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Related Concept Videos

RNA Structure01:23

RNA Structure

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...
RNA Structure01:23

RNA Structure

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...
RNA Structure01:19

RNA Structure

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.
Different Types of RNA Have the Same Basic Structure
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...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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 has a double-helix structure. The...
DNA Helicases00:55

DNA Helicases

DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...

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Related Experiment Videos

Predicting helical coaxial stacking in RNA multibranch loops.

Rahul Tyagi1, David H Mathews

  • 1Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.

RNA (New York, N.Y.)
|May 18, 2007
PubMed
Summary

Predicting RNA coaxial stacking using free energy minimization shows moderate accuracy. Optimizing with partition function calculations and a probability threshold improves prediction of direct helix stacking over noncanonical interactions.

Related Experiment Videos

Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • RNA coaxial stacking is crucial for RNA structure and function.
  • Accurate prediction of RNA secondary structures is essential for understanding RNA-protein interactions and catalytic activity.
  • Nearest-neighbor parameters are commonly used to model RNA thermodynamics.

Purpose of the Study:

  • To evaluate the accuracy of predicting RNA coaxial stacking using free energy minimization with nearest-neighbor parameters.
  • To assess the utility of partition function calculations for improving coaxial stack predictions.
  • To investigate factors influencing prediction accuracy, such as helix separation and loop complexity.

Main Methods:

  • Utilized free energy minimization to predict RNA coaxial stacking configurations.
  • Employed nearest-neighbor thermodynamic parameters for energy calculations.
  • Performed partition function calculations to determine the probability of stacking configurations.
  • Compared predicted structures with experimentally determined crystal structures.
  • Analyzed prediction accuracy based on probability thresholds and loop complexity.

Main Results:

  • The lowest free energy configuration achieved 58.2% positive predictive value (PPV) and 65.7% sensitivity compared to crystal structures.
  • A probability threshold of 0.7, derived from partition function calculations, yielded 66.7% PPV and 51.9% sensitivity.
  • Direct coaxial stacks (unseparated helices) were predicted with higher accuracy (74.0% PPV, 66.1% sensitivity) than those mediated by noncanonical base pairs (55.9% PPV, 36.5% sensitivity).
  • Prediction accuracy did not correlate with multibranch loop complexity.

Conclusions:

  • Free energy minimization using nearest-neighbor parameters offers a baseline for predicting RNA coaxial stacking.
  • Partition function calculations and probability thresholds enhance prediction accuracy, particularly for direct helix stacking.
  • The method's performance is significantly influenced by the nature of helix separation and base pairing within loops.