Evidence map›Paper›PMID 34680052›Full record

ArticleBiomolecules2021

Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA.

Liudmila A Abrosimova, Nikita A Kuznetsov, Natalia A Astafurova, Anastasiia R Samsonova, Andrey S Karpov, Tatiana A Perevyazova, Tatiana S Oretskaya, Olga S Fedorova, Elena A Kubareva

Open access · goldAbstract read
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In one paragraph

Article in Biomolecules, 2021. 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
0.1field-weighted citation impact, top 55% 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, 3 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

9 authors at 4 institutions in 2 countries.

Liudmila A AbrosimovaDepartment of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.ORCID 0000-0002-8975-8285
Nikita A KuznetsovInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia.ORCID 0000-0002-4016-198X
Natalia A AstafurovaDepartment of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.
Anastasiia R SamsonovaSAS Synhelix, Genopole Campus 3, 4 Rue Pierre Fontaine, 91058 Evry-Courcouronnes, France.
Andrey S KarpovDepartment of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.
Tatiana A PerevyazovaInstitute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya Str. 3, 142290 Puschino, Russia.
Tatiana S OretskayaBelozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.ORCID 0000-0002-2262-117X
Olga S FedorovaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia.ORCID 0000-0002-4001-7187
Elena A KubarevaBelozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.
Lomonosov Moscow State University · RUInstitute of Chemical Biology and Fundamental Medicine · RUGenopole (France) · FRInstitute of Theoretical and Experimental Biophysics · RU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Nicking endonucleases (NEs) are enzymes that incise only one strand of the duplex to produce a DNA molecule that is 'nicked' rather than cleaved in two. Since these precision tools are used in genetic engineering and genome editing, information about their mechanism of action at all stages of DNA recognition and phosphodiester bond hydrolysis is essential. For the first time, fast kinetics of the Nt.BspD6I interaction with DNA were studied by the stopped-flow technique, and changes of optical characteristics were registered for the enzyme or DNA molecules. The role of divalent metal cations was estimated at all steps of Nt.BspD6I-DNA complex formation. It was demonstrated that divalent metal ions are not required for the formation of a non-specific complex of the protein with DNA. Nt.BspD6I bound five-fold more efficiently to its recognition site in DNA than to a random DNA. DNA bending was confirmed during the specific binding of Nt.BspD6I to a substrate. The optimal size of Nt.BspD6I's binding site in DNA as determined in this work should be taken into account in methods of detection of nucleic acid sequences and/or even various base modifications by means of NEs.

Indexed as

BacillusDeoxyribonuclease IDNADNA-Binding ProteinsEndonucleasesKineticsMultiprotein ComplexesNucleic Acid ConformationDeoxyribonuclease IDNADNA-Binding ProteinsEndonucleasesMultiprotein ComplexesDNA-protein interactionkinetic mechanismnicking endonucleasepre–steady-state kinetics

Identifiers

PMID34680052
PMCPMC8533099
OpenAlexW3202034904

What Socratic holds

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Registered trials

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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 Socratic graph.