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Related Concept Videos

RNA-seq03:21

RNA-seq

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.

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Updated: Jun 5, 2026

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

Nonparametric clustering for studying RNA conformations.

Xavier Le Faucheur1, Eli Hershkovits, Rina Tannenbaum

  • 1School of Electrical and Computer Engineering, Georgia Institute of Technology, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332-0535, USA. xavier@gatech.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|December 22, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a novel clustering method for RNA structures, analyzing conformational spaces using a Potts model. The technique accurately classifies RNA conformations, including base stacking geometries, aiding in understanding RNA function.

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Last Updated: Jun 5, 2026

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • The local conformation of RNA molecules is crucial for their catalytic and binding functions.
  • Analyzing RNA conformations is challenging due to numerous degrees of freedom, including torsion angles and interatomic distances.

Purpose of the Study:

  • To develop and apply an automated nearest-neighbor search method for clustering RNA conformational space.
  • To analyze single residue conformations, base pair geometries, and base stacking geometries.

Main Methods:

  • Utilized a nearest-neighbor search algorithm based on the statistical mechanical Potts model.
  • Applied the method to RNA conformational data, including single residue (4-7 torsion angles) and base pair (2D) geometries.
  • Investigated base stacking geometries, validating classifications with geometrical constraints.

Main Results:

  • The clustering method demonstrated a high degree of accuracy in classifying single residue and base pair conformations, closely matching known classifications.
  • New clusters for base stacking geometries were identified and characterized by their content and geometry.
  • The technique proved effective even without prior knowledge of the data space structure.

Conclusions:

  • The proposed Potts model-based clustering method is a powerful and largely automated tool for analyzing RNA conformational space.
  • This approach facilitates the discovery and classification of RNA structural motifs, including novel base stacking arrangements.
  • The findings contribute to a deeper understanding of structure-function relationships in RNA molecules.