Evidence map›Paper›PMID 38584614›Full record

ArticleArXiv2024

Spectroscopic approaches for studies of site-specific DNA base and backbone 'breathing' using exciton-coupled dimer-labeled DNA.

Andrew H Marcus, Spiridoula Matsika, Dylan Heussman, Mohammed I Sorour, Jack Maurer, Claire S Albrecht, Lulu Enkhbaatar, Patrick Herbert, Kurt A Kistler, Peter H von Hippel

Open access · greenAbstract readPreprint
PubMed Full text at PMC
In one paragraph

Article in ArXiv, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
1.5field-weighted citation impact, top 25% of its field
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

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

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

0 citing papers in PubMed, 1 citations in OpenAlex.

No citing paper in PubMed yet.

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

10 authors at 4 institutions in 1 country.

Andrew H MarcusCenter for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403.
Spiridoula MatsikaDepartment of Chemistry, Temple University, Philadelphia, Pennsylvania 19122.
Dylan HeussmanCenter for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403.
Mohammed I SorourDepartment of Chemistry, Temple University, Philadelphia, Pennsylvania 19122.
Jack MaurerCenter for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403.
Claire S AlbrechtCenter for Optical, Molecular and Quantum Science, Department of Physics, University of Oregon, Eugene, Oregon 97403.
Lulu EnkhbaatarCenter for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403.
Patrick HerbertCenter for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403.
Kurt A KistlerDepartment of Chemistry, Brandywine Campus, The Pennsylvania State University, Media, Pennsylvania 19063.
Peter H von HippelInstitute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403.
University of Oregon · USTemple University · USOregon Research Institute · USPennsylvania State University · US

Funding

STRUCTURE AND RELATIONS OF PROTEINS AND NUCLEIC ACIDSR01GM015792 · NIGMS · UNIVERSITY OF OREGON · PI MARCUS, ANDREW HADLEY · 1985 to 2025
$10.2M
NIGMS NIH HHS R01 GM015792
6 · The paper itself

Abstract

DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.

Indexed as

DNA ‘breathing’exciton-coupled dimer probeexciton-coupled probe spectroscopyfluorescent base analogueFourier transform spectroscopyfree energy surfacepolarization-sweep single-molecule fluorescence (PS-SMF) microscopyprotein-DNA interactionstwo-dimensional coherent spectroscopytwo-dimensional fluorescence spectroscopy (2DFS)two-photon excitation

Identifiers

PMID38584614
PMCPMC10996769
OpenAlexW4393213137

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.