Evidence map›Paper›PMID 26348651›Full record

ArticleArchives of biochemistry and biophysics2015

Characterization of the structural and protein recognition properties of hybrid PNA-DNA four-way junctions.

Douglas Iverson, Crystal Serrano, Ann Marie Brahan, Arik Shams, Filbert Totsingan, Anthony J Bell

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Archives of biochemistry and biophysics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Douglas IversonDepartment of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA.
Crystal SerranoDepartment of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA.
Ann Marie BrahanDepartment of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA.
Arik ShamsDepartment of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA.
Filbert TotsinganDepartment of Chemistry, New York University, New York, NY, USA.
Anthony J BellDepartment of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA. Electronic address: Anthony.Bell@usm.edu.

Funding

Training and Mentoring Core P20GM103476 · NIGMS · UNIVERSITY OF SOUTHERN MISSISSIPPI · PI MICHAEL R GARRETT · 2012 to 2026
$60.2M
NIGMS NIH HHS P20 GM103476NIGMS NIH HHS P20GM103476
6 · The paper itself

Abstract

The objective of this study is to evaluate the structure and protein recognition properties of hybrid four-way junctions (4WJs) composed of DNA and peptide nucleic acid (PNA) strands. We compare a classic immobile DNA junction, J1, vs. six PNA-DNA junctions, including a number with blunt DNA ends and multiple PNA strands. Circular dichroism (CD) analysis reveals that hybrid 4WJs are composed of helices that possess structures intermediate between A- and B-form DNA, the apparent level of A-form structure correlates with the PNA content. The structure of hybrids that contain one PNA strand is sensitive to Mg(+2). For these constructs, the apparent B-form structure and conformational stability (Tm) increase in high Mg(+2). The blunt-ended junction, b4WJ-PNA3, possesses the highest B-form CD signals and Tm (40.1 °C) values vs. all hybrids and J1. Protein recognition studies are carried out using the recombinant DNA-binding protein, HMGB1b. HMGB1b binds the blunt ended single-PNA hybrids, b4WJ-PNA1 and b4WJ-PNA3, with high affinity. HMGB1b binds the multi-PNA hybrids, 4WJ-PNA1,3 and b4WJ-PNA1,3, but does not form stable protein-nucleic acid complexes. Protein interactions with hybrid 4WJs are influenced by the ratio of A- to B-form helices: hybrids with helices composed of higher levels of B-form structure preferentially associate with HMGB1b.

Indexed as

AnimalsBase SequenceDNA, A-FormDNA, B-FormHMGB1 ProteinMagnesiumModels, MolecularMolecular Sequence DataNucleic Acid ConformationPeptide Nucleic AcidsProtein BindingRatsDNA, A-FormDNA, B-FormHMGB1 ProteinMagnesiumPeptide Nucleic AcidsA-DNA helicesB-DNA helicesFour-way junctionsHigh mobility group proteins (HMG)Peptide nucleic acids (PNAs)

Identifiers

PMID26348651
PMCPMC4852880

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