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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.
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Updated: Oct 14, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

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Refinement of RNA Structures Using Amber Force Fields.

Jonathon G Gray¹, David A Case¹

¹Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.

|November 8, 2021

Summary

This summary is machine-generated.

This study introduces force-field energy gradients to refine atomic models of nucleic acids, improving structural details like torsion angles and hydrogen bonds. This method enhances atomic models derived from X-ray diffraction data.

Keywords:

RNA crystallographic refinement force fields

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Area of Science:

Structural Biology
Biophysics
Computational Chemistry

Background:

Atomic models for nucleic acids from X-ray diffraction offer insights but can have structural ambiguities.
Conventional refinement uses geometric restraints based on small molecule data, which may not fully represent nucleic acid environments.

Purpose of the Study:

To explore the replacement of traditional geometric restraints with force-field energy gradients for refining nucleic acid atomic models.
To evaluate the impact of including solvent effects, such as water molecules and ions, on model refinement.

Main Methods:

Utilized force-field energy gradients, including integral equation models for solvent effects, to refine atomic models.
Compared conventional refinement with force-field based refinement for 22 RNA crystal structures (1.1–3.6 Å resolution).

Main Results:

Force-field refinement improved torsion angles and hydrogen-bonding interactions in nucleic acid models.
Unfavorable atomic clashes were significantly reduced.
Agreement with observed X-ray diffraction scattering intensities was maintained or improved.
Solvent screening of charge-charge interactions was found to be important in crowded nucleic acid crystal environments.

Conclusions:

Force-field based refinement offers an improved approach for developing accurate atomic models of nucleic acids from X-ray diffraction data.
Accounting for solvent effects is crucial for precise structural modeling of nucleic acids in crystalline states.
This method enhances the quality of structural models, leading to better understanding of nucleic acid structure and function.