(Q38354518)

English

Local conformations and competitive binding affinities of single- and double-stranded primer-template DNA at the polymerization and editing active sites of DNA polymerases

scientific article

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

Local conformations and competitive binding affinities of single- and double-stranded primer-template DNA at the polymerization and editing active sites of DNA polymerases (English)

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

author name string

Kausiki Datta

1

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

Neil P Johnson

2

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

Vince J LiCata

3

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

Peter H von Hippel

4

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

language of work or name

0 references

publication date

1 May 2009

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

Journal of Biological Chemistry

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

284

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

25

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

17180-17193

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

describes a project that uses

1 reference

Europe PubMed Central

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2719356/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

Spectroscopic studies of position-specific DNA "breathing" fluctuations at replication forks and primer-template junctions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Dimerization of the Klenow fragment of Escherichia coli DNA polymerase I is linked to its mode of DNA binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Low energy CD of RNA hairpin unveils a loop conformation required for lambdaN antitermination activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Sedimentation velocity analysis of heterogeneous protein-protein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Sedimentation velocity analysis of heterogeneous protein-protein interactions: sedimentation coefficient distributions c(s) and asymptotic boundary profiles from Gilbert-Jenkins theory

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

DNA polymerase fidelity: kinetics, structure, and checkpoints

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Low-energy circular dichroism of 2-aminopurine dinucleotide as a probe of local conformation of DNA and RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Participation of active-site carboxylates of Escherichia coli DNA polymerase I (Klenow fragment) in the formation of a prepolymerase ternary complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Determinants of DNA mismatch recognition within the polymerase domain of the Klenow fragment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Probing DNA polymerase fidelity mechanisms using time-resolved fluorescence anisotropy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Structure of the replicating complex of a pol alpha family DNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Exonuclease-polymerase active site partitioning of primer-template DNA strands and equilibrium Mg2+ binding properties of bacteriophage T4 DNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Structure of DNA polymerase I Klenow fragment bound to duplex DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Proofreading DNA: recognition of aberrant DNA termini by the Klenow fragment of DNA polymerase I

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Deoxynucleoside triphosphate and pyrophosphate binding sites in the catalytically competent ternary complex for the polymerase reaction catalyzed by DNA polymerase I (Klenow fragment).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Crystal structure of Thermus aquaticus DNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Isolation of an E. coli Strain with a Mutation affecting DNA Polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Cocrystal structure of an editing complex of Klenow fragment with DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Exonucleolytic proofreading

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Genetic and crystallographic studies of the 3',5'-exonucleolytic site of DNA polymerase I.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Metal binding to DNA polymerase I, its large fragment, and two 3',5'-exonuclease mutants of the large fragment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

6 September 2017

Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

23 June 2018

Purification of Escherichia coli DNA polymerase I and Klenow fragment.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

23 June 2018

Enzymatic synthesis of deoxyribonucleic acid. 36. A proofreading function for the 3' leads to 5' exonuclease activity in deoxyribonucleic acid polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

23 June 2018

Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

23 June 2018

An intramolecular FRET system monitors fingers subdomain opening in Klentaq1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

31 August 2018

Using 2-aminopurine fluorescence to detect bacteriophage T4 DNA polymerase-DNA complexes that are important for primer extension and proofreading reactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

31 August 2018

Salt dependence of DNA binding by Thermus aquaticus and Escherichia coli DNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719356

31 August 2018

Identification of a new motif required for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I (Klenow fragment): the RRRY motif is necessary for the binding of single-stranded DNA substrate and the template strand of the mismatched

1 reference

https://pubmed.ncbi.nlm.nih.gov/19411253

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Interaction of DNA polymerase I (Klenow fragment) with the single-stranded template beyond the site of synthesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/19411253

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Deoxyribonucleic acid polymerase: two distinct enzymes in one polypeptide. I. A proteolytic fragment containing the polymerase and 3' leads to 5' exonuclease functions

1 reference

https://pubmed.ncbi.nlm.nih.gov/19411253

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Effects of mutations on the partitioning of DNA substrates between the polymerase and 3'-5' exonuclease sites of DNA polymerase I (Klenow fragment)

1 reference

https://pubmed.ncbi.nlm.nih.gov/19411253

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mapping the conformation of the nucleic acid framework of the T7 RNA polymerase elongation complex in solution using low-energy CD and fluorescence spectroscopy

1 reference

https://pubmed.ncbi.nlm.nih.gov/19411253

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Probing DNA polymerase-DNA interactions: examining the template strand in exonuclease complexes using 2-aminopurine fluorescence and acrylamide quenching

1 reference

https://pubmed.ncbi.nlm.nih.gov/19411253

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1074/JBC.M109.007641

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

2 September 2017

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q38354518&oldid=1755644862"