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Related Concept Videos

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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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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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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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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DCJ-RNA - double cut and join for RNA secondary structures.

Ghada H Badr1,2, Haifa A Al-Aqel3

  • 1IRI- The City of Scientific Research and Technological Applications, University and Research District, P. O. 21934, New Borg Alarab, Alexandria, Egypt. badrghada@hotmail.com.

BMC Bioinformatics
|October 27, 2017
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Summary
This summary is machine-generated.

This study introduces a novel algorithm for analyzing genome rearrangements based on RNA secondary structures, not just sequences. This method efficiently calculates the minimum operations needed to compare and align RNA structures, aiding evolutionary and functional studies.

Keywords:
DCJGenome RearrangementRNA Secondary StructureSimilarity MeasureSorting Scenario

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Genome rearrangements drive evolution and create diverse genome architectures.
  • Existing algorithms focus on sequence-based genome rearrangements, not secondary structures.
  • RNA secondary structures preserve genome functionality, making them crucial for evolutionary analysis.

Purpose of the Study:

  • To propose an efficient algorithm for comparing RNA secondary structures based on rearrangement operations.
  • To enable the description of evolutionary scenarios using secondary structures instead of sequences.
  • To facilitate researchers' comparison of two ribonucleic acid (RNA) secondary structures.

Main Methods:

  • Development of the double cut and join for RNA secondary structures (DCJ-RNA) algorithm.
  • Application of the DCJ-RNA algorithm to real biological datasets.
  • Analysis of rearrangement operations on RNA secondary structures.

Main Results:

  • The DCJ-RNA algorithm efficiently counts the minimum rearrangement operations between RNA secondary structures.
  • The algorithm reports optimal scenarios to enhance structural similarity.
  • Validation using real datasets demonstrates the algorithm's effectiveness.

Conclusions:

  • The DCJ-RNA algorithm calculates structural distances and suggests rearrangement scenarios.
  • It identifies the minimum operations to align RNA secondary structures.
  • This facilitates the identification of common functionalities across different species.