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.

Influence of Nanochannel Inlet Structure Upon DNA Capture Ratio

2011 ◽  
Author(s):  
Jiahao Wu ◽  
Hong Wang ◽  
Jinsoo Kim ◽  
Freddy Murphy ◽  
Steven A. Soper ◽  
...  
Keyword(s):  
Real Time ◽  
Persistence Length ◽  
Contour Length ◽  
Dna Molecules ◽  
Channel Diameter ◽  
Dna Molecule ◽  
Capture Ratio ◽  
Sequence Variations ◽  
Dna Capture ◽  
Dna Chain

DNA molecule will be stretched to its near full contour length inside a nanochannel when the channel diameter is less than the DNA persistence length.1–3 It provides the possibility of real time lab-free-analysis of analysis, such as screening of sequence variations of DNA molecules.3 The key process for this nanochannel-based analysis is to drive DNA molecule electrophoretically through the nanochannel and read out the information of the DNA chain while it is passing the channel.2, 3

scholarly journals Measurement of DNA Length Changes upon CpG Hypermethylation by Microfluidic Molecular Stretching

Cell Medicine ◽  
2017 ◽  
Vol 9 (1-2) ◽  
pp. 61-66 ◽  
Author(s):  
Daisuke Onoshima ◽  
Naoko Kawakita ◽  
Daiki Takeshita ◽  
Hirohiko Niioka ◽  
Hiroshi Yukawa ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Culture Conditions ◽  
Polymer Chains ◽  
Dna Molecules ◽  
Fluidic Channel ◽  
Molecular Feature ◽  
Single Dna Molecules ◽  
Length Changes ◽  
Cpg Hypermethylation

Abnormal DNA methylation in CpG-rich promoters is recognized as a distinct molecular feature of precursor lesions to cancer. Such unintended methylation can occur during in vitro differentiation of stem cells. It takes place in a subset of genes during the differentiation or expansion of stem cell derivatives under general culture conditions, which may need to be monitored in future cell transplantation studies. Here we demonstrate a microfluidic device for investigating morphological length changes in DNA methylation. Arrayed polymer chains of single DNA molecules were fluorescently observed by parallel trapping and stretching in the micro-fluidic channel. This observational study revealed that the shortened DNA length is due to the increased rigidity of the methylated DNA molecule. The trapping rate of the device for DNA molecules was substantially unaffected by changes in the CpG methylation.

scholarly journals A simple DNA stretching method for fluorescence imaging of single DNA molecules

2006 ◽  
Vol 34 (17) ◽  
pp. e113-e113 ◽  
Author(s):  
Ting-Fung Chan ◽  
Connie Ha ◽  
Angie Phong ◽  
Dongmei Cai ◽  
Eunice Wan ◽  
...  
Keyword(s):  
Fluorescence Imaging ◽  
Dna Molecules ◽  
Dna Stretching ◽  
Single Dna Molecules

scholarly journals Scaling Concepts in Serpin Polymer Physics

Materials ◽  
2021 ◽  
Vol 14 (10) ◽  
pp. 2577
Author(s):  
Samuele Raccosta ◽  
Fabio Librizzi ◽  
Alistair M. Jagger ◽  
Rosina Noto ◽  
Vincenzo Martorana ◽  
...  
Keyword(s):  
Persistence Length ◽  
Time Lapse ◽  
Polymer Physics ◽  
Contour Length ◽  
Force Microscopy ◽  
Negative Stain ◽  
Atomic Force ◽  
Linear Chains ◽  
End Distance ◽  
Polymer Size

α1-Antitrypsin is a protease inhibitor belonging to the serpin family. Serpin polymerisation is at the core of a class of genetic conformational diseases called serpinopathies. These polymers are known to be unbranched, flexible, and heterogeneous in size with a beads-on-a-string appearance viewed by negative stain electron microscopy. Here, we use atomic force microscopy and time-lapse dynamic light scattering to measure polymer size and shape for wild-type (M) and Glu342→Lys (Z) α1-antitrypsin, the most common variant that leads to severe pathological deficiency. Our data for small polymers deposited onto mica and in solution reveal a power law relation between the polymer size, namely the end-to-end distance or the hydrodynamic radius, and the polymer mass, proportional to the contour length. We use the scaling concepts of polymer physics to assess that α1-antitrypsin polymers are random linear chains with a low persistence length.

Electrically Tethered DNA Stretching in Nanochannels

2009 ◽  
Author(s):  
Byung Chul Lee ◽  
Chanmin Kang ◽  
Jinsik Kim ◽  
Ji Yoon Kang ◽  
Hyun-Joon Shin ◽  
...  
Keyword(s):  
Fem Simulation ◽  
Transverse Plane ◽  
Contour Length ◽  
Chain Model ◽  
Dna Molecules ◽  
Elongation Ratio ◽  
Dna Stretching ◽  
Cross Sectional ◽  
Electrical Fields ◽  
Measured Relaxation

In present study, stretching dynamics of electrically tethered λ-DNA (48.5kbp) in SiO2 nanochannels has been investigated. At high electrical fields (above 20kV/m), elongations of electrically tethered DNA molecules were observed. At high E-fields, DNAs were tethered in nanochannels and were spontaneously elongated along the nanochannels up to about 90 percent of its contour length. With E-field turned off, the measured relaxation time was about 10 sec from stretching with 20kV/m. In current study, observed behaviors of DNA molecules in nanochannels were explained by field-induced dielectrophoretic DNA trap due to the particular cross-sectional geometry of nanochannels. Also the elongation ratio between 20kV/m and 60kV/m cases and the effect of E-field distribution in the transverse plane on field-induced dielectrophoretic tethering force are discussed based on “worm-like chain” model. The FEM simulation was done to verify induced dielectrophoretic tethering force into the nanohorn.

Thermoplastic Nanofluidic Devices for Identifying Abasic Sites in Single DNA Molecules

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Steven A Soper ◽  
Swarnagowri Vaidyanathan ◽  
Franklin Uba ◽  
Bo Hu ◽  
David Kaufman ◽  
...  
Keyword(s):  
Dna Damage ◽  
Therapeutic Efficacy ◽  
Double Strand Breaks ◽  
Dna Molecules ◽  
Strand Breaks ◽  
Single Dna Molecules ◽  
Abasic Sites ◽  
Nanofluidic Devices ◽  
Ap Sites

DNA damage can take many forms such as double-strand breaks and/or the formation of abasic (apurinic/apyrimidinic; AP) sites. The presence of AP sites can be used to determine therapeutic efficacy...

scholarly journals Active Delivery of Single DNA Molecules into a Plasmonic Nanopore for Label-Free Optical Sensing

Nano Letters ◽  
2018 ◽  
Vol 18 (12) ◽  
pp. 8003-8010 ◽  
Author(s):  
Xin Shi ◽  
Daniel V. Verschueren ◽  
Cees Dekker
Keyword(s):  
Optical Sensing ◽  
Label Free ◽  
Dna Molecules ◽  
Single Dna Molecules
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