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

Thermodynamic Properties of the Specific Binding Between Ag+Ions and C:C Mismatched Base Pairs in Duplex DNA

2011 ◽  
Vol 30 (2) ◽  
pp. 149-167 ◽  
Author(s):  
Hidetaka Torigoe ◽  
Yukako Miyakawa ◽  
Akira Ono ◽  
Tetsuo Kozasa
Keyword(s):  
Thermodynamic Properties ◽  
Specific Binding ◽  
Duplex Dna ◽  
Base Pairs

scholarly journals Transient Hoogsteen base pairs in canonical duplex DNA

Nature ◽  
2011 ◽  
Vol 470 (7335) ◽  
pp. 498-502 ◽  
Author(s):  
Evgenia N. Nikolova ◽  
Eunae Kim ◽  
Abigail A. Wise ◽  
Patrick J. O’Brien ◽  
Ioan Andricioaei ◽  
...  
Keyword(s):  
Duplex Dna ◽  
Base Pairs

scholarly journals A historical account of hoogsteen base-pairs in duplex DNA

Biopolymers ◽  
2013 ◽  
pp. n/a-n/a ◽  
Author(s):  
Evgenia N. Nikolova ◽  
Huiqing Zhou ◽  
Federico L. Gottardo ◽  
Heidi S. Alvey ◽  
Isaac J. Kimsey ◽  
...  
Keyword(s):  
Duplex Dna ◽  
Historical Account ◽  
Base Pairs

scholarly journals Binding of Pseudomonas aeruginosa AlgZ to Sites Upstream of the algZ Promoter Leads to Repression of Transcription

2005 ◽  
Vol 187 (13) ◽  
pp. 4430-4443 ◽  
Author(s):  
Deborah M. Ramsey ◽  
Patricia J. Baynham ◽  
Daniel J. Wozniak
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Binding Sites ◽  
Transcriptional Control ◽  
Specific Binding ◽  
Transcriptional Start Site ◽  
Opportunistic Pathogen ◽  
Single Copy ◽  
Amino Acid Identity ◽  
Mobility Shift ◽  
Base Pairs

ABSTRACT Mucoid variants of the opportunistic pathogen Pseudomonas aeruginosa produce the exopolysaccharide alginate and colonize the respiratory tracts of cystic fibrosis patients. The genes encoding the alginate biosynthetic enzymes are clustered in a single operon, which is under tight transcriptional control. One essential activator of the alginate operon is AlgZ, a proposed ribbon-helix-helix DNA binding protein that shares 30% amino acid identity with the Mnt repressor of Salmonella enterica serovar Typhimurium bacteriophage P22. In the current study, we examined the role of AlgZ as an autoregulator. Using single-copy algZ-lacZ transcription fusions, an increase in algZ transcription was observed in an algZ mutant compared to the isogenic wild-type strain, suggesting that AlgZ may have an additional role as a repressor. To identify the AlgZ binding site, overlapping regions upstream of algZ were incubated with AlgZ and analyzed by electrophoretic mobility shift assays. Specific binding activity was localized to a region spanning from 66 to 185 base pairs upstream of the algZ transcriptional start site. Two AlgZ binding sites were defined using copper-phenanthroline footprinting and deletion analyses, with one site centered at 93 base pairs and the other centered at 161 base pairs upstream of the algZ promoter. Deletion of both binding sites resulted in the loss of AlgZ binding. These results indicate that AlgZ represses algZ transcription, and this activity is mediated by multiple AlgZ-DNA interactions.

scholarly journals DNA polymerase β: effects of gapped DNA substrates on dNTP specificity, fidelity, processivity and conformational changes1

1998 ◽  
Vol 331 (1) ◽  
pp. 79-87 ◽  
Author(s):  
Jinwoo AHN ◽  
Vadim S. KRAYNOV ◽  
Xuejun ZHONG ◽  
Brian G. WERNEBURG ◽  
Ming-Daw TSAI
Keyword(s):  
Conformational Change ◽  
Dna Polymerase ◽  
Catalytic Efficiency ◽  
Duplex Dna ◽  
Gap Filling ◽  
Dna Polymerase Β ◽  
Base Pairs ◽  
Single Nucleotide ◽  
Dna Substrates ◽  
Gapped Dna

Pre-steady-state kinetic analysis was used to compare the catalytic properties of DNA polymerase β (Pol β) for single-base gap-filling and regular duplex DNA synthesis. The rate of polymerization (kpol) and the apparent equilibrium dissociation constant of dNTP (Kd) were determined with single-nucleotide gapped DNA substrates for all four possible correct base pairs and twelve possible incorrect base pairs, and the results were compared with those obtained previously with non-gapped primer/template duplex DNA substrates. For correct dNTP incorporation, the use of single-nucleotide gapped DNA led to significant decreases in the Kd of dNTP. Although kpol was little affected, the catalytic efficiency kpol/Kd increased significantly owing to the decreases in Kd. In contrast, for incorrect dNTP incorporation, the use of single-nucleotide gapped DNA substrates did not affect the Kd of dNTP appreciably but caused the kpol (and thus kpol/Kd) for incorrect dNTP incorporation to increase. As a consequence the fidelity of Pol β was not significantly affected by the use of single-nucleotide gapped DNA substrates. In addition we show that under processive polymerization conditions the processivity of Pol β increases in the gap-filling synthesis owing to a decreased rate of DNA dissociation. Finally, with a single-nucleotide gapped DNA substrate the rate-limiting conformational change step before chemistry was also observed. However, the preceding fast conformational change observed with duplex DNA substrates was not clearly detected. A possible cause is that in the complex with the gapped DNA, the 8 kDa N-terminal domain of Pol β already exists in a closed conformation. This interpretation was supported by tryptic digestion experiments.

scholarly journals Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Heidi S. Alvey ◽  
Federico L. Gottardo ◽  
Evgenia N. Nikolova ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Duplex Dna ◽  
Base Pairs

scholarly journals SEARCHING FOR TARGETS ON A MODEL DNA: EFFECTS OF INTER-SEGMENT HOPPING, DETACHMENT, AND RE-ATTACHMENT

2009 ◽  
Vol 20 (06) ◽  
pp. 817-830
Author(s):  
DEBANJAN CHOWDHURY
Keyword(s):  
Binding Site ◽  
Specific Binding ◽  
Specific Site ◽  
Search Process ◽  
Biological Processes ◽  
Base Pairs ◽  
Successful Search ◽  
Single Protein ◽  
Relevant Quantity

For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base-pairs while the DNA is usually several millions of base-pairs long. How does the protein search for the target site? What is the most efficient mechanism for a successful search? Motivated by these fundamental questions on intracellular biological processes, we have developed a model for searching a specific site on a model DNA by a single protein. We have made a comparative quantitative study on the efficiencies of sliding, inter-segmental hoppings and detachment/re-attachments of the particle during its search for the specific site on the DNA. We also introduce some new quantitative measures of efficiency of a search process by defining a relevant quantity, which can be measured in in-vitro experiments.

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