Impact of target mRNA structure on siRNA silencing efficiency: A large-scale study (Q37135903)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18306428%20AND%20SRC:MED&resulttype=core&format=json

3 January 2020

title

Impact of target mRNA structure on siRNA silencing efficiency: A large-scale study (English)

1 reference

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3 January 2020

3

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3 January 2020

author name string

Joseph A Gredell

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18306428%20AND%20SRC:MED&resulttype=core&format=json

3 January 2020

Angela K Berger

series ordinal

2

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18306428%20AND%20SRC:MED&resulttype=core&format=json

3 January 2020

publication date

1 July 2008

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18306428%20AND%20SRC:MED&resulttype=core&format=json

Biotechnology and Bioengineering

3 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18306428%20AND%20SRC:MED&resulttype=core&format=json

3 January 2020

volume

100

1 reference

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3 January 2020

issue

4

1 reference

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3 January 2020

page(s)

744-755

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18306428%20AND%20SRC:MED&resulttype=core&format=json

Effect of target secondary structure on RNAi efficiency

3 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Molecular basis for target RNA recognition and cleavage by human RISC.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

RNA helicase A interacts with RISC in human cells and functions in RISC loading

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Comparison of approaches for rational siRNA design leading to a new efficient and transparent method

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Designing siRNA that distinguish between genes that differ by a single nucleotide

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Off-target effects by siRNA can induce toxic phenotype

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Induction of the interferon response by siRNA is cell type- and duplex length-dependent

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Computational models with thermodynamic and composition features improve siRNA design

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Thermodynamics of RNA-RNA binding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

DINAMelt web server for nucleic acid melting prediction

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

siRNA target site secondary structure predictions using local stable substructures

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

A protein sensor for siRNA asymmetry

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Revealing the world of RNA interference

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Sfold web server for statistical folding and rational design of nucleic acids

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Kinetic analysis of the RNAi enzyme complex

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Mechanistic insights into the kinetics of HIV-1 nucleocapsid protein-facilitated tRNA annealing to the primer binding site

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Effects on RNAi of the tight structure, sequence and position of the targeted region.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Rational siRNA design for RNA interference

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Functional siRNAs and miRNAs Exhibit Strand Bias

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Asymmetry in the assembly of the RNAi enzyme complex

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Activation of the interferon system by short-interfering RNAs

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Vienna RNA secondary structure server

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Mfold web server for nucleic acid folding and hybridization prediction

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Expression profiling reveals off-target gene regulation by RNAi

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Analysis of gene function in somatic mammalian cells using small interfering RNAs

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

RNA interference is mediated by 21- and 22-nucleotide RNAs

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Effects of RNA secondary structure on cellular antisense activity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Prediction of antisense oligonucleotide binding affinity to a structured RNA target

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

A systematic analysis of the effect of target RNA structure on RNA interference

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Local RNA target structure influences siRNA efficacy: a systematic global analysis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Coupling of RNAi-mediated target downregulation with gene replacement

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

RISC is a 5' phosphomonoester-producing RNA endonuclease

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Determinants of targeting by endogenous and exogenous microRNAs and siRNAs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Specific residues at every third position of siRNA shape its efficient RNAi activity

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Selecting effective siRNAs based on guide RNA structure.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Potent effect of target structure on microRNA function.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Sequence characteristics of functional siRNAs

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2658823

Target accessibility dictates the potency of human RISC

3 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18306428

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18306428

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

How to design an antisense oligodeoxynucleotide experiment: a consensus approach

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18306428

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/BIT.21798

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18306428%20AND%20SRC:MED&resulttype=core&format=json

3 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18306428%20AND%20SRC:MED&resulttype=core&format=json

3 January 2020

1 reference