M6-4 Development of coarse graining DNA model with single nucleotide resolution and analysis of electrophoresis (M6 Bio Sensor and System)

2009 ◽  
Vol 2009.1 (0) ◽  
pp. 101-102
Author(s):  
Kentaro Doi ◽  
Yukihiro Toyokita ◽  
Satoyuki Kawano
Keyword(s):  
Coarse Graining ◽  
Single Nucleotide ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Development of coarse-graining DNA models for single-nucleotide resolution analysis

2010 ◽  
Vol 368 (1920) ◽  
pp. 2615-2628 ◽  
Author(s):  
Kentaro Doi ◽  
Tomoaki Haga ◽  
Hirofumi Shintaku ◽  
Satoyuki Kawano
Keyword(s):  
Dna Sequences ◽  
Persistence Length ◽  
Analytical Techniques ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Wide Range ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Recently, analytical techniques have been developed for detecting single-nucleotide polymorphisms in DNA sequences. Improvements of the sequence identification techniques has attracted much attention in several fields. However, there are many things that have not been clarified about DNA. In the present study, we have developed a coarse-graining DNA model with single-nucleotide resolution, in which potential functions for hydrogen bonds and the π -stack effect are taken into account. Using Langevin-dynamics simulations, several characteristics of the coarse-grained DNA have been clarified. The validity of the present model has been confirmed, compared with other experimental and computational results. In particular, the melting temperature and persistence length are in good agreement with the experimental results for a wide range of salt concentrations.

scholarly journals Chemical probing of the homopurine·homopyrimidine tract in supercoiled DNA at single-nucleotide resolution

FEBS Letters ◽  
1988 ◽  
Vol 234 (2) ◽  
pp. 295-299 ◽  
Author(s):  
M. Vojtíšková ◽  
S. Mirkin ◽  
V. Lyamichev ◽  
O. Voloshin ◽  
M. Frank-Kamenetskii ◽  
...  
Keyword(s):  
Single Nucleotide ◽  
Supercoiled Dna ◽  
Chemical Probing ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Identifying DNA mismatches at single-nucleotide resolution by probing individual surface potentials of DNA-capped nanoparticles

Nanoscale ◽  
2018 ◽  
Vol 10 (2) ◽  
pp. 538-547 ◽  
Author(s):  
Hyungbeen Lee ◽  
Sang Won Lee ◽  
Gyudo Lee ◽  
Wonseok Lee ◽  
Kihwan Nam ◽  
...  
Keyword(s):  
Kelvin Probe Force Microscopy ◽  
Powerful Method ◽  
Kelvin Probe ◽  
Single Nucleotide ◽  
Force Microscopy ◽  
Surface Potentials ◽  
Dna Mismatches ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Here, we demonstrate a powerful method to discriminate DNA mismatches at single-nucleotide resolution from 0 to 5 mismatches (χ0 to χ5) using Kelvin probe force microscopy (KPFM).

scholarly journals Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

2015 ◽  
Vol 12 (8) ◽  
pp. 767-772 ◽  
Author(s):  
Bastian Linder ◽  
Anya V Grozhik ◽  
Anthony O Olarerin-George ◽  
Cem Meydan ◽  
Christopher E Mason ◽  
...  
Keyword(s):  
Single Nucleotide ◽  
Resolution Mapping ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution
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