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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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RNA Structure01:23

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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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DNA Topoisomerases02:02

DNA Topoisomerases

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Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
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Crystal Field Theory - Tetrahedral and Square Planar Complexes02:46

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Tetrahedral Complexes
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Cycloheptatriene is a neutral monocyclic unsaturated hydrocarbon that consists of an odd number of carbon atoms and an intervening sp3 carbon in the ring. The three double bonds in the ring correspond to 6 π electrons, which is a Huckel number, and therefore satisfies the criteria of 4n + 2 π electrons. However, the intervening sp3 carbon disrupts the continuous overlap of p orbitals. As a result, cycloheptatriene is not aromatic.
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Nucleic Acid Structure01:25

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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.
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Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping
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Topology-based classification of tetrads and quadruplex structures.

Mariusz Popenda1, Joanna Miskiewicz2, Joanna Sarzynska1

  • 1Department of Structural Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland.

Bioinformatics (Oxford, England)
|October 8, 2019
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Summary

Researchers developed a new method to classify and identify nucleic acid quadruplexes, including non-canonical forms, advancing their study for therapeutic applications.

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Area of Science:

  • Bio-science
  • Structural Biology
  • Bioinformatics

Background:

  • Quadruplexes are crucial tertiary motifs in nucleic acids involved in various biological processes.
  • They hold significant therapeutic potential for anticancer and neurological disease treatments.
  • Current analysis methods for quadruplexes are limited to canonical motifs based on sequence or 3D structure.

Purpose of the Study:

  • To develop a novel classification system for tetrads and quadruplexes based on secondary structure topology.
  • To implement an automated method for recognizing quadruplex types, including non-canonical forms.
  • To statistically analyze the occurrence of these motifs in experimentally determined nucleic acid structures.

Main Methods:

  • Analysis of tetrads and quadruplexes in the Protein Data Bank.
  • Development of new dot-bracket and arc representations for secondary structure topology.
  • Implementation of an automated recognition method based on a new classification system.
  • Statistical analysis of identified quadruplex motifs.

Main Results:

  • A novel classification for tetrads and quadruplexes was defined, accommodating both canonical and non-canonical structures.
  • An automated method was successfully implemented to recognize and classify these motifs.
  • Statistical analysis provided insights into the distribution of quadruplexes within nucleic acid structures.

Conclusions:

  • The new classification and automated method enhance the analysis of diverse quadruplex structures.
  • This work facilitates further research into the biological roles and therapeutic applications of quadruplexes.
  • The findings contribute to a deeper understanding of nucleic acid structural diversity.