Evidence map›Paper›PMID 27926785›Full record

ArticleFEBS letters2017

Identification of proximal sites for unwound DNA substrate in Escherichia coli topoisomerase I with oxidative crosslinking.

Bokun Cheng, Qingxuan Zhou, Liwei Weng, John D Leszyk, Marc M Greenberg, Yuk-Ching Tse-Dinh

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

Article in FEBS letters, 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, top 90% 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

6 authors at 4 institutions in 1 country.

Bokun ChengDepartment of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, USA.
Qingxuan ZhouDepartment of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.
Liwei WengDepartment of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
John D LeszykDepartment of Biochemistry and Molecular Pharmacology and Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, MA, USA.
Marc M GreenbergDepartment of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
Yuk-Ching Tse-DinhDepartment of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.
Florida International University · USJohns Hopkins University · USNew York Medical College · USUniversity of Massachusetts Chan Medical School · US

Funding

Mechanistic Studies of Nucleic Acid Damage and Their Applications.R01GM054996 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI GREENBERG, MARC M · 1997 to 2019
$5.4M
Supplement for undergraduate research participant to promote diversityR01GM054226 · NIGMS · NEW YORK MEDICAL COLLEGE · PI TSE-DINH, YUK-CHING · 1996 to 2020
$4.6M
NIGMS NIH HHS R01 GM054226NIGMS NIH HHS R01 GM054996
6 · The paper itself

Abstract

Topoisomerases catalyze changes in DNA topology by directing the movement of DNA strands through consecutive cleavage-rejoining reactions of the DNA backbone. We describe the use of a phenylselenyl-modified thymidine incorporated into a specific position of a partially unwound DNA substrate in crosslinking studies of Escherichia coli topoisomerase I to gain new insights into its catalytic mechanism. Crosslinking of the phenylselenyl-modified thymidine to the topoisomerase protein was achieved by the addition of a mild oxidant. Following nuclease and trypsin digestion, lysine residues on topoisomerase I crosslinked to the modified thymidine were identified by mass spectrometry. The crosslinked sites may correspond to proximal sites for the unwound DNA strand as it interacts with enzyme in the different stages of the catalytic cycle.

Indexed as

Amino Acid SequenceBase SequenceCross-Linking ReagentsDNA, BacterialDNA, SuperhelicalDNA Topoisomerases, Type IEscherichia coliLysineMicrococcal NucleaseOligonucleotidesOxidation-ReductionPeptidesSubstrate SpecificityCross-Linking ReagentsDNA, BacterialDNA, SuperhelicalDNA Topoisomerases, Type ILysineMicrococcal NucleaseOligonucleotidesPeptidescrosslinkingDNA-protein interactionstopoisomerase

Identifiers

PMID27926785
PMCPMC5235945
OpenAlexW2560709084

What OpenQuestion holds

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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.