Evidence map›Paper›PMID 28062036›Full record

ArticleMethods in enzymology2017

Inserting Extrahelical Structures into Long DNA Substrates for Single-Molecule Studies of DNA Mismatch Repair.

M W Brown, A de la Torre, I J Finkelstein

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Methods in enzymology, 2017. 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
–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

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.

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

3 authors.

M W BrownInstitute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.
A de la TorreInstitute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.
I J FinkelsteinInstitute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, United States. Electronic address: ifinkelstein@cm.utexas.edu.

Funding

Mechanistic Characterization of the First Steps of Human DNA Break RepairR01GM120554 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI FINKELSTEIN, ILYA J · 2016 to 2020
$1.5M
Mechanisms of chromatin remodeling and roadblock clearance by DNA motor proteinsR00GM097177 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI FINKELSTEIN, ILYA J · 2013 to 2015
$747k
Mechanisms of chromatin remodeling and roadblock clearance by DNA motor proteinsK99GM097177 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI FINKELSTEIN, ILYA J · 2011 to 2012
$114k
NIGMS NIH HHS K99 GM097177NIGMS NIH HHS R00 GM097177NIGMS NIH HHS R01 GM120554
6 · The paper itself

Abstract

The DNA mismatch repair (MMR) system corrects errors that occur during DNA replication. MMR needs the coordinated and highly dynamic assembly of repair enzymes at the site of the lesion. By visualizing transient intermediates of these assemblies, single-molecule approaches have shed critical insights into the mechanisms of MMR. These studies frequently require long (>20kb) DNA substrates with lesions and other extrahelical structures inserted at defined positions. DNA derived from bacteriophage λ (λ-DNA) is a high quality long (48.5kb) DNA substrate that is frequently used in single-molecule studies. Here we provide detailed protocols for site-specific incorporation of recombinant sequences and extrahelical structures into λ-DNA. We also describe how to assemble DNA curtains, and how to collect and analyze single-molecule observations of lesion recognition by MMR proteins diffusing on these DNA curtains. These protocols will facilitate future single-molecule studies of DNA transcription, replication, and repair.

Indexed as

Bacteriophage lambdaDNADNA Mismatch RepairDNA ReplicationNucleic Acid ConformationProteinsSingle Molecule ImagingDNAProteinsDNA curtainsNicking enzymeRecombineeringSingle-molecule imaging

Identifiers

PMID28062036
PMCPMC6637764

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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.