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Nucleic Acids02:43

Nucleic Acids

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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids09:04

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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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Structural Properties of Small Single-Stranded Circular Nucleic Acids.

Parth Chaturvedi1, Lela Vuković1

  • 1Department of Chemistry and Biochemistry , University of Texas at El Paso , El Paso , Texas 79968 , United States.

The Journal of Physical Chemistry. B
|September 10, 2019
PubMed
Summary

Circular nucleic acids (circNAs) offer stability for biomedical uses. Molecular dynamics simulations reveal circNAs

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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Chemistry

Background:

  • Nucleic acids are prone to degradation in biomedical applications.
  • Circular nucleic acids (circNAs) are a strategy to enhance stability.
  • Understanding circNA structure and dynamics is crucial for their application.

Purpose of the Study:

  • To investigate the structural properties of flexible, non-base-paired circNAs.
  • To analyze the impact of circular geometry on DNA and RNA structures.
  • To explore the behavior of circNAs in aqueous solution at physiological conditions.

Main Methods:

  • Microsecond-long molecular dynamics simulations.
  • Analysis of conformational ensembles for circular DNA (circDNA) and RNA (circRNA).
  • Examination of molecules ranging from 6 to 48 nucleotides.

Main Results:

  • Circular DNA (circDNA) exhibits greater bending and flexibility than circular RNA (circRNA).
  • Distinct arrangements of phosphate backbones and bases were observed between circDNA and circRNA.
  • Small circNAs (6-8 nucleotides) sequester counterions, forming crown ether-like structures.
  • At millimolar concentrations, circNAs aggregate into linear chain shapes.

Conclusions:

  • The circular geometry significantly influences circNA structure and dynamics.
  • CircNAs display unique counterion sequestration and aggregation behaviors compared to linear counterparts.
  • These findings provide insights into the fundamental properties of circNAs for potential applications.