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Nucleic Acid Structure

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...

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Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit

Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit

Published on: June 28, 2013

Solving nucleic acid structures by molecular replacement: examples from group II intron studies.

Marco Marcia¹, Elisabeth Humphris-Narayanan, Kevin S Keating

¹Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.

Acta Crystallographica. Section D, Biological Crystallography

|November 6, 2013

Summary

Molecular replacement is becoming crucial for analyzing nucleic acid crystal structures. This technique offers flexible strategies for understanding RNA and DNA folding, aiding cellular viability research.

Keywords:

RCrane RNA structure de novo structure design homology modeling long noncoding RNA nucleic acid sequence homology

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Last Updated: May 6, 2026

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Published on: June 28, 2013

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Area of Science:

Structural biology
Biochemistry
Molecular biology

Background:

Cellular viability relies on structured RNA molecules.
The function of nucleic acids is increasingly linked to their tertiary structures.
The number of determined nucleic acid crystal structures is rapidly growing.

Purpose of the Study:

To discuss strategies for selecting, creating, and refining molecular replacement search models for nucleic acids.
To highlight the potential of molecular replacement for phasing crystallographic data of nucleic acids.
To encourage further crystallographic studies on noncoding transcripts.

Main Methods:

Review of molecular replacement strategies for nucleic acid structure determination.
Application of examples from group II intron research.
Comparison of molecular replacement approaches for nucleic acids versus proteins.

Main Results:

Nucleic acids are suitable for molecular replacement phasing.
Molecular replacement searches for nucleic acids can be more flexible and sophisticated than for proteins.
Established strategies are effective for creating and refining search models.

Conclusions:

Molecular replacement is a valuable and evolving technique for nucleic acid crystallography.
The flexibility of molecular replacement for nucleic acids opens new avenues for structural studies.
Further research into noncoding transcripts using these methods is encouraged.