Fifty years of DNA "breathing": Reflections on old and new approaches (Q38120510)

29 August 2017

Fifty years of DNA "breathing": Reflections on old and new approaches (English)

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29 August 2017

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Peter H von Hippel

1

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PMCID

4313903

29 August 2017

Neil P Johnson

series ordinal

2

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PMCID

4313903

29 August 2017

Andrew H Marcus

series ordinal

3

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29 August 2017

1 December 2013

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29 August 2017

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29 August 2017

99

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29 August 2017

12

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29 August 2017

923-954

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Solution conformation of 2-aminopurine (2-AP) dinucleotide determined by ultraviolet 2D fluorescence spectroscopy (UV-2D FS).

29 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Single-molecule FRET and linear dichroism studies of DNA breathing and helicase binding at replication fork junctions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

A single-molecule view of the assembly pathway, subunit stoichiometry, and unwinding activity of the bacteriophage T4 primosome (helicase-primase) complex

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Temperature-dependent conformations of a membrane supported zinc porphyrin tweezer by 2D fluorescence spectroscopy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Breathing fluctuations in position-specific DNA base pairs are involved in regulating helicase movement into the replication fork

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Assembly and subunit stoichiometry of the functional helicase-primase (primosome) complex of bacteriophage T4.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Characterization of the 6-methyl isoxanthopterin (6-MI) base analog dimer, a spectroscopic probe for monitoring guanine base conformations at specific sites in nucleic acids

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Conformation of self-assembled porphyrin dimers in liposome vesicles by phase-modulation 2D fluorescence spectroscopy.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

DNA conformational changes at the primer-template junction regulate the fidelity of replication by DNA polymerase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Timing, coordination, and rhythm: acrobatics at the DNA replication fork.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Single-molecule measurements of DNA topology and topoisomerases.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Nonlinear analysis of the dynamics of DNA breathing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

DNA models of trinucleotide frameshift deletions: the formation of loops and bulges at the primer-template junction

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Fluorescence-detected two-dimensional electronic coherence spectroscopy by acousto-optic phase modulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Investigating local conformations of double-stranded DNA by low-energy circular dichroism of pyrrolo-cytosine

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Observing spontaneous branch migration of Holliday junctions one step at a time

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Degradation of ribonuclease by subtilisin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

HYDROGEN EXCHANGE STUDIES OF DNA STRUCTURE

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Structural considerations in the interaction of DNA and acridines

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Chemistry. Optical analogs of 2D NMR.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Helicase mechanisms and the coupling of helicases within macromolecular machines. Part I: Structures and properties of isolated helicases

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

A general model for nucleic acid helicases and their "coupling" within macromolecular machines

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Molecular dynamics simulation of nucleic acids

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Reconstruction of bacteriophage T4 DNA replication apparatus from purified components: rolling circle replication following de novo chain initiation on a single-stranded circular DNA template

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Formaldehyde as a probe of DNA structure. 4. Mechanism of the initial reaction of formaldehyde with DNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

DNA Modification and Cancer

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Open states in native polynucleotides. II. Hydrogen-exchange study of cytosine-containing double helices

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Open states in native polynucleotides. I. Hydrogen-exchange study of adenine-containing double helices

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Formaldehyde as a probe of DNA structure. II. Reaction with endocyclic imino groups of DNA bases

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

DNA replication by bacteriophage T4 proteins. The T4 43, 32, 44–62, And 45 proteins are required for strand displacement synthesis at nicks in duplex DNA

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

DNA replication with bacteriophage T4 proteins. Purification of the proteins encoded by T4 genes 41, 45, 44, and 62 using a complementation assay

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Conformation and electronic population transfer in membrane-supported self-assembled porphyrin dimers by 2D fluorescence spectroscopy

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Transient Hoogsteen base pairs in canonical duplex DNA.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

A HYDROGEN EXCHANGE METHOD USING TRITIUM AND SEPHADEX: ITS APPLICATION TO RIBONUCLEASE.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

T4 Bacteriophage Gene 32: A Structural Protein in the Replication and Recombination of DNA

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Formaldehyde as a probe of DNA structure. 3. Equilibrium denaturation of DNA and synthetic polynucleotides

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Bubble Dynamics in Double-Stranded DNA

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Kinetics of hydrogen exchange in deoxyribonucleic acid. ph and salt effects

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313903

Enzymatic synthesis of deoxyribonucleic acid. II. General properties of the reaction

31 August 2018

1 reference

12 December 2020

Hydrogen exchange as a probe of the dynamic structure of DNA. I. General acid-base catalysis

1 reference

12 December 2020

The phage T4-coded DNA replication helicase (gp41) forms a hexamer upon activation by nucleoside triphosphate

1 reference

12 December 2020

A denaturation map of the lambda phage DNA molecule determined by electron microscopy

1 reference

12 December 2020

The pH-dependence of the deuterium exchange of insulin

1 reference

12 December 2020

Studies of base pair kinetics by NMR measurement of proton exchange

1 reference

12 December 2020

Characterization of the bacteriophage T4 gene 41 DNA helicase

1 reference

12 December 2020

Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions

1 reference

12 December 2020

Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA

1 reference

12 December 2020

The ATP-activated hexameric helicase of bacteriophage T4 (gp41) forms a stable primosome with a single subunit of T4-coded primase (gp61)

1 reference

12 December 2020

Hydrogen exchange as a probe of the dynamic structure of DNA. II. Effects of base composition and destabilizing salts

1 reference

12 December 2020

INTERACTION OF ETHIDIUM BROMHYDRATE (BET) WITH NUCLEIC ACIDS (NA). SPECTROFLUORIMETRIC STUDY

1 reference

12 December 2020

A single mode of DNA base-pair opening drives imino proton exchange

1 reference

12 December 2020

Deuterium exchange between myoglobin and water

1 reference

12 December 2020

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

12 December 2020

Identifiers

DOI

10.1002/BIP.22347

1 reference

29 August 2017

1 reference

29 August 2017

1 reference

PMCID

4313903