Evidence map›Paper›PMID 36892773›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

Adoption of A-Z Junctions in RNAs by Binding of Zα Domains.

Parker J Nichols, Shaun Bevers, Morkos A Henen, Jeffrey S Kieft, Quentin Vicens, Beat Vögeli

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Parker J NicholsDepartment of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA.
Shaun BeversDepartment of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA.
Morkos A HenenDepartment of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA.
Jeffrey S KieftDepartment of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA.
Quentin VicensDepartment of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA. quentin.vicens@cuanschutz.edu.
Beat VögeliDepartment of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA. beat.vogeli@cuanschutz.edu.

Funding

University of Colorado Cancer Center Support Grant - Lung Cancer Patient-Derived Xenografts with Autologous Human Immune SystemsP30CA046934 · NCI · UNIVERSITY OF COLORADO DENVER · PI James V Degregori · 1988 to 2026
$117.0M
Structure, function, and dynamics of viral RNAs and RNA-containing complexesR35GM118070 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI Jeffrey S Kieft · 2016 to 2026
$10.6M
600 MHz NMR console and cold probeS10OD025020 · OD · UNIVERSITY OF COLORADO DENVER · PI JONES, DAVID NIGEL · 2018 to 2018
$501k
A-Z junction formation drives recognition of Alu RNAs by ADAR1 and supports viral infectivity and replicationF31AI167396 · NIAID · UNIVERSITY OF COLORADO DENVER · PI NICHOLS, PARKER J · 2022 to 2024
$109k
NCI NIH HHS P30 CA046934NIAID NIH HHS F31 AI167396NIGMS NIH HHS R35 GM118070NIH HHS S10 OD025020
6 · The paper itself

Abstract

While DNA and RNA helices often adopt the canonical B- or A-conformation, the fluid conformational landscape of nucleic acids allows for many higher energy states to be sampled. One such state is the Z-conformation of nucleic acids, which is unique in that it is left-handed and has a "zigzag" backbone. The Z-conformation is recognized and stabilized by Z-DNA/RNA binding domains called Zα domains. We recently demonstrated that a wide range of RNAs can adopt partial Z-conformations termed "A-Z junctions" upon binding to Zα and that the formation of such conformations may be dependent upon both sequence and context. In this chapter, we present general protocols for characterizing the binding of Zα domains to A-Z junction-forming RNAs for the purpose of determining the affinity and stoichiometry of interactions as well as the extent and location of Z-RNA formation.

Indexed as

DNA, Z-FormDNANucleic Acid ConformationProtein Structure, SecondaryRNADNADNA, Z-FormRNAAnalytical ultracentrifugationA–Z junctionsCircular dichroismEz scoreIsothermal titration calorimetryNuclear magnetic resonanceZ-RNAZα domains

Identifiers

PMID36892773
PMCPMC10083127

What Socratic holds

Textmetadata
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Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.