Sequence-Dependent DNA Dynamics: The Regulator of DNA-Mediated Charge Transport

2006 ◽  
pp. 27-75 ◽  
Author(s):  
Melanie A. O'Neill ◽  
Jacqueline K. Barton
Keyword(s):  
Charge Transport ◽  
Dna Dynamics ◽  
Sequence Dependent

scholarly journals Sequence-Dependent DNA Dynamics by Scanning Force Microscopy Time-Resolved Imaging

2002 ◽  
Vol 9 (12) ◽  
pp. 1315-1321 ◽  
Author(s):  
Anita Scipioni ◽  
Giampaolo Zuccheri ◽  
Claudio Anselmi ◽  
Anna Bergia ◽  
Bruno Samorı̀ ◽  
...  
Keyword(s):  
Scanning Force Microscopy ◽  
Dna Dynamics ◽  
Time Resolved ◽  
Force Microscopy ◽  
Sequence Dependent ◽  
Scanning Force ◽  
Time Resolved Imaging

DNA sequence-dependent variation in nucleosome structure, stability, and dynamics detected by a FRET-based analysisThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 323-335 ◽  
Author(s):  
L. Kelbauskas ◽  
N. Woodbury ◽  
D. Lohr
Keyword(s):  
Dna Sequence ◽  
Peer Review Process ◽  
Regulatory Element ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
5S Rdna ◽  
Structure Stability ◽  
Dna Dynamics ◽  
Nucleosome Structure ◽  
Sequence Dependent

Förster resonance energy transfer (FRET) techniques provide powerful and sensitive methods for the study of conformational features in biomolecules. Here, we review FRET-based studies of nucleosomes, focusing particularly on our work comparing the widely used nucleosome standard, 5S rDNA, and 2 promoter-derived regulatory element-containing nucleosomes, mouse mammary tumor virus (MMTV)-B and GAL10. Using several FRET approaches, we detected significant DNA sequence-dependent structure, stability, and dynamics differences among the three. In particular, 5S nucleosomes and 5S H2A/H2B-depleted nucleosomal particles have enhanced stability and diminished DNA dynamics, compared with MMTV-B and GAL10 nucleosomes and particles. H2A/H2B-depleted nucleosomes are of interest because they are produced by the activities of many transcription-associated complexes. Significant location-dependent (intranucleosomal) stability and dynamics variations were also observed. These also vary among nucleosome types. Nucleosomes restrict regulatory factor access to DNA, thereby impeding genetic processes. Eukaryotic cells possess mechanisms to alter nucleosome structure, to generate DNA access, but alterations often must be targeted to specific nucleosomes on critical regulatory DNA elements. By endowing specific nucleosomes with intrinsically higher DNA accessibility and (or) enhanced facility for conformational transitions, DNA sequence-dependent nucleosome dynamics and stability variations have the potential to facilitate nucleosome recognition and, thus, aid in the crucial targeting process. This and other nucleosome structure and function conclusions from FRET analyses are discussed.

THE SEQUENCE-DEPENDENT TRANSMISSION PROPERTIES THROUGH DOUBLE HELIX DNA MOLECULES

2008 ◽  
Vol 22 (18) ◽  
pp. 1767-1776
Author(s):  
RUI-XIN DONG ◽  
XUN-LING YAN ◽  
BING YANG
Keyword(s):  
Charge Transport ◽  
Double Helix ◽  
Transmission Spectra ◽  
Dna Molecules ◽  
Transmission Characteristics ◽  
Periodic Sequences ◽  
Transmission Properties ◽  
Dna Molecule ◽  
Sequence Dependent

In this paper, a double helix model of charge transport in a DNA molecule is presented, and the transmission spectra and I–V curves of four kinds of periodic sequences DNA are obtained. The results show that the transmission characteristics of DNA are not only related to the longitudinal transport but also to the transverse transport of the molecule. The more the composition of bases, the bigger the percent of θ-direction, and the conductive ability reduces. For a different sequence with same composition, the less the number of consecutive appearance of the same base is, the lower the conductive ability.

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 The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry

2017 ◽  
Vol 8 ◽  
Author(s):  
Takeru Kameda ◽  
Shuhei Isami ◽  
Yuichi Togashi ◽  
Hiraku Nishimori ◽  
Naoaki Sakamoto ◽  
...  
Keyword(s):  
Network Model ◽  
Dna Dynamics ◽  
Elastic Network Model ◽  
Elastic Network ◽  
Sequence Dependent
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