Predicting oligonucleotide affinity to nucleic acid targets (Q24539440)

6 July 2017

Predicting oligonucleotide affinity to nucleic acid targets (English)

1 reference

ORCID Public Data File 2021

6 July 2017

1 reference

author name string

D H Mathews

1

1 reference

6 July 2017

M E Burkard

2

1 reference

6 July 2017

S M Freier

3

1 reference

6 July 2017

J R Wyatt

4

1 reference

6 July 2017

D H Turner

5

1 reference

6 July 2017

language of work or name

English

0 references

publication date

1 November 1999

1 reference

6 July 2017

1 reference

6 July 2017

5

1 reference

6 July 2017

1458-1469

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6 July 2017

11

1 reference

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

6 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

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

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

A dynamic programming algorithm for RNA structure prediction including pseudoknots

24 March 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

24 March 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Selecting effective antisense reagents on combinatorial oligonucleotide arrays

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

On finding all suboptimal foldings of an RNA molecule

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Mapping of a protein-RNA kissing hairpin interface: Rom and Tar-Tar*

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Antisense binding enhanced by tertiary interactions: binding of phosphorothioate and N3'-->P5' phosphoramidate hexanucleotides to the catalytic core of a group I ribozyme from the mammalian pathogen Pneumocystis carinii

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

A Pneumocystis carinii group I intron ribozyme that does not require 2' OH groups on its 5' exon mimic for binding to the catalytic core

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA:RNA duplexes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Inhibition of human TNF alpha and LT in cell-free extracts and in cell culture by antisense oligonucleotides.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Potent antisense oligonucleotides to the human multidrug resistance-1 mRNA are rationally selected by mapping RNA-accessible sites with oligonucleotide libraries

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Reduction of expression of the multidrug resistance protein (MRP) in human tumor cells by antisense phosphorothioate oligonucleotides

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Characterization of a "kissing" hairpin complex derived from the human immunodeficiency virus genome

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Minor groove recognition of the conserved G.U pair at the Tetrahymena ribozyme reaction site

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Antisense gene suppression against human ICAM-1, ELAM-1, and VCAM-1 in cultured human umbilical vein endothelial cells.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Inhibition of endothelial cell adhesion molecule expression with antisense oligonucleotides.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Probing the structure of RNAs in solution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: evidence for ribozyme specific interactions with 2' OH groups

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Ribozyme recognition of RNA by tertiary interactions with specific ribose 2′-OH groups

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Inhibition of interleukin-1 type I receptor expression in human cell-lines by an antisense phosphorothioate oligodeoxynucleotide

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Probing accessible sites for ribozymes on human acetylcholinesterase RNA.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Phylogenetic comparative analysis of RNA secondary structure

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Antisense oligonucleotides inhibit intercellular adhesion molecule 1 expression by two distinct mechanisms

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Thermal unfolding of yeast glycine transfer RNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Ribozyme-mediated repair of sickle beta-globin mRNAs in erythrocyte precursors

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Inhibition of protein kinase C-alpha expression in human A549 cells by antisense oligonucleotides inhibits induction of intercellular adhesion molecule 1 (ICAM-1) mRNA by phorbol esters.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Determinants of RNA hairpin loop-loop complex stability.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1369867

Mitogen-activated protein (MAP) kinase is regulated by the MAP kinase phosphatase (MKP-1) in vascular smooth muscle cells. Effect of actinomycin D and antisense oligonucleotides

29 November 2018

1 reference

12 December 2020

Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes

1 reference

12 December 2020

Improved nearest-neighbor parameters for predicting DNA duplex stability

1 reference

12 December 2020

Combinatorial screening and rational optimization for hybridization to folded hepatitis C virus RNA of oligonucleotides with biological antisense activity

1 reference

12 December 2020

Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3' terminal intron components

1 reference

12 December 2020

Kinetic intermediates in RNA folding

1 reference

12 December 2020

Thermodynamics and NMR of internal G.T mismatches in DNA

1 reference

12 December 2020

Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries

1 reference

12 December 2020

Tetranucleotide GGGA motif in primary RNA transcripts. Novel target site for antisense design

1 reference

12 December 2020

Prediction of antisense oligonucleotide efficacy by in vitro methods

1 reference

12 December 2020

Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches

1 reference

12 December 2020

The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA

1 reference

12 December 2020

Free energy contributions of G.U and other terminal mismatches to helix stability

1 reference

12 December 2020

Enzymatic approaches to probing of RNA secondary and tertiary structure

1 reference

12 December 2020

Blocking of heart allograft rejection by intercellular adhesion molecule-1 antisense oligonucleotides alone or in combination with other immunosuppressive modalities

1 reference

12 December 2020

10.1017/S1355838299991148

Identifiers

DOI

1 reference

OpenCitations bibliographic resource ID

6 July 2017

4285050

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

6 July 2017

1 reference