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Related Concept Videos

RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Nucleic Acid Structure01:25

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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RNA Stability01:53

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Bacterial RNA Polymerase00:43

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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Sequence Design Using RNAstructure.

Mingyi Zhu1, David H Mathews2

  • 1Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)
|September 23, 2024
PubMed
Summary
This summary is machine-generated.

This study introduces RNA design software for creating specific RNA structures. It addresses challenges in RNA sequence design, offering tools for both structured and unstructured RNA.

Keywords:
Genetic algorithmInverse foldingNonstructural designRNA structure design

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • RNA's known role in protein expression has expanded to include catalysis and gene regulation via noncoding RNA.
  • Recent research highlights the importance of specific RNA structures for various applications.
  • RNA design software development is advancing, driven by RNA secondary structure prediction methods.

Purpose of the Study:

  • To provide protocols for RNA sequence design software.
  • To address challenges in designing RNA sequences with specific secondary structures.
  • To introduce tools for both structured and unstructured RNA design.

Main Methods:

  • Utilized the RNAstructure package, specifically the "Design" tool for structured RNA.
  • Employed the "orega" tool for unstructured RNA sequence design.
  • Focused on protocols for in silico RNA design.

Main Results:

  • Presented protocols for two RNA design software tools.
  • Facilitated the design of RNA sequences meeting specific secondary structure requirements.
  • Addressed computational challenges associated with RNA secondary structure design.

Conclusions:

  • RNA design software is crucial for experimental and therapeutic applications.
  • The "Design" and "orega" tools offer solutions for complex RNA sequence design.
  • Overcoming NP-hard computational challenges is key to advancing RNA design.