scholarly journals New 3D graphical representation for RNA structure analysis and its application in the pre-miRNA identification of plants

RSC Advances ◽  
2018 ◽  
Vol 8 (54) ◽  
pp. 30833-30841 ◽  
Author(s):  
Xiangzheng Fu ◽  
Bo Liao ◽  
Wen Zhu ◽  
Lijun Cai
Keyword(s):  
Structure Analysis ◽  
Rna Structure ◽  
Graphical Representation ◽  
Transcriptional Regulators ◽  
Mirna Identification ◽  
Non Coding Rnas ◽  
3D Graphical Representation

MicroRNAs (miRNAs) are a family of short non-coding RNAs that play significant roles as post-transcriptional regulators.

scholarly journals A Dynamic 3D Graphical Representation for RNA Structure Analysis and Its Application in Non-Coding RNA Classification

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0152238 ◽  
Author(s):  
Yi Zhang ◽  
Haiyun Huang ◽  
Xiaoqing Dong ◽  
Yiliang Fang ◽  
Kejing Wang ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Rna Structure ◽  
Graphical Representation ◽  
Non Coding Rna ◽  
3D Graphical Representation ◽  
Rna Classification

scholarly journals Viral RNA structure analysis using DMS-MaPseq

Methods ◽  
2020 ◽  
Vol 183 ◽  
pp. 68-75 ◽  
Author(s):  
Phillip Tomezsko ◽  
Harish Swaminathan ◽  
Silvi Rouskin
Keyword(s):  
Structure Analysis ◽  
Rna Structure ◽  
Viral Rna

RNA Structure Analysis by Chemical Probing with DMS and CMCT

2019 ◽  
pp. 209-223
Author(s):  
José M. Andrade ◽  
Ricardo F. dos Santos ◽  
Cecília M. Arraiano
Keyword(s):  
Structure Analysis ◽  
Rna Structure ◽  
Chemical Probing

scholarly journals Large-Scale in Vitro Transcription, RNA Purification and Chemical Probing Analysis

2018 ◽  
Vol 48 (5) ◽  
pp. 1915-1927 ◽  
Author(s):  
Fariha Kanwal ◽  
Ting Chen ◽  
Yunlon Zhang ◽  
Altaf Simair ◽  
Cai Rujie ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Rna Structure ◽  
In Vitro Transcription ◽  
Size Exclusion ◽  
Nucleoside Triphosphate ◽  
Separation Procedure ◽  
Rna Purification ◽  
Chemical Probing ◽  
Rna Interaction

Background/Aims: RNA elements such as catalytic RNA, riboswitch, microRNA, and long non coding RNA (lncRNA) play central roles in many cellular processes. Studying diverse RNA functions require large quantities of RNA for precise structure analysis. Current RNA structure and function studies can benefit from improved RNA quantity and quality, simpler separation procedure and enhanced accuracy of structural analysis. Methods: Here we present an optimized protocol for analyzing the structure of any RNA, including in vitro transcription, size-exclusion chromatography (SEC) based denaturing purification and improved secondary structure analysis by chemical probing. Results: We observed that higher Mg2+, nucleoside triphosphate (NTP) concentrations and longer reaction duration can improve the RNA yield from in vitro transcription, specifically for longer and more complicated constructs. Our improved SEC-based denaturing RNA purification effectively halved the experiment duration and labor without introducing any contaminant. Finally, this study increased the accuracy and signal-to-noise ratio (SNR) of selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing for analyzing RNA structure. Conclusion: Part or all of our modified method can improve almost any RNA-related study from protein-RNA interaction analysis to crystallography.

scholarly journals MicroRNA-based therapeutics in cardiovascular disease: screening and delivery to the target

2017 ◽  
Vol 46 (1) ◽  
pp. 11-21 ◽  
Author(s):  
David Mellis ◽  
Andrea Caporali
Keyword(s):  
Targeted Delivery ◽  
Transcriptional Regulators ◽  
Messenger Rnas ◽  
Biological Responses ◽  
Cardiovascular Biology ◽  
Non Coding Rnas ◽  
Novel Approaches ◽  
Cardiovascular Cells ◽  
Mirna Therapeutics ◽  
Mirna Targeting

MicroRNAs (miRNAs) are small non-coding RNAs of ∼22 nucleotides, which have increasingly been recognized as potent post-transcriptional regulators of gene expression. MiRNA targeting is defined by the complementarities between positions 2–8 of miRNA 5′-end with generally the 3′-untranslated region of target mRNAs (messenger RNAs). The capacity of miRNAs to simultaneously inhibit many different mRNAs allows for an amplification of biological responses. Hence, miRNAs are extremely attractive targets for therapeutic regulation in several diseases, including cardiovascular. Novel approaches are emerging to identify the miRNA functions in cardiovascular biology processes and to improve miRNA delivery in the heart and vasculature. In the present study, we provide an overview of current studies of miRNA functions in cardiovascular cells by the use of high-content screening. We also discuss the challenge to achieve a safe and targeted delivery of miRNA therapeutics in cardiovascular cells.

scholarly journals RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core

2013 ◽  
Vol 32 (21) ◽  
pp. 2804-2818 ◽  
Author(s):  
Maria Anokhina ◽  
Sergey Bessonov ◽  
Zhichao Miao ◽  
Eric Westhof ◽  
Klaus Hartmuth ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Rna Structure ◽  
Catalytic Core
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