scholarly journals Optical Microlever Assisted DNA Stretching

2021 ◽  
Author(s):  
Philippa-Kate Andrew ◽  
Ebubekir Avci ◽  
Bill Williams ◽  
Daniel Fan ◽  
Allan Raudsepp ◽  
...  
Keyword(s):  
Dna Stretching

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.

scholarly journals Theory of high-force DNA stretching and overstretching

2003 ◽  
Vol 67 (5) ◽  
Author(s):  
C. Storm ◽  
P. C. Nelson
Keyword(s):  
Dna Stretching

scholarly journals DNA Interactions Kinetics of HIV-1 Nucleocapsid Proteins by Single Molecule DNA Stretching

2012 ◽  
Vol 102 (3) ◽  
pp. 484a
Author(s):  
Jialin Li ◽  
Robert Gorelick ◽  
Ioulia Rouzina ◽  
Karin Musier-Forsyth ◽  
Mark Williams
Keyword(s):  
Single Molecule ◽  
Dna Interactions ◽  
Dna Stretching ◽  
Nucleocapsid Proteins ◽  
Kinetics Of ◽  
Hiv 1

scholarly journals Optimization of Dielectrophoretic DNA Stretching in Microfabricated Devices

2006 ◽  
Vol 78 (9) ◽  
pp. 2939-2947 ◽  
Author(s):  
Kyung Eun Sung ◽  
Mark A. Burns
Keyword(s):  
Dna Stretching ◽  
Microfabricated Devices

Simple method of DNA stretching on glass substrate for fluorescence imaging and spectroscopy

2014 ◽  
Vol 19 (5) ◽  
pp. 051210 ◽  
Author(s):  
Guru P. Neupane ◽  
Krishna P. Dhakal ◽  
Min Su Kim ◽  
Hyunsoo Lee ◽  
Martin Guthold ◽  
...  
Keyword(s):  
Fluorescence Imaging ◽  
Glass Substrate ◽  
Dna Stretching ◽  
Simple Method ◽  
Imaging And Spectroscopy

scholarly journals Sample preparation method to improve the efficiency of high-throughput single-molecule force spectroscopy

2019 ◽  
Vol 5 (4) ◽  
pp. 176-183 ◽  
Author(s):  
Lei Jin ◽  
Li Kou ◽  
Yanan Zeng ◽  
Chunguang Hu ◽  
Xiaodong Hu
Keyword(s):  
Sample Preparation ◽  
High Throughput ◽  
Single Molecule ◽  
Preparation Method ◽  
Force Spectroscopy ◽  
Experimental Result ◽  
Sample Preparation Method ◽  
Dna Stretching ◽  
Single Molecule Force Spectroscopy ◽  
Preparation Methods

Abstract Inefficient sample preparation methods hinder the performance of high-throughput single-molecule force spectroscopy (H-SMFS) for viscous damping among reactants and unstable linkage. Here, we demonstrated a sample preparation method for H-SMFS systems to achieve a higher ratio of effective target molecules per sample cell by gas-phase silanization and reactant hydrophobization. Digital holographic centrifugal force microscopy (DH-CFM) was used to verify its performance. The experimental result indicated that the DNA stretching success ratio was improved from 0.89% to 13.5%. This enhanced efficiency preparation method has potential application for force-based DNA stretching experiments and other modifying procedures.

scholarly journals Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations

Polymers ◽  
2018 ◽  
Vol 11 (1) ◽  
pp. 15 ◽  
Author(s):  
Seonghyun Lee ◽  
Yelin Lee ◽  
Yongkyun Kim ◽  
Cong Wang ◽  
Jungyul Park ◽  
...  
Keyword(s):  
Ionic Strength ◽  
Double Helix ◽  
Persistence Length ◽  
Polymer Physics ◽  
Structural Deformation ◽  
Contour Length ◽  
Dna Molecules ◽  
Dna Stretching ◽  
Single Dna Molecules ◽  
Length Changes

Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes.

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