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Updated: Aug 5, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.

Xiaoli Chen¹, Shaojie Zhang¹

¹Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.

Nucleic Acids Research

|March 29, 2023

Summary

This summary is machine-generated.

Researchers developed CircularSTAR3D, a novel tool for analyzing non-coding RNA 3D structures. It identifies conserved substructures, even with rearranged sequences, enhancing functional analysis and complementing existing RNA alignment methods.

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Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Area of Science:

Structural Biology
Bioinformatics
Computational Biology

Background:

Non-coding RNA functions are intrinsically linked to their three-dimensional (3D) structures.
Comparing RNA 3D structures is essential for understanding their biological roles.
Existing structural alignment tools often fail to detect functional similarities between RNAs with permuted sequence orders.

Purpose of the Study:

To address the limitation of current RNA 3D structural alignment tools.
To define and computationally solve the RNA 3D structure circular matching problem.
To introduce CircularSTAR3D, a software tool for identifying circular RNA substructures.

Main Methods:

Definition of the RNA 3D structure circular matching problem.
Development of the CircularSTAR3D software.
Identification of conserved stacks to pinpoint internal loops and multiloops.
Iterative local extension to delineate entire circular matched substructures.

Main Results:

Computational experiments confirmed the prevalence of circular matching in RNA structures.
CircularSTAR3D successfully detected conserved substructures missed by conventional alignment tools.
The tool identified conserved motifs and structures across diverse riboswitches and ribozymes.

Conclusions:

Circular matching represents a significant, previously underappreciated aspect of RNA 3D structure.
CircularSTAR3D offers a novel approach to RNA structural comparison and functional analysis.
The tool is expected to be a valuable addition to the suite of RNA 3D structure analysis techniques.