Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity (Q34474076)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20805246%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

review article

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title

Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity (English)

1 reference

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13 February 2020

1 reference

2 August 2019

1 reference

28 September 2019

1

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13 February 2020

author name string

Barry L Stoddard

series ordinal

2

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13 February 2020

Shuang-Yong Xu

series ordinal

3

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13 February 2020

language of work or name

English

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publication date

30 August 2010

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13 February 2020

published in

Nucleic Acids Research

4 references

18 June 2019

2 August 2019

28 September 2019

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13 February 2020

volume

39

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13 February 2020

page(s)

1-18

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issue

1

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Creative Commons Attribution-NonCommercial 2.5 Generic

13 February 2020

copyright license

3 references

18 June 2019

2 August 2019

A unified genetic, computational and experimental framework identifies functionally relevant residues of the homing endonuclease I-BmoI.

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Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site

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Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit

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Vitamin D receptor polymorphisms and the risk of cutaneous melanoma: a systematic review and meta-analysis

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Specific versus nonspecific isothermal DNA amplification through thermophilic polymerase and nicking enzyme activities

6 July 2018

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Engineering variants of the I-SceI homing endonuclease with strand-specific and site-specific DNA-nicking activity

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Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway

6 July 2018

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Labeling of unique sequences in double-stranded DNA at sites of vicinal nicks generated by nicking endonucleases.

6 July 2018

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MeCP2 binding to DNA depends upon hydration at methyl-CpG

6 July 2018

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Enzymatic signal amplification of molecular beacons for sensitive DNA detection

6 July 2018

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A novel sequence-specific RNA quantification method using nicking endonuclease, dual-labeled fluorescent DNA probe, and conformation-interchangeable oligo-DNA

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Coevolution of a Homing Endonuclease and Its Host Target Sequence

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6 July 2018

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6 July 2018

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6 July 2018

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Nickase and a protein encoded by an open reading frame downstream from the nickase BspD6I gene form a restriction endonuclease complex

6 July 2018

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When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I.

6 July 2018

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6 July 2018

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SNP-RFLPing: restriction enzyme mining for SNPs in genomes

6 July 2018

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Homing endonuclease structure and function

6 July 2018

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A single catalytic domain of the junction-resolving enzyme T7 endonuclease I is a non-specific nicking endonuclease

6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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How restriction enzymes became the workhorses of molecular biology

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6 July 2018

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6 July 2018

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6 July 2018

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Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease

6 July 2018

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6 July 2018

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The isolation of strand-specific nicking endonucleases from a randomized SapI expression library

6 July 2018

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Group I intron homing in Bacillus phages SPO1 and SP82: a gene conversion event initiated by a nicking homing endonuclease

6 July 2018

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Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI.

6 July 2018

1 reference

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Engineering strand-specific DNA nicking enzymes from the type IIS restriction endonucleases BsaI, BsmBI, and BsmAI.

6 July 2018

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The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity

6 July 2018

1 reference

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Cloning and sequencing of the gene of site-specific nickase N.BspD6I

6 July 2018

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Host controlled variation in bacterial viruses

6 July 2018

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A nonhereditary, host-induced variation of bacterial viruses

6 July 2018

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The nicking homing endonuclease I-BasI is encoded by a group I intron in the DNA polymerase gene of the Bacillus thuringiensis phage Bastille

6 July 2018

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Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI

6 July 2018

1 reference

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How the Bfi I restriction enzyme uses one active site to cut two DNA strands

6 July 2018

1 reference

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Isothermal reactions for the amplification of oligonucleotides

6 July 2018

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A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes

6 July 2018

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The metal-independent type IIs restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre

6 July 2018

1 reference

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Catalytic mechanisms of restriction and homing endonucleases

6 July 2018

1 reference

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Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI

6 July 2018

1 reference

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Comprehensive human genome amplification using multiple displacement amplification

6 July 2018

1 reference

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Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA.

6 July 2018

1 reference

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Simple and rapid preparation of gapped plasmid DNA for incorporation of oligomers containing specific DNA lesions

6 July 2018

1 reference

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Engineering a nicking endonuclease N.AlwI by domain swapping

6 July 2018

1 reference

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Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility

6 July 2018

1 reference

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Converting MlyI endonuclease into a nicking enzyme by changing its oligomerization state

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

The nicking endonuclease N.BstNBI is closely related to type IIs restriction endonucleases MlyI and PleI

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

The minimal repression domain of MBD2b overlaps with the methyl-CpG-binding domain and binds directly to Sin3A

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Crystal structure of a phospholipase D family member

