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Nucleic Acids02:43

Nucleic Acids

49.9K
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.
DNA and RNA
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.
DNA and RNA
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 Structure01:23

RNA Structure

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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...
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From DNA to Protein03:06

From DNA to Protein

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The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
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DNA Isolation01:34

DNA Isolation

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DNA from cells is required for many biotechnology and research applications, such as molecular cloning. To remove and purify DNA from cells, researchers use various methods of DNA extraction. While the specifics of different protocols may vary, some general concepts underlie the process of DNA extraction.
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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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Updated: Jan 24, 2026

High-Density DNA and RNA microarrays - Photolithographic Synthesis, Hybridization and Preparation of Large Nucleic Acid Libraries
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HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures.

Jiahua He1, Jun Wang1, Huanyu Tao1

  • 1Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China.

Nucleic Acids Research
|May 23, 2019
PubMed
Summary

HNADOCK is a new web server for modeling 3D structures of nucleic acid (NA)-NA complexes. It accurately predicts RNA-RNA and DNA-DNA interactions, aiding in understanding cellular mechanisms.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Nucleic acid (NA) interactions, including RNA-RNA and DNA-DNA, are fundamental to cellular processes like gene regulation and protein synthesis.
  • Understanding the 3D structures of these NA complexes is critical for elucidating their molecular mechanisms.

Purpose of the Study:

  • To develop and present HNADOCK, a user-friendly web server for nucleic acid-nucleic acid docking.
  • To model 3D complex structures between two RNAs or two DNAs, accepting sequence and/or structure inputs.

Main Methods:

  • HNADOCK accepts sequence and structure inputs for RNA-RNA docking, and structure inputs for DNA-DNA docking.
  • Performance was evaluated using a benchmark of 60 RNA-RNA complexes, comparing HNADOCK against the SimRNA algorithm.
  • The impact of incorporating inter-RNA base-pairing information on docking accuracy was assessed.

Main Results:

  • HNADOCK achieved a 71.7% success rate for top 10 predictions with structure inputs, outperforming SimRNA (58.3%).
  • For sequence inputs, HNADOCK showed 83.3% success with bound RNA templates and 53.3% without.
  • Including inter-RNA base-pairing information significantly improved docking accuracy, particularly for top predictions.

Conclusions:

  • HNADOCK is an effective and efficient web server for predicting nucleic acid complex structures.
  • The tool facilitates research into RNA-RNA and DNA-DNA interactions, crucial for understanding cellular functions.
  • HNADOCK offers a valuable resource for the scientific community, with rapid computation times (approx. 10 minutes).