(Q35024188)

English

Tertiary structural and functional analyses of a viroid RNA motif by isostericity matrix and mutagenesis reveal its essential role in replication

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scholarly article

1 reference

Europe PubMed Central

5 August 2017

Tertiary structural and functional analyses of a viroid RNA motif by isostericity matrix and mutagenesis reveal its essential role in replication (English)

1 reference

Europe PubMed Central

5 August 2017

author name string

Xuehua Zhong

1

1 reference

Europe PubMed Central

5 August 2017

Neocles Leontis

2

1 reference

Europe PubMed Central

5 August 2017

Shuiming Qian

3

1 reference

Europe PubMed Central

5 August 2017

Asuka Itaya

4

1 reference

Europe PubMed Central

5 August 2017

Yijun Qi

5

1 reference

Europe PubMed Central

5 August 2017

Kathleen Boris-Lawrie

6

1 reference

Europe PubMed Central

5 August 2017

Biao Ding

7

1 reference

Europe PubMed Central

5 August 2017

language of work or name

0 references

publication date

1 September 2006

1 reference

Europe PubMed Central

5 August 2017

Journal of Virology

1 reference

Europe PubMed Central

5 August 2017

80

1 reference

Europe PubMed Central

5 August 2017

17

1 reference

Europe PubMed Central

5 August 2017

8566-8581

1 reference

Europe PubMed Central

5 August 2017

Mutational analysis of potato spindle tuber viroid reveals complex relationships between structure and infectivity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Viroids and viroid-host interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

RNA replication without RNA-dependent RNA polymerase: surprises from hepatitis delta virus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Dissecting RNA silencing in protoplasts uncovers novel effects of viral suppressors on the silencing pathway at the cellular level

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Viroids: unusual small pathogenic RNAs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

RNA silencing in plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Viroids: petite RNA pathogens with distinguished talents

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

An mRNA structure in bacteria that controls gene expression by binding lysine

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Mfold web server for nucleic acid folding and hybridization prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Replication of human hepatitis delta virus: recent developments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Identification of a minimal sequence required for activation of the tomato golden mosaic virus coat protein promoter in protoplasts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

A mini-RNA containing the tetraloop, wobble-pair and loop E motifs of the central conserved region of potato spindle tuber viroid is processed into a minicircle

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

The non-Watson-Crick base pairs and their associated isostericity matrices

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Detection and analysis of hairpin II, an essential metastable structural element in viroid replication intermediates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

The antiquity of RNA-based evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

In vivo RNA-directed transcription, with template switching, by a mammalian RNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Geometric nomenclature and classification of RNA base pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Conserved geometrical base-pairing patterns in RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Multiple pathways of reversion in viroids for conservation of structural elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

The conformation of loop E of eukaryotic 5S ribosomal RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

The sarcin/ricin loop, a modular RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

An infectious viroid RNA replicon evolved from an in vitro-generated non-infectious viroid deletion mutant via a complementary deletion in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Only one of four possible secondary structures of the central conserved region of potato spindle tuber viroid is a substrate for processing in a potato nuclear extract

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

A Replication Cycle for Viroids and Other Small Infectious RNA's

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Potato spindle tuber "virus". IV. A replicating, low molecular weight RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Ultraviolet light-induced crosslinking reveals a unique region of local tertiary structure in potato spindle tuber viroid and HeLa 5S RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Effects of random mutagenesis upon potato spindle tuber viroid replication and symptom expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Accurate in vitro transcription of plant promoters with nuclear extracts prepared from cultured plant cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Nucleotide sequence and secondary structure of potato spindle tuber viroid

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Structure and structure formation of viroids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Fine structure melting of viroids as studied by kinetic methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

8 July 2018

Inhibition of cell growth and shoot development by a specific nucleotide sequence in a noncoding viroid RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

25 October 2018

Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

25 October 2018

Restoration of secondary hairpin II is associated with restoration of infectivity of a non-viable recombinant viroid

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

25 October 2018

CEVd-induced symptom modification as a response to a host-specific temperature-sensitive reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

25 October 2018

RNA structural features responsible for potato spindle tuber viroid pathogenicity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

25 October 2018

Isolates of citrus exocortis viroid recovered by host and tissue selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

25 October 2018

Nucleotide sequence and secondary structure of citrus exocortis and chrysanthemum stunt viroid.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563885

25 October 2018

Replication of Potato spindle tuber viroid in cultured cells of tobacco and Nicotiana benthamiana: the role of specific nucleotides in determining replication levels for host adaptation

1 reference

https://pubmed.ncbi.nlm.nih.gov/16912306

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Destabilization of potato spindle tuber viroid by mutations in the left terminal loop

1 reference

https://pubmed.ncbi.nlm.nih.gov/16912306

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcription of potato spindle tuber viroid by RNA polymerase II starts in the left terminal loop

1 reference

https://pubmed.ncbi.nlm.nih.gov/16912306

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Site-specific mutagenesis of potato spindle tuber viroid cDNA: : Alterations within premelting region 2 that abolish infectivity

1 reference

https://pubmed.ncbi.nlm.nih.gov/16912306

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Movement of potato spindle tuber viroid reveals regulatory points of phloem-mediated RNA traffic

1 reference

https://pubmed.ncbi.nlm.nih.gov/16912306

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A single nucleotide substitution converts potato spindle tuber viroid (PSTVd) from a noninfectious to an infectious RNA for nicotiana tabacum

1 reference

https://pubmed.ncbi.nlm.nih.gov/16912306

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Secondary structure probing of potato spindle tuber viroid (PSTVd) and sequence comparison with other small pathogenic RNA replicons provides evidence for central non-canonical base-pairs, large A-rich loops, and a terminal branch

1 reference

https://pubmed.ncbi.nlm.nih.gov/16912306

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Role of the variable domain in modulating potato spindle tuber viroid replication

1 reference

https://pubmed.ncbi.nlm.nih.gov/16912306

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structural Characterization of the 69 Nucleotide Potato Spindle Tuber Viroid Left-terminal Domain by NMR and Thermodynamic Analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/16912306

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Origin of life: The RNA world

1 reference

4 November 2023

https://opencitations.net/index/coci/api/v1/citations/10.1038/319618A0

Identifiers

10.1128/JVI.00837-06

1 reference

Europe PubMed Central

5 August 2017

1 reference

Europe PubMed Central

5 August 2017

1 reference

Europe PubMed Central

5 August 2017

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