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

FokI dimerization is required for DNA cleavage

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Structure of FokI has implications for DNA cleavage

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Cloning and analysis of the four genes coding for Bpu10I restriction-modification enzymes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Homing endonucleases: keeping the house in order

6 July 2018

1 reference

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Structure of the multimodular endonuclease FokI bound to DNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Beyond homing: competition between intron endonucleases confers a selective advantage on flanking genetic markers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Mechanisms of intron mobility.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Intron-encoded endonuclease I-TevI binds as a monomer to effect sequential cleavage via conformational changes in the td homing site.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Introns as mobile genetic elements

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron-exon junctions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

The site-specific DNA endonuclease encoded by a group I intron in the Chlamydomonas pallidostigmatica chloroplast small subunit rRNA gene introduces a single-strand break at low concentrations of Mg2+

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

In vivo cleavage of cytosine-containing bacteriophage T4 DNA to genetically distinct, discretely sized fragments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

A restriction enzyme from Hemophilus influenzae. I. Purification and general properties

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Group I introns as mobile genetic elements: facts and mechanistic speculations--a review

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Class-IIS restriction enzymes--a review

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Characterization of MeCP2, a vertebrate DNA binding protein with affinity for methylated DNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Detection of two restriction endonuclease activities in Haemophilus parainfluenzae using analytical agarose--ethidium bromide electrophoresis

6 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Cloning of Nt.CviQII nicking endonuclease and its cognate methyltransferase: M.CviQII methylates AG sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

I-BasI and I-HmuI: two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA specificities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Generation of the BfiI restriction endonuclease from the fusion of a DNA recognition domain to a non-specific nuclease from the phospholipase D superfamily

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Structural and mechanistic basis of immunity toward endonuclease colicins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

HNH family subclassification leads to identification of commonality in the His-Me endonuclease superfamily

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

In vitro analysis of the relationship between endonuclease and maturase activities in the bi-functional group I intron-encoded protein, I-AniI.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Isothermal DNA amplification with gold nanosphere-based visual colorimetric readout for herpes simplex virus detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Isothermal DNA amplification coupled with DNA nanosphere-based colorimetric detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Molecular detection of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

RAG proteins shepherd double-strand breaks to a specific pathway, suppressing error-prone repair, but RAG nicking initiates homologous recombination.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Pyrosequencing on nicked dsDNA generated by nicking endonucleases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Preparation of heteroduplex enhanced green fluorescent protein plasmid for in vivo mismatch repair activity assay

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Targeting DNA 5mCpG sites with chimeric endonucleases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ742

Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017599

Strand-specific contacts and divalent metal ion regulate double-strand break formation by the GIY-YIG homing endonuclease I-BmoI

27 October 2018

1 reference

12 December 2020

FokI requires two specific DNA sites for cleavage

1 reference

12 December 2020

Mismatch repair in human nuclear extracts. Quantitative analyses of excision of nicked circular mismatched DNA substrates, constructed by a new technique employing synthetic oligonucleotides

1 reference

12 December 2020

Physical mapping of the HindIII, EcoRI, Sal and Sma restriction endonuclease cleavage fragments from bacteriophage T5 DNA

1 reference

12 December 2020

Atypical DNA-binding properties of class-IIS restriction endonucleases: evidence for recognition of the cognate sequence by a FokI monomer

1 reference

12 December 2020

Cleavage of Individual DNA Strands by the Different Subunits of the Heterodimeric Restriction Endonuclease BbvCI

1 reference

12 December 2020

Significant enhancement of fluorescence on hybridization of a molecular beacon to a target DNA in the presence of a site-specific DNA nickase

1 reference

12 December 2020

Domain organization and metal ion requirement of the Type IIS restriction endonuclease MnlI

1 reference

12 December 2020

Changing the enzymatic activity of T7 endonuclease by mutations at the beta-bridge site: alteration of substrate specificity profile and metal ion requirements by mutation distant from the catalytic domain

1 reference

12 December 2020

Nucleotide sequences at the cleavage sites of two restriction endonucleases from Hemophilus parainfluenzae

1 reference

12 December 2020

EcoRI endonuclease cleavage map of bacteriophage P4-DNA

1 reference

12 December 2020

DeepSAGE: higher sensitivity and multiplexing of samples using a simpler experimental protocol

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKQ742

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20805246%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

DBLP publication ID

journals/nar/ChanSX11

1 reference

DBLP Dataset 2021-01-02

release_domihqprkra2tfcy43cwzxvnvu

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/domihqprkra2tfcy43cwzxvnvu

24 November 2022

mapped directly with Wikidata item

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20805246%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1 reference