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Related Concept Videos

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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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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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-seq03:21

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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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Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Improving RNA Branching Predictions: Advances and Limitations.

Svetlana Poznanović1, Carson Wood1, Michael Cloer1

  • 1School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634, USA.

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Optimizing RNA structure prediction involves refining thermodynamic models. A new algorithm finds optimal parameters for multiloop energetics, improving accuracy and enabling analysis of longer RNA sequences.

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Area of Science:

  • Computational biology
  • Biophysics
  • Bioinformatics

Background:

  • RNA secondary structure prediction relies on the Nearest Neighbor Thermodynamics Model.
  • Prediction accuracy varies, influenced by multiloop energetics and branching thermodynamics.
  • Previous studies identified a linear model for multiloop energetics as optimal.

Purpose of the Study:

  • To develop an algorithm for finding optimal parameters in RNA secondary structure prediction.
  • To enhance the accuracy of minimum free energy predictions.
  • To investigate the feasibility of analyzing longer RNA sequences.

Main Methods:

  • Developed a branch-and-bound algorithm to identify optimal thermodynamic parameters.
  • Performed parametric analysis on tRNA and 5S rRNA sequences.
  • Evaluated parameter set performance on training and testing datasets.

Main Results:

  • The branch-and-bound algorithm efficiently finds optimal parameters.
  • Previously determined ad hoc parameters show near-optimal accuracy for tRNA and 5S rRNA.
  • Cross-family parameter optimization is challenging due to competing parameter preferences.
  • Restricting unpaired nucleotide penalties improves analysis feasibility for longer sequences.

Conclusions:

  • Optimal parameterization significantly enhances RNA secondary structure prediction accuracy.
  • The developed algorithm provides a robust method for parameter optimization.
  • Findings support the use of reduced unpaired nucleotide penalties for analyzing longer RNA sequences.