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Related Concept Videos

Nucleic Acid Structure01:25

Nucleic Acid Structure

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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
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Molecular Models02:00

Molecular Models

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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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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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Molecular Shapes01:18

Molecular Shapes

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Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
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DNA as a Genetic Template02:05

DNA as a Genetic Template

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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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Analyzing and Building Nucleic Acid Structures with 3DNA
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Analyzing and Building Nucleic Acid Structures with 3DNA

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Molecular modeling of nucleic Acid structure: setup and analysis.

Rodrigo Galindo-Murillo1, Christina Bergonzo, Thomas E Cheatham

  • 1Vanderbilt University; Rega Institute for Medical Research; Hokkaido University; Rasayan Inc.

Current Protocols in Nucleic Acid Chemistry
|January 22, 2015
PubMed
Summary

This unit guides researchers in molecular modeling of nucleic acids. It covers selecting force fields, setting up simulations in explicit solvents, and analyzing molecular dynamics trajectories for accurate results.

Keywords:
force field reviewnucleic acid chemistrynucleic acid structure and foldingsampling methodssimulation protocolssimulation setup and analysis

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Molecular Biology

Background:

  • Molecular modeling is crucial for understanding nucleic acid structure and function.
  • Accurate simulations require careful selection of parameters and methodologies.

Purpose of the Study:

  • To provide a comprehensive guide for molecular modeling of nucleic acids.
  • To address key challenges in simulating nucleic acids in explicit solvents.
  • To detail methods for setting up, running, and analyzing molecular dynamics simulations.

Main Methods:

  • Selection of appropriate molecular mechanics force fields.
  • System setup and equilibration for molecular dynamics (MD) or Monte Carlo (MC) simulations.
  • Analysis of molecular dynamics trajectories.

Main Results:

  • Provides a framework for choosing suitable force fields.
  • Outlines protocols for preparing and equilibrating complex biological systems.
  • Offers guidance on interpreting simulation data.

Conclusions:

  • This unit equips researchers with essential knowledge for accurate nucleic acid modeling.
  • Effective molecular modeling enhances the study of DNA and RNA dynamics.
  • The described methods facilitate deeper insights into nucleic acid behavior.