NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome (Q37469625)

20 August 2017

NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome (English)

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20 August 2017

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Sarah C Keane

1

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20 August 2017

Verna Van

2

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20 August 2017

Heather M Frank

3

1 reference

20 August 2017

Carly A Sciandra

4

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20 August 2017

Sayo McCowin

5

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20 August 2017

Justin Santos

6

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20 August 2017

Xiao Heng

7

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20 August 2017

Michael F Summers

8

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20 August 2017

language of work or name

English

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publication date

10 October 2016

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Proceedings of the National Academy of Sciences of the United States of America

20 August 2017

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20 August 2017

113

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20 August 2017

46

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20 August 2017

13033-13038

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describes a project that uses

20 August 2017

ImageJ

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5135362/fullTextXML

inferred from PubMed Central ID database lookup

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Conserved determinants of lentiviral genome dimerization

23 August 2017

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Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

23 August 2017

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RNA structure. Structure of the HIV-1 RNA packaging signal

23 August 2017

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In-gel probing of individual RNA conformers within a mixed population reveals a dimerization structural switch in the HIV-1 leader

23 August 2017

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Dimeric RNA recognition regulates HIV-1 genome packaging

23 August 2017

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Database proton NMR chemical shifts for RNA signal assignment and validation

23 August 2017

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23 August 2017

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Identification of a minimal region of the HIV-1 5'-leader required for RNA dimerization, NC binding, and packaging

23 August 2017

1 reference

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NMR detection of structures in the HIV-1 5'-leader RNA that regulate genome packaging

23 August 2017

1 reference

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Structural determinants and mechanism of HIV-1 genome packaging

23 August 2017

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Probing the HIV-1 genomic RNA trafficking pathway and dimerization by genetic recombination and single virion analyses

23 August 2017

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The remarkable frequency of human immunodeficiency virus type 1 genetic recombination

23 August 2017

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The secondary structure of the human immunodeficiency virus type 1 transcript modulates viral splicing and infectivity

23 August 2017

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RNA structure modulates splicing efficiency at the human immunodeficiency virus type 1 major splice donor

23 August 2017

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Contribution of Recombination to the Evolution of Human Immunodeficiency Viruses Expressing Resistance to Antiretroviral Treatment

23 August 2017

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Dimer initiation signal of human immunodeficiency virus type 1: its role in partner selection during RNA copackaging and its effects on 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=5135362

Effects of mutations in the human immunodeficiency virus type 1 Gag gene on RNA packaging and 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=5135362

A new NMR solution structure of the SL1 HIV-1Lai loop-loop dimer

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

How retroviruses select their genomes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Using NMRView to visualize and analyze the NMR spectra of macromolecules

23 August 2017

1 reference

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The retroviral RNA dimer linkage: different structures may reflect different roles

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

A proton-coupled dynamic conformational switch in the HIV-1 dimerization initiation site kissing complex

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

A simple and efficient method to reduce nontemplated nucleotide addition at the 3 terminus of RNAs transcribed by T7 RNA polymerase

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Structure of the dimer initiation complex of HIV-1 genomic RNA

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Role of the DIS hairpin in replication of human immunodeficiency virus 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=5135362

A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

The human immunodeficiency virus type 1 encapsidation site is a multipartite RNA element composed of functional hairpin structures

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

The human immunodeficiency virus type 1 5' packaging signal structure affects translation but does not function as an internal ribosome entry site structure

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Characterization of human immunodeficiency virus type 1 dimeric RNA from wild-type and protease-defective virions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Synthesis of small RNAs using T7 RNA polymerase

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Genetic consequences of packaging two RNA genomes in one retroviral particle: pseudodiploidy and high rate of genetic 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=5135362

Retroviral Recombination and Reverse Transcription

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Rapid NMR screening of RNA secondary structure and binding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Life of psi: how full-length HIV-1 RNAs become packaged genomes in the viral particles

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

HIV RNA dimerisation interference by antisense oligonucleotides targeted to the 5' UTR structural elements

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Solution studies of the dimerization initiation site of HIV-1 genomic RNA.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Structure, Replication, and Recombination of Retrovirus Genomes: Some Unifying Hypotheses

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

An efficient and economic site-specific deuteration strategy for NMR studies of homologous oligonucleotide repeat sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Role of the 5' TAR stem--loop and the U5-AUG duplex in dimerization of HIV-1 genomic RNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

HIV-1 viral RNA is selected in the form of monomers that dimerize in a three-step protease-dependent process; the DIS of stem-loop 1 initiates viral RNA dimerization

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Deficient dimerization of human immunodeficiency virus type 1 RNA caused by mutations of the u5 RNA sequences

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Structural investigation of HIV-1 genomic RNA dimerization process reveals a role for the Major Splice-site Donor stem loop.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing-duplex structural transition

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

HIV-1 genome dimerization: kissing-loop hairpin dictates whether nucleotides downstream of the 5' splice junction contribute to loose and tight dimerization of human immunodeficiency virus RNA.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Annealing to sequences within the primer binding site loop promotes an HIV-1 RNA conformation favoring RNA dimerization and packaging

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Dominant role of the 5' TAR bulge in dimerization of HIV-1 genomic RNA, but no evidence of TAR-TAR kissing during in vivo virus assembly

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Structural requirement for the two-step dimerization of human immunodeficiency virus type 1 genome

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

NMR structure of the mature dimer initiation complex of HIV-1 genomic RNA.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

Mutational analysis of the bipartite dimer linkage structure of human immunodeficiency virus type 1 genomic RNA.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5135362

NMR analysis of intra- and inter-molecular stems in the dimerization initiation site of the HIV-1 genome

2 September 2018

1 reference

12 December 2020

Ultrastructure of HIV-1 genomic RNA

1 reference

12 December 2020

NCp7 activates HIV-1Lai RNA dimerization by converting a transient loop-loop complex into a stable dimer

1 reference

12 December 2020

The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation

1 reference

12 December 2020

A short sequence upstream of the 5' major splice site is important for encapsidation of HIV-1 genomic RNA

1 reference

12 December 2020

A kissing complex together with a stable dimer is involved in the HIV-1Lai RNA dimerization process in vitro

1 reference

12 December 2020

Kissing-loop model of HIV-1 genome dimerization: HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensable for dimer formation

1 reference

12 December 2020

Dimerization of HIV-1Lai RNA at low ionic strength. An autocomplementary sequence in the 5' leader region is evidenced by an antisense oligonucleotide

1 reference

12 December 2020

Variant effects of non-native kissing-loop hairpin palindromes on HIV replication and HIV RNA dimerization: role of stem-loop B in HIV replication and HIV RNA dimerization

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1614785113

1 reference

20 August 2017

1 reference

20 August 2017

PubMed publication ID

27791166

1 reference