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Related Concept Videos

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...
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...
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Unit Cells01:18

Unit Cells

A crystal's internal structure is an orderly array of atoms, ions, or molecules, and the details of this array significantly influence the solid's properties. In a crystal, periodically repeating 'structural motifs' - which could be atoms, molecules, or groups thereof - create a 'space lattice.' This is essentially a three-dimensional, infinite array of points, each surrounded by its neighbors in an identical way, forming the basic structure of the crystal.A 'unit cell' is a theoretical...

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Related Experiment Video

Updated: Jul 2, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

RNA structure alignment by a unit-vector approach.

Emidio Capriotti1, Marc A Marti-Renom

  • 1Bioinformatics and Genomics Department, Structural Genomics Unit, Centro de Investigación Príncipe Felipe, Valencia, Spain.

Bioinformatics (Oxford, England)
|August 12, 2008
PubMed
Summary
This summary is machine-generated.

A new algorithm, SARA, aligns RNA structures using a unit-vector approach. This method improves RNA structure comparison and aids in functional annotation, outperforming existing tools.

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Last Updated: Jul 2, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

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Published on: April 26, 2013

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • RNA's biological activity is determined by its 3D structure, not just its sequence.
  • Accurate RNA structure comparison is crucial for functional annotation.
  • Existing methods for RNA structure comparison need improvement in accuracy and automation.

Purpose of the Study:

  • To introduce a novel algorithm for RNA structure alignment.
  • To implement this algorithm in the SARA program for pairwise RNA structure comparison.
  • To provide statistically significant RNA structure alignments.

Main Methods:

  • Developed a new RNA structure alignment algorithm based on a unit-vector approach.
  • Implemented the algorithm in the SARA program.
  • Benchmarked SARA against the ARTS program using 1275 non-redundant alignments.

Main Results:

  • SARA provides general applicability, even without secondary structure information.
  • SARA identified approximately 6% more alignments than ARTS, with significant structural superposition.
  • SARA achieved >60% accuracy in assigning deep SCOR functional classifications.

Conclusions:

  • SARA offers an accurate and automatic method for RNA structure comparison.
  • The SARA program enhances the functional annotation of RNA molecules.
  • SARA is freely available, facilitating broader research applications.