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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
DNA...
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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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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.
Two regions of electron density in a diatomic...
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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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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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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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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...
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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.

Rodrigo Galindo-Murillo1, Christina Bergonzo1, Thomas E Cheatham1

  • 1Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah.

Current Protocols in Nucleic Acid Chemistry
|February 11, 2014
PubMed
Summary

This study introduces molecular modeling for analyzing nucleic acid structures. It covers computer simulations, static models, graphics, energy calculations, and 3D structure characterization.

Keywords:
experimental determination of structurefolding and conformational changenucleic acid chemistrynucleic acid structure and foldingstructural analysis of biomolecules

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Molecular modeling is crucial for understanding complex biological molecules.
  • Nucleic acid structure analysis benefits from computational approaches.
  • This unit is the first in a series on nucleic acid structure analysis using molecular modeling.

Purpose of the Study:

  • To provide an overview of computer simulations for nucleic acids.
  • To introduce fundamental concepts in molecular modeling of nucleic acids.
  • To lay the groundwork for advanced analysis in subsequent units.

Main Methods:

  • Overview of static structure models for nucleic acids.
  • Introduction to computational graphics and energy models.
  • Methods for generating initial molecular models.
  • Techniques for characterizing three-dimensional nucleic acid structures.

Main Results:

  • Establishes a foundational understanding of nucleic acid computer simulation.
  • Details key components: static models, graphics, and energy potentials.
  • Explains the process of initial model generation.
  • Outlines methods for 3D structure characterization.

Conclusions:

  • Computer simulation and molecular modeling are essential tools for nucleic acid structure analysis.
  • This unit provides a comprehensive introduction to the core concepts.
  • The methods discussed are foundational for further exploration of nucleic acid dynamics and interactions.