scholarly journals Insights Into Sequence Dependent Effects on DNA Elasticity Using Single Molecule Techniques

2011 ◽  
Vol 100 (3) ◽  
pp. 75a
Author(s):  
Krishnan Raghunathan ◽  
Yih-Fan Chen ◽  
Joshua Milstein ◽  
Benjamin Juliar ◽  
Justin Blaty ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Elasticity ◽  
Sequence Dependent

Theory of sequence-dependent DNA elasticity

2003 ◽  
Vol 118 (15) ◽  
pp. 7127-7140 ◽  
Author(s):  
Bernard D. Coleman ◽  
Wilma K. Olson ◽  
David Swigon
Keyword(s):  
Dna Elasticity ◽  
Sequence Dependent

scholarly journals A Single-Molecule Technique to Study Sequence-Dependent Transcription Pausing

2004 ◽  
Vol 87 (6) ◽  
pp. 3945-3953 ◽  
Author(s):  
Alla Shundrovsky ◽  
Thomas J. Santangelo ◽  
Jeffrey W. Roberts ◽  
Michelle D. Wang
Keyword(s):  
Single Molecule ◽  
Sequence Dependent

Using DNA looping to measure sequence dependent DNA elasticity

2012 ◽  
Author(s):  
Alan Kandinov ◽  
Krishnan Raghunathan ◽  
Jens-Christian Meiners
Keyword(s):  
Dna Looping ◽  
Dna Elasticity ◽  
Sequence Dependent

scholarly journals Study Of Sequence Dependent Homolog Pairing With A Single Molecule Assay

2009 ◽  
Vol 96 (3) ◽  
pp. 345a-346a
Author(s):  
Claudia Danilowicz ◽  
Chiu H. Lee ◽  
Kristi Hatch ◽  
Vincent W. Coljee ◽  
Nancy Kleckner ◽  
...  
Keyword(s):  
Single Molecule ◽  
Homolog Pairing ◽  
Sequence Dependent

scholarly journals Homology sensing via non-linear amplification of sequence-dependent pausing by RecQ helicase

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Yeonee Seol ◽  
Gábor M Harami ◽  
Mihály Kovács ◽  
Keir C Neuman
Keyword(s):  
Single Molecule ◽  
Magnetic Tweezers ◽  
Dependent Manner ◽  
Linear Amplification ◽  
Recq Helicases ◽  
The Core ◽  
Sequence Dependent ◽  
Non Linear ◽  
Dna Strand ◽  
The Stability

RecQ helicases promote genomic stability through their unique ability to suppress illegitimate recombination and resolve recombination intermediates. These DNA structure-specific activities of RecQ helicases are mediated by the helicase-and-RNAseD like C-terminal (HRDC) domain, via unknown mechanisms. Here, employing single-molecule magnetic tweezers and rapid kinetic approaches we establish that the HRDC domain stabilizes intrinsic, sequence-dependent, pauses of the core helicase (lacking the HRDC) in a DNA geometry-dependent manner. We elucidate the core unwinding mechanism in which the unwinding rate depends on the stability of the duplex DNA leading to transient sequence-dependent pauses. We further demonstrate a non-linear amplification of these transient pauses by the controlled binding of the HRDC domain. The resulting DNA sequence- and geometry-dependent pausing may underlie a homology sensing mechanism that allows rapid disruption of unstable (illegitimate) and stabilization of stable (legitimate) DNA strand invasions, which suggests an intrinsic mechanism of recombination quality control by RecQ helicases.

scholarly journals Sequence-Dependent Dynamics of Synthetic and Endogenous RSSs in V(D)J Recombination

2019 ◽  
Author(s):  
Soichi Hirokawa ◽  
Griffin Chure ◽  
Nathan M. Belliveau ◽  
Geoffrey A. Lovely ◽  
Michael Anaya ◽  
...  
Keyword(s):  
Single Molecule ◽  
Large Scale ◽  
Antigen Receptor ◽  
Quantitative Information ◽  
Dna Dynamics ◽  
Endogenous Gene ◽  
Quantitative Studies ◽  
Recombination Signal Sequences ◽  
Sequence Dependent ◽  
Dna Nicking

Developing lymphocytes in the immune system of jawed vertebrates assemble antigen-receptor genes by undergoing large-scale reorganization of spatially separated V, D, and J gene segments through a process known as V(D)J recombination. The RAG protein initiates this process by binding and cutting recombination signal sequences (RSSs) composed of conserved heptamer and nonamer sequences flanking less well-conserved 12- or 23-bp spacers. Little quantitative information is known about the contributions of individual RSS positions over the course of the RAG-RSS interaction. We employ a single-molecule method known as tethered particle motion to quantify the formation, stability, and cleavage of the RAG-12RSS-23RSS paired complex (PC) for numerous synthetic and endogenous 12RSSs. We thoroughly investigate the sequence space around a RSS by making 40 different single-bp changes and characterizing the reaction dynamics. We reveal that single-bp changes affect RAG function based on their position: loss of cleavage function (first three positions of the heptamer); reduced propensity for forming the PC (the nonamer and last four bp of the heptamer); or variable effects on PC formation (spacer). We find that the rare usage of some endogenous gene segments can be mapped directly to their adjacent 12RSSs to which RAG binds weakly. The 12RSS, however, cannot explain the high-frequency usage of other gene segments. Finally, we find that RSS nicking, while not required for PC formation, substantially stabilizes the PC. Our findings provide detailed insights into the contribution of individual RSS positions to steps of the RAG-RSS re-action that previously have been difficult to assess quantitatively.SummaryV(D)J recombination is a genomic cut-and-paste process for generating diverse antigen-receptor repertoires. The RAG enzyme brings separate gene segments together by binding the neighboring sequences called RSSs, forming a paired complex (PC) before cutting the DNA. There are limited quantitative studies of the sequence-dependent dynamics of the crucial inter-mediate steps of PC formation and cleavage. Here, we quantify individual RAG-DNA dynamics for various RSSs. While RSSs of frequently-used segments do not comparatively enhance PC formation or cleavage, the rare use of some segments can be explained by their neighboring RSSs crippling PC formation and/or cleavage. Furthermore, PC lifetimes reveal DNA-nicking is not required for forming the PC, but PCs with nicks are more stable.

scholarly journals Modulation Of Sequence-dependent Pausing Of RNA Polymerase By The Accessory Factor Nusa: A Single-molecule Study

2009 ◽  
Vol 96 (3) ◽  
pp. 57a
Author(s):  
Jing Zhou ◽  
Kook Sun Ha ◽  
Arthur La Porta ◽  
Robert Landick ◽  
Steven M. Block
Keyword(s):  
Rna Polymerase ◽  
Single Molecule ◽  
Sequence Dependent ◽  
Accessory Factor

The main role of the sequence-dependent DNA elasticity in determining the free energy of nucleosome formation on telomeric DNAs

2000 ◽  
Vol 83 (3) ◽  
pp. 223-237 ◽  
Author(s):  
Ilaria Filesi ◽  
Stefano Cacchione ◽  
Pasquale De Santis ◽  
Luigi Rossetti ◽  
Maria Savino
Keyword(s):  
Free Energy ◽  
Main Role ◽  
Dna Elasticity ◽  
Sequence Dependent ◽  
Nucleosome Formation
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