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Related Concept Videos

RNA Structure01:23

RNA Structure

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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. 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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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.
DNA Structure
DNA has a double-helix structure. The...
Point and Frameshift Mutations01:30

Point and Frameshift Mutations

Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
Mutations01:35

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

A two-dimensional mutate-and-map strategy for non-coding RNA structure.

Wipapat Kladwang1, Christopher C VanLang, Pablo Cordero

  • 1Department of Biochemistry, Stanford University, Stanford, California 94305, USA.

Nature Chemistry
|November 24, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new "mutate-and-map" method to accurately determine RNA structures. This technique precisely maps RNA base-pairing, aiding genetic regulation and protein synthesis research.

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Non-coding RNAs (ncRNAs) are crucial for genetic regulation and protein synthesis.
  • Accurate determination of ncRNA secondary and tertiary structures is essential but challenging.
  • Existing chemical and computational methods have limitations in RNA structure prediction.

Purpose of the Study:

  • To develop and validate a novel strategy for accurate RNA base-pair inference.
  • To determine secondary and tertiary structures of various non-coding RNAs.
  • To investigate RNA structure-function relationships, including ligand-binding cooperativity.

Main Methods:

  • Coupling systematic mutagenesis with high-throughput chemical mapping ('mutate-and-map').
  • Application to ribosomal RNA, ribozymes, and riboswitches, including a six-RNA benchmark.
  • Integration with Rosetta/FARFAR algorithm for 3D structure modeling.

Main Results:

  • Achieved accurate base-pair inference for RNA domains.
  • Secondary structures agreed with crystallography (2% helix error rate) on a challenging benchmark.
  • Generated nucleotide-resolution 3D models of an adenine riboswitch (5.7 Å RMSD).
  • Enabled testing of an interdomain helix-swap hypothesis in a glycine riboswitch.

Conclusions:

  • The 'mutate-and-map' strategy provides a robust method for RNA secondary structure determination.
  • This approach facilitates the inference of tertiary contacts and 3D RNA models.
  • Establishes a powerful 2D chemical strategy for understanding ncRNA structure and function.