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.

Electron microscopic assays of restriction endonuclease cutting, exonuclease digestion, and hybridization

1984 ◽  
Vol 42 ◽  
pp. 686-687
Author(s):  
Mark Hannibal ◽  
Jacob Varkey ◽  
Michael Beer
Keyword(s):  
Electron Microscope ◽  
Low Temperature ◽  
Restriction Endonuclease ◽  
Double Helix ◽  
Test Material ◽  
Electron Microscopic ◽  
Exonuclease Iii ◽  
Dna Molecule ◽  
Linear Molecules ◽  
Exonuclease Digestion

Workman and Langmore have recently proposed a procedure for isolating particular chromatin fragments. The method requires restriction endonuclease cutting of the chromatin and a probe, their digestion with two exonucleases which leave complimentary single strand termini and low temperature hybridization of these. We here report simple electron microscopic monitoring of the four reactions involved.Our test material was ϕX-174 RF DNA which is cut once by restriction endonuclease Xho I. The conversion of circles to linear molecules was followed in Kleinschmidt spreads. Plate I shows a circular and a linear DNA molecule. The rate of cutting is shown in Figure 1.After completion of the endonuclease cutting, one portion of the DNA was treated with exonuclease III, an enzyme known to digest the 3' terminals of double helical DNA. Aliquots when examined in the electron microscope reveal a decreasing length of double helix and increasing bushes at the ends.

scholarly journals Replication forms of the gene-sized DNA molecules of hypotrichous ciliates.

1983 ◽  
Vol 3 (9) ◽  
pp. 1562-1566 ◽  
Author(s):  
K G Murti ◽  
D M Prescott
Keyword(s):  
Electron Microscopy ◽  
S Phase ◽  
Origin Of Replication ◽  
Dna Molecules ◽  
Linear Dna ◽  
Dna Molecule ◽  
Independent Unit

Using a method for obtaining DNA from 10 to 40 macronuclei for electron microscopy, we analyzed the structure of gene-sized, linear DNA molecules from S-phase macronuclei of two hypotrichous ciliates, Euplotes eurystomus and Styx sp. Three types of putative replicating intermediates were observed: (i) molecules with a bubble close to one end, (ii) molecules with single forks, and (iii) molecules with two forks. We conclude that: (i) each macronuclear DNA molecule replicates as an independent unit, (ii) the molecules contain an origin of replication close to one or both ends, and (iii) the mode of replication is bidirectional.

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 Ensemble of DNA Kinks

2019 ◽  
Vol 224 ◽  
pp. 03005 ◽  
Author(s):  
Ludmila V. Yakushevich ◽  
Larisa A. Krasnobaeva
Keyword(s):  
Hydrogen Bonds ◽  
Dynamic Characteristics ◽  
Dynamic Properties ◽  
Double Helix ◽  
Statistical Properties ◽  
Dna Molecule ◽  
Open States

The DNA open states, which are locally unwound regions of the double helix within which hydrogen bonds between complementary nitrous bases are broken, are often modeled as quasiparticles – DNA kinks. Most of the works on the DNA kinks are devoted to the studies of their dynamic properties, as well as their role in the functioning of the molecule. However, if not one but N open states are formed in the DNA molecule it is reasonable to consider the problem of the statistics of the ensemble of N DNA kinks. The statistical properties of such an ensemble are still poorly understood. In the present work, we study these properties applying new data on the dynamic characteristics of DNA kinks.

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.

Effects of dynamic disorder on the charge transport via DNA molecules

2005 ◽  
Vol 7 (7) ◽  
pp. 1514 ◽  
Author(s):  
J. Matulewski ◽  
S. D. Baranovskii ◽  
P. Thomas
Keyword(s):  
Charge Transport ◽  
Dna Molecules ◽  
Dynamic Disorder

DNA Base Identification by Electron Microscopy

2012 ◽  
Vol 18 (5) ◽  
pp. 1049-1053 ◽  
Author(s):  
David C. Bell ◽  
W. Kelley Thomas ◽  
Katelyn M. Murtagh ◽  
Cheryl A. Dionne ◽  
Adam C. Graham ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Base Pair ◽  
Heavy Atom ◽  
Genomic Research ◽  
Biological Research ◽  
Template Molecule ◽  
Dna Molecules ◽  
Base Pairs ◽  
Dna Molecule ◽  
Dna Base

AbstractAdvances in DNA sequencing, based on fluorescent microscopy, have transformed many areas of biological research. However, only relatively short molecules can be sequenced by these technologies. Dramatic improvements in genomic research will require accurate sequencing of long (>10,000 base-pairs), intact DNA molecules. Our approach directly visualizes the sequence of DNA molecules using electron microscopy. This report represents the first identification of DNA base pairs within intact DNA molecules by electron microscopy. By enzymatically incorporating modified bases, which contain atoms of increased atomic number, direct visualization and identification of individually labeled bases within a synthetic 3,272 base-pair DNA molecule and a 7,249 base-pair viral genome have been accomplished. This proof of principle is made possible by the use of a dUTP nucleotide, substituted with a single mercury atom attached to the nitrogenous base. One of these contrast-enhanced, heavy-atom-labeled bases is paired with each adenosine base in the template molecule and then built into a double-stranded DNA molecule by a template-directed DNA polymerase enzyme. This modification is small enough to allow very long molecules with labels at each A-U position. Image contrast is further enhanced by using annular dark-field scanning transmission electron microscopy (ADF-STEM). Further refinements to identify additional base types and more precisely determine the location of identified bases would allow full sequencing of long, intact DNA molecules, significantly improving the pace of complex genomic discoveries.

Sign in / Sign up

Export Citation Format

Share Document