scholarly journals Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics

2012 ◽  
Vol 116 (5) ◽  
pp. 3376-3393 ◽  
Author(s):  
Jeffrey Comer ◽  
Aleksei Aksimentiev
Keyword(s):  
Dna Sequence ◽  
Brownian Dynamics ◽  
Ion Current ◽  
Atomic Resolution ◽  
Sequence Dependence

DFT study of DNA sequence dependence at the level of dinucleoside monophosphates

2011 ◽  
Vol 975 (1-3) ◽  
pp. 69-75 ◽  
Author(s):  
V.I. Poltev ◽  
V.M. Anisimov ◽  
V.I. Danilov ◽  
D. Garcia ◽  
A. Deriabina ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dft Study ◽  
Sequence Dependence ◽  
Dinucleoside Monophosphates

scholarly journals The DNA Sequence-dependence of Nucleosome Positioningin vivoandin vitro

2010 ◽  
Vol 27 (6) ◽  
pp. 713-724 ◽  
Author(s):  
Andrew Travers ◽  
Edwige Hiriart ◽  
Mark Churcher ◽  
Micaela Caserta ◽  
Ernesto Di Mauro
Keyword(s):  
Dna Sequence ◽  
Sequence Dependence

scholarly journals Molecular Dynamics Study of MspA Arginine Mutants Predicts Slow DNA Translocations and Ion Current Blockades Indicative of DNA Sequence

ACS Nano ◽  
2012 ◽  
Vol 6 (8) ◽  
pp. 6960-6968 ◽  
Author(s):  
Swati Bhattacharya ◽  
Ian M. Derrington ◽  
Mikhail Pavlenok ◽  
Michael Niederweis ◽  
Jens H. Gundlach ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Dna Sequence ◽  
Ion Current

scholarly journals DNA sequence-dependent ionic currents in ultra-small solid-state nanopores

Nanoscale ◽  
2016 ◽  
Vol 8 (18) ◽  
pp. 9600-9613 ◽  
Author(s):  
Jeffrey Comer ◽  
Aleksei Aksimentiev
Keyword(s):  
Solid State ◽  
Dna Sequence ◽  
Ionic Current ◽  
Ionic Currents ◽  
Atomic Resolution ◽  
Sequence Dependent ◽  
Dna Strand

Atomic resolution simulations elucidate the effect of DNA sequence and conformation on the ionic current blockades produced by the presence of a DNA strand in an ultra-small solid-state nanopore.

scholarly journals DNA sequence preferences of GAL4 and PPR1: how a subset of Zn2 Cys6 binuclear cluster proteins recognizes DNA.

1996 ◽  
Vol 16 (7) ◽  
pp. 3773-3780 ◽  
Author(s):  
S D Liang ◽  
R Marmorstein ◽  
S C Harrison ◽  
M Ptashne
Keyword(s):  
Crystal Structure ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Tight Binding ◽  
Recognition Sequence ◽  
Sequence Dependence ◽  
Network Of Hydrogen Bonds ◽  
Dna Binding Assay ◽  
Related Proteins

Biophysical and genetic experiments have defined how the Saccharomyces cerevisiae protein GAL4 and a subset of related proteins recognize specific DNA sequences. We assessed DNA sequence preferences of GAL4 and a related protein, PPR1, in an in vitro DNA binding assay. For GAL4, the palindromic CGG triplets at the ends of the 17-bp recognition site are essential for tight binding, whereas the identities of the internal 11 bp are much less important, results consistent with the GAL4-DNA crystal structure. Small reductions in affinity due to mutations at the center-most 5 bp are consistent with the idea that an observed constriction in the minor groove in the crystalline GAL4-DNA complex is sequence dependent. The crystal structure suggests that this sequence dependence is due to phosphate contacts mediated by arginine 51, as part of a network of hydrogen bonds. Here we show that the mutant protein GAL4(1-100)R51A fails to discriminate sites with alterations in the center of the site from the wild-type site. PPR1, a relative of GAL4, also recognizes palindromic CGG triplets at the ends of its 12-bp recognition sequence. The identities of the internal 6 bp do not influence the binding of PPR1. We also show that the PPR1 site consists of a 12-bp duplex rather than 16 bp as reported previously: the two T residues immediately 5' to the CGG sequence in each half site, although highly conserved, are not important for binding by PPR1. Thus, GAL4 and PPR1 share common CGG half sites, but they prefer DNA sequences with the palindromic CGG separated by the appropriate number of base pairs, 11 for GAL4 and 6 for PPR1.

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