scholarly journals Elementary processes of DNA surface hybridization resolved by single-molecule kinetics: implication for macroscopic device performance

2021 ◽  
Author(s):  
Takanori Harashima ◽  
Yusuke Hasegawa ◽  
Satoshi Kaneko ◽  
Yuki Jono ◽  
Shintaro Fujii ◽  
...  
Keyword(s):  
Single Molecule ◽  
Electrical Conductance ◽  
Device Performance ◽  
Elementary Processes ◽  
Dna Concentration ◽  
Dna Molecule ◽  
Hybridization Efficiency ◽  
Single Dna Molecule

Hybridization of a single DNA molecule on a surface was investigated by electrical conductance measurements. The hybridization efficiency increases with increasing the DNA concentration, in contrast to preceding studies with ensemble studies.

Genomics via Optical Mapping (I): 0-1 Laws for Mapping with Single Molecules

2013 ◽  
Author(s):  
Thomas Anantharaman ◽  
Bud (Bhubaneswar) Mishra
Keyword(s):  
Single Molecule ◽  
Optical Mapping ◽  
Single Molecules ◽  
Upper Bounds ◽  
Optical Methods ◽  
Lower And Upper Bounds ◽  
Mapping Data ◽  
Dna Molecule ◽  
Experimental Parameters ◽  
Single Dna Molecule

The genomic data that can be collected from a single DNA molecule by the best chemical and optical methods (e.g., using technologies from OpGen, BioNanoGenomics, NABSys, PacBio, etc.) are badly corrupted by many poorly understood noise processes. Thus, single molecule technology derives its utility through powerful probabilistic modeling, which can provide precise lower and upper bounds on various experimental parameters to create the correct map or validate sequence assembly. As an example, this analysis shows how as the number of "imaged" single molecules (i.e., coverage) is increased in the optical mapping data, the probability of successful computation of the map jumps from 0 to 1 for fairly small number of molecules.

scholarly journals Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis

2021 ◽  
Author(s):  
Robin Öz ◽  
Jing L Wang ◽  
Raphael Guerois ◽  
Gaurav Goyal ◽  
Sriram KK ◽  
...  
Keyword(s):  
Single Molecule ◽  
End Joining ◽  
Complementary Dna ◽  
Dna Molecule ◽  
Dna Junctions ◽  
Non Homologous End Joining ◽  
Single Dna Molecule ◽  
Dna Ends ◽  
Shed Light

Abstract We use single-molecule techniques to characterize the dynamics of prokaryotic DNA repair by non-homologous end-joining (NHEJ), a system comprised only of the dimeric Ku and Ligase D (LigD). The Ku homodimer alone forms a ∼2 s synapsis between blunt DNA ends that is increased to ∼18 s upon addition of LigD, in a manner dependent on the C-terminal arms of Ku. The synapsis lifetime increases drastically for 4 nt complementary DNA overhangs, independently of the C-terminal arms of Ku. These observations are in contrast to human Ku, which is unable to bridge either of the two DNA substrates. We also demonstrate that bacterial Ku binds the DNA ends in a cooperative manner for synapsis initiation and remains stably bound at DNA junctions for several hours after ligation is completed, indicating that a system for removal of the proteins is active in vivo. Together these experiments shed light on the dynamics of bacterial NHEJ in DNA end recognition and processing. We speculate on the evolutionary similarities between bacterial and eukaryotic NHEJ and discuss how an increased understanding of bacterial NHEJ can open the door for future antibiotic therapies targeting this mechanism.

The elastic theory of a single DNA molecule

Pramana ◽  
2003 ◽  
Vol 61 (2) ◽  
pp. 353-360
Author(s):  
Haijun Zhou ◽  
Yang Zhang ◽  
Zhang-Can Ou-Yang
Keyword(s):  
Elastic Theory ◽  
Dna Molecule ◽  
Single Dna Molecule

Label-free plasmonic assisted optical trapping of single DNA molecule

2021 ◽  
Author(s):  
Lei Chen ◽  
Wei Liu ◽  
Dongyi Shen ◽  
Zhihao Zhou ◽  
Yuehan Liu ◽  
...  
Keyword(s):  
Optical Trapping ◽  
Label Free ◽  
Dna Molecule ◽  
Single Dna Molecule

Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method

1994 ◽  
Vol 14 (2) ◽  
pp. 1520-1529
Author(s):  
C Liang ◽  
S A Gerbi
Keyword(s):  
Three Dimensional ◽  
Dna Amplification ◽  
Gel Method ◽  
Dna Molecule ◽  
Cutting Out ◽  
Origin Region ◽  
2D Gel ◽  
Third Dimension ◽  
Single Dna Molecule ◽  
Replication Intermediates

The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.

scholarly journals Determining Trap Compliances, Microsphere Size Variations, and Response Linearities in Single DNA Molecule Elasticity Measurements with Optical Tweezers

2021 ◽  
Vol 8 ◽  
Author(s):  
Youbin Mo ◽  
Mounir Fizari ◽  
Kristina Koharchik ◽  
Douglas E. Smith
Keyword(s):  
Optical Tweezers ◽  
Dna Elasticity ◽  
Dna Stretching ◽  
Dna Molecule ◽  
Scale Factors ◽  
Length Measurements ◽  
Microsphere Size ◽  
Force Range ◽  
Single Dna Molecule ◽  
Displacement Measurements

We previously introduced the use of DNA molecules for calibration of biophysical force and displacement measurements with optical tweezers. Force and length scale factors can be determined from measurements of DNA stretching. Trap compliance can be determined by fitting the data to a nonlinear DNA elasticity model, however, noise/drift/offsets in the measurement can affect the reliability of this determination. Here we demonstrate a more robust method that uses a linear approximation for DNA elasticity applied to high force range (25–45 pN) data. We show that this method can be used to assess how small variations in microsphere sizes affect DNA length measurements and demonstrate methods for correcting for these errors. We further show that these measurements can be used to check assumed linearities of system responses. Finally, we demonstrate methods combining microsphere imaging and DNA stretching to check the compliance and positioning of individual traps.

Thermophilic Topoisomerase I on a Single DNA Molecule

2003 ◽  
Vol 329 (2) ◽  
pp. 271-282 ◽  
Author(s):  
N.H Dekker ◽  
T Viard ◽  
C.Bouthier de La Tour ◽  
M Duguet ◽  
D Bensimon ◽  
...  
Keyword(s):  
Topoisomerase I ◽  
Dna Molecule ◽  
Single Dna Molecule
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