Thermodynamic and structural properties of the specific binding between Ag+ ion and C:C mismatched base pair in duplex DNA to form C–Ag–C metal-mediated base pair

Biochimie ◽  
2012 ◽  
Vol 94 (11) ◽  
pp. 2431-2440 ◽  
Author(s):  
Hidetaka Torigoe ◽  
Itaru Okamoto ◽  
Takenori Dairaku ◽  
Yoshiyuki Tanaka ◽  
Akira Ono ◽  
...  
Keyword(s):  
Structural Properties ◽  
Base Pair ◽  
Specific Binding ◽  
Duplex Dna ◽  
Mismatched Base Pair

HgIIIon Specifically Binds with T:T Mismatched Base Pair in Duplex DNA

2010 ◽  
Vol 16 (44) ◽  
pp. 13218-13225 ◽  
Author(s):  
Hidetaka Torigoe ◽  
Akira Ono ◽  
Tetsuo Kozasa
Keyword(s):  
Base Pair ◽  
Duplex Dna ◽  
Mismatched Base Pair

scholarly journals Detection of the C-C mismatched base pair by small ligands

2003 ◽  
Vol 3 (1) ◽  
pp. 131-132 ◽  
Author(s):  
A. Kobori ◽  
H. Suda ◽  
K. Nakatani ◽  
I. Saito
Keyword(s):  
Base Pair ◽  
Mismatched Base Pair ◽  
Small Ligands

scholarly journals Supercoiling DNA locates mismatches

2017 ◽  
Author(s):  
Andrew Dittmore ◽  
Sumitabha Brahmachari ◽  
Yasuhara Takagi ◽  
John F. Marko ◽  
Keir C. Neuman
Keyword(s):  
Dna Sequence ◽  
Base Pair ◽  
Dna Supercoiling ◽  
Magnetic Tweezers ◽  
Relative Probability ◽  
Base Pairs ◽  
Damage Sensing ◽  
Mismatched Base Pair ◽  
Monovalent Salt

We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.5 pN force and show that, under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under physiologically relevant conditions. Based on this estimate, we propose that DNA supercoiling could contribute to mismatch and damage sensing in vivo.

Transposable element-mediated enhancement of gene expression in Saccharomyces cerevisiae involves sequence-specific binding of a trans-acting factor

1988 ◽  
Vol 8 (6) ◽  
pp. 2572-2580
Author(s):  
A Goel ◽  
R E Pearlman
Keyword(s):  
Gene Expression ◽  
Base Pair ◽  
Specific Binding ◽  
Adjacent Gene ◽  
Cis Acting ◽  
Contact Sites ◽  
Cell Extracts ◽  
Single Base Pair ◽  
Beta Galactosidase

In our studies on the regulation of adjacent-gene expression by Ty sequences, we demonstrated that a single-base-pair change (T-A----C-G) in the epsilon sequence of Ty917-derived elements is primarily responsible for enhancement of beta-galactosidase expression from lacZ fusion plasmids. Using an electrophoretic gel mobility assay, we showed that the same base pair transition is required for binding of a trans-acting factor, TyBF, from crude cell extracts in vitro. We identified the site of TyBF binding and determined the guanine nucleotide contact sites required for TyBF interaction. We propose that TyBF binding to cis-acting Ty2 sequences activates adjacent-gene transcription.

scholarly journals Isosteric and fluorescent DNA base pair formed by 4-amino-phthalimide and 2,4-diaminopyrimidine: melting, structure, and THz polar solvation dynamics

2016 ◽  
Vol 18 (9) ◽  
pp. 6813-6820 ◽  
Author(s):  
L. Dehmel ◽  
F. Berndt ◽  
M. Weinberger ◽  
M. Sajadi ◽  
I. Ioffe ◽  
...  
Keyword(s):  
Base Pair ◽  
Solvation Dynamics ◽  
Duplex Dna ◽  
Dna Base ◽  
Dna Base Pair ◽  
Polar Solvation

An artificial base pair in duplex DNA, formed by 2,4-diaminopyrimidine and fluorescent 4-aminophthalimide C-nucleosides, is characterized spectroscopically, for use in femtosecond solvation dynamics.

scholarly journals Nucleosomes around a mismatched base pair are excluded via an Msh2-dependent reaction with the aid of SNF2 family ATPase Smarcad1

2018 ◽  
Vol 32 (11-12) ◽  
pp. 806-821 ◽  
Author(s):  
Riki Terui ◽  
Koji Nagao ◽  
Yoshitaka Kawasoe ◽  
Kanae Taki ◽  
Torahiko L. Higashi ◽  
...  
Keyword(s):  
Base Pair ◽  
Mismatched Base Pair

Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA

2012 ◽  
Vol 532 ◽  
pp. 28-35 ◽  
Author(s):  
Hidetaka Torigoe ◽  
Yukako Miyakawa ◽  
Akira Ono ◽  
Tetsuo Kozasa
Keyword(s):  
Specific Binding ◽  
Duplex Dna ◽  
Base Pairs ◽  
Positive Cooperativity
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