stranded DNA as judged from thermal denaturation studies and DNA unwinding experiments.

scholarly journals Functional aspects of the nuclear matrix.

1995 ◽  
Vol 42 (2) ◽  
pp. 127-131 ◽  
Author(s):  
F Wanka
Keyword(s):  
Dna Sequences ◽  
Nuclear Matrix ◽  
Specific Protein ◽  
Dna Unwinding ◽  
Replication Origins ◽  
Repeated Dna ◽  
Chromosomal Dna ◽  
Double Stranded Dna ◽  
Functional Aspects ◽  
The Matrix

A model is proposed of the way in which the unwinding of the chromosomal DNA loops is controlled during DNA replication. It is based on the observation of a permanent binding of replication origins to the nuclear matrix and of a transient attachment of replicating DNA regions to sites in the immediate neighbourhood. DNA unwinding is controlled while the replicating loops are reeled through the replication binding sites. Also a mechanism is proposed to explain how the once-per-cycle replication of individual replicons can be controlled. DNA synthesis is initiated at single-stranded loops exposed by tandemly repeated DNA sequences at the replication origins. The single-stranded loops turn into fully double-stranded DNA during replication, becoming inaccessible for a second initiation during the same cell cycle. The configuration competent for initiation is restored by specific protein-DNA rearrangements coupled to mitotic condensation of the matrix into chromosomal scaffolds and its reversal.

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