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Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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Related Experiment Video

Updated: Mar 11, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

RNA Secondary Structure Prediction.

David H Mathews¹, Douglas H Turner¹, Richard M Watson¹

¹University of Rochester, Rochester, New York.

Current Protocols in Nucleic Acid Chemistry

|December 3, 2016

Summary

This summary is machine-generated.

This study provides protocols for predicting RNA secondary structure and oligonucleotide binding sites using the RNAstructure software. These methods enable the analysis of RNA folding and interactions for biological research.

Keywords:

RNA folding RNA secondary structure prediction binding affinity free energy minimization partition function thermodynamics

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Published on: March 12, 2012

Area of Science:

Computational Biology
Bioinformatics
Molecular Biology

Background:

RNA secondary structure prediction is crucial for understanding RNA function.
Accurate prediction methods are needed for analyzing RNA-ligand interactions.
Computational tools simplify complex RNA structure analysis.

Purpose of the Study:

To provide protocols for RNA secondary structure prediction using RNAstructure.
To present methods for identifying high-affinity oligonucleotide binding sites on structured RNAs.
To offer user-friendly computational tools for RNA analysis.

Main Methods:

Utilizing the RNAstructure desktop program for minimum free energy and suboptimal structure prediction.
Employing the RNAstructure Web server for accessible RNA structure predictions.
Implementing algorithms to predict oligonucleotide binding sites on RNA targets.

Main Results:

Successful prediction of minimum free energy RNA secondary structures.
Generation of sets of suboptimal RNA structures with comparable free energies.
Identification of potential high-affinity binding sites for oligonucleotides on structured RNAs.

Conclusions:

RNAstructure provides effective tools for RNA secondary structure prediction.
The software facilitates the analysis of RNA-oligonucleotide interactions.
These protocols enhance the study of RNA folding and binding in molecular biology.