To Validate A Nucleic Acid Structure

Question

[Angel]

Hi Biostars!

How can we validate a nucleic structure model using any bioinformatics tool? as in case of protein we use ramachandran plot to validate protein model.

Answer 1

[Neilfws]

As seidel suggested, software cannot validate a predicted structure. You need experimental data to do that.

What software can do is identify obvious problems with a model. You mention the Ramachandran plot. This will identify amino acid residues which appear to lie outside of the expected "allowed" conformations. However, a model with acceptable psi/phi values would not be validated - just plausible.

In terms of similar software for nucleic acids:

• MolProbity - a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes [paper | website]
• Phenix states that "comprehensive validation of nucleic acid structures is planned for a future release"
• Table 1 in this PDF, found via web search, is titled "Overview of nucleic acid structure validation software"

There are probably a few more.

[seidel]

Thanks neilfws. Well said.

[Angel]

Thanks neilfws ..

Answer 2

[seidel]

It depends on what kind of structure you want to validate. For small RNAs you can use NMR (nuclear magnetic resonance) to get structural information. For various RNA structures you can use primer extension methods whereby primers are designed to suspected single stranded regions, and the primers can be extended until a structured region is encountered. The results are viewed by running the extended fragments on sequencing gels. There are chemical probing methods that rely on the fact that RNA in single or double stranded regions is differentially sensitive to chemical modifying agents (hydroxyl radicals, DMS, etc.). The modifications can serve as fragmentation points, that can be observed on a gel. There are methods involving nuclease accessibility. Some of these same principles apply to DNA.

Oh look there's a wikipedia page (which is much better than my cloudy memory): http://en.wikipedia.org/wiki/Nucleic_acid_structure_determination

[Angel]

@seidel sorry i was asking for bioinformatics tool

[seidel]

Thanks for editing the question for clarity. For me, validation means go into the lab and measure something :)