Generating idealized A-form RNA structures of generic sequence

Over the years, the fiber utility program has become a handy way to generate standard B-DNA and A-DNA structures, as evident from citations to 3DNA. Nevertheless, the currently collected 55 experimental fiber models, comprehensive as they are, do not include one for canonical double-stranded (ds) RNA or single-stranded (ss) RNA structures of generic A/C/G/U sequence.

This situation is best illustrated by a recent article by Charles Brooks and Hashim Al-Hashimi and their co-workers, titled Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch [Nucleic Acids Research, 40(3) 1345–1355 (2012)] , where they wrote:

Idealized A-form structures were constructed using Insight II (Molecular Simulations, Inc.) correcting the propeller twist angles from +15° to –15° using an in-house program, as previously described (47). The complementary strand was removed and the resulting ssRNA used in NMR data analysis. B-form helices were constructed using W3DNA (48).

As of 3DNA v2.1, however, that’s no longer the case: now the fiber utility provides direct support for generating idealized dsRNA or ssRNA structures of arbitrary A/C/G/U sequence. As always, the new functionality can be best illustrated with examples. Let’s build ssRNAs of the wild-type (5’-AUAAAAAACUAA-3’) and A29C mutated form (5’-AUAACAAACUAA-3’) used in the work cited above:

fiber -r -s -seq=AUAAAAAACUAA wt-12nt.pdb
fiber -r -s -seq=AUAACAAACUAA mt-12nt.pdb

Here the -r option is for RNA, -s for a ss structure, and -seq for the specific base sequence. The generated ssRNA structure for the wild-type sequence is named wt-12nt.pdb, and that for the mutated sequence named mt-12nt.pdb.

Note that the new RNA model is based on Struther Arnott’s work of fiber