(Q37606980)

21 August 2017

Reprogramming homing endonuclease specificity through computational design and directed evolution (English)

1 reference

21 August 2017

0 references

1 reference

Justin Ashworth

8

0 references

Tony Nolan

object named as

Tony Nolan

4

0 references

David Baker

object named as

David Baker

9

0 references

author name string

Summer B Thyme

1

1 reference

21 August 2017

Sandrine J S Boissel

2

1 reference

21 August 2017

S Arshiya Quadri

3

1 reference

21 August 2017

Dean A Baker

5

1 reference

21 August 2017

Rachel U Park

6

1 reference

21 August 2017

Lara Kusak

7

1 reference

21 August 2017

language of work or name

English

0 references

publication date

21 November 2013

1 reference

21 August 2017

Nucleic Acids Research

1 reference

21 August 2017

42

1 reference

21 August 2017

4

1 reference

21 August 2017

2564-2576

1 reference

Creative Commons Attribution 3.0 Unported

21 August 2017

start time

10 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

ImageJ

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3936771/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination

1 reference

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CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity

23 August 2017

1 reference

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High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

23 August 2017

1 reference

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Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

23 August 2017

1 reference

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DNA targeting specificity of RNA-guided Cas9 nucleases

23 August 2017

1 reference

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Protospacer recognition motifs: mixed identities and functional diversity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

RNA-guided human genome engineering via Cas9

23 August 2017

1 reference

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Multiplex genome engineering using CRISPR/Cas systems

23 August 2017

1 reference

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Modelling dynamics in protein crystal structures by ensemble refinement

23 August 2017

1 reference

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A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

23 August 2017

1 reference

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Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

A new method for evaluating the specificity of indirect readout in protein-DNA recognition

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Non-specific protein-DNA interactions control I-CreI target binding and cleavage

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Automated selection of stabilizing mutations in designed and natural proteins

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Comprehensive homing endonuclease target site specificity profiling reveals evolutionary constraints and enables genome engineering applications

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Tapping natural reservoirs of homing endonucleases for targeted gene modification

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Mining endonuclease cleavage determinants in genomic sequence data.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

A synthetic homing endonuclease-based gene drive system in the human malaria mosquito

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Meganucleases and other tools for targeted genome engineering: perspectives and challenges for gene therapy

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

A TALE nuclease architecture for efficient genome editing

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Genome editing with engineered zinc finger nucleases

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Structure-based DNA-binding prediction and design.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Exploitation of binding energy for catalysis and design

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Motif-directed flexible backbone design of functional interactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Assessment of the optimization of affinity and specificity at protein-DNA interfaces

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Cluster expansion models for flexible-backbone protein energetics.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Coevolution of a Homing Endonuclease and Its Host Target Sequence

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Computational redesign of endonuclease DNA binding and cleavage specificity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Directed evolution and substrate specificity profile of homing endonuclease I-SceI.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Protein production by auto-induction in high density shaking cultures

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Enhancing Gene Targeting with Designed Zinc Finger Nucleases

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Design, activity, and structure of a highly specific artificial endonuclease

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

The pathophysiology and treatment of hereditary tyrosinemia type 1.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

XRCC3 promotes homology-directed repair of DNA damage in mammalian cells

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Bayesian statistical analysis of protein side‐chain rotamer preferences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Efficient site-directed mutagenesis using uracil-containing DNA.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Chemical and biological approaches to improve the efficiency of homologous recombination in human cells mediated by artificial restriction DNA cutter

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Functional interplay of the Mre11 nuclease and Ku in the response to replication-associated DNA damage

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Determining the specificity of protein–DNA interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

The monomeric homing endonuclease PI-SceI has two catalytic centres for cleavage of the two strands of its DNA substrate

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Quantitative specificity of the Mnt repressor

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Specificity, free energy and information content in protein-DNA interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Canine models of gene-modified hematopoiesis

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

A simple physical model for the prediction and design of protein-DNA interactions

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936771

Zinc fingers hit off target

1 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24270794

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Specificity by design

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1093/NAR/GKT1212

Identifiers

DOI

10.1093/NAR/GKT1212

1 reference

21 August 2017

1 reference

21 August 2017

PubMed publication ID

24270794

1 reference