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Related Concept Videos

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...
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...
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

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Related Experiment Video

Updated: Jun 20, 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

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Evolutionary triplet models of structured RNA.

Robert K Bradley1, Ian Holmes

  • 1Biophysics Graduate Group, University of California, Berkeley, California, United States of America.

Plos Computational Biology
|August 29, 2009
PubMed
Summary

Reconstructing ancestral RNA structures is now possible with new bioinformatics methods. A novel transducer composition algorithm enables accurate RNA sequence and structure alignment for evolutionary studies.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Paleogenetics

Background:

  • Reconstructing ancestral RNA sequences and structures is a key challenge in paleogenetics.
  • Existing bioinformatics methods require enhancement for accurate phylogenetic analysis of RNA evolution.

Purpose of the Study:

  • To develop novel bioinformatics methods for the reconstruction and synthesis of ancestral RNAs.
  • To extend pairwise probabilistic models of RNA structural evolution to multiple sequences using phylogenetic trees.

Main Methods:

  • Developed a "transducer composition" algorithm based on computational linguistics and phylogenetic methods.
  • Generated multiple-sequence stochastic context-free grammars and employed dynamic programming for parsing.
  • Implemented algorithms for maximum likelihood (ML) alignment and ancestral structure inference.

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Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
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Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

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Chemical Triphosphorylation of Oligonucleotides
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Chemical Triphosphorylation of Oligonucleotides

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Related Experiment Videos

Last Updated: Jun 20, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

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Published on: December 9, 2022

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
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Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Published on: February 27, 2026

Chemical Triphosphorylation of Oligonucleotides
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Chemical Triphosphorylation of Oligonucleotides

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Main Results:

  • The transducer composition algorithm successfully extends pairwise RNA models to phylogenetic contexts.
  • Incorporating basepair structure significantly improved alignment accuracy.
  • Posterior-decoding heuristics offered a faster alternative to exact phylogenetic inference.

Conclusions:

  • The developed algorithms provide a robust framework for ancestral RNA reconstruction and structural alignment.
  • Basepair structure is crucial for accurate inference, with posterior-decoding offering computational advantages.
  • This work advances paleogenetics by enabling the study of ancient RNA molecules.