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Related Concept Videos

RNA Structure01:19

RNA Structure

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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.
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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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Viruses with RNA Genomes

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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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Size and Structure of Viral Genomes01:26

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Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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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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Related Experiment Video

Updated: Nov 13, 2025

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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HIV-1 genomic RNA U3 region forms a stable quadruplex-hairpin structure.

Chelsea Harpster1, Elaina Boyle1, Karin Musier-Forsyth1

  • 1Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.

Biophysical Chemistry
|March 13, 2021
PubMed
Summary

The HIV-1 LTR-III RNA forms a stable quadruplex-hairpin structure, unlike its DNA counterpart. This RNA structure

Keywords:
DNAHIV-1Quadruplex topologyQuadruplexesRNAThermodynamics

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Virology

Background:

  • The human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) U3 promoter region can form G-quadruplex structures.
  • Previous studies identified LTR-III as the most stable G-quadruplex in vitro, with NMR revealing a quadruplex-hairpin DNA structure.
  • The formation and role of this hairpin in RNA G-quadruplexes remain uncharacterized.

Purpose of the Study:

  • To investigate the formation of the hairpin structure in the LTR-III RNA element.
  • To characterize the role of the hairpin in the structure and stability of RNA G-quadruplexes.
  • To compare the stability and structural properties of RNA and DNA LTR-III G-quadruplexes.

Main Methods:

  • Optical spectroscopy techniques were employed to study RNA and DNA structures.
  • Thermodynamic analyses were performed to assess structural stability.
  • Comparative studies were conducted on wild-type and variant RNA sequences.

Main Results:

  • Wild-type LTR-III RNA forms a stable, monomolecular quadruplex with parallel topology.
  • The RNA quadruplex incorporates a hairpin loop element within its structure.
  • Compared to DNA, the RNA LTR-III structures exhibit greater stability and homogeneity.

Conclusions:

  • The RNA quadruplex-hairpin structure is more stable and homogeneous than the analogous DNA structure.
  • The hairpin loop element plays a crucial role in the stability of the RNA quadruplex.
  • The enhanced stability of the RNA quadruplex-hairpin suggests its potential as a therapeutic target for HIV-1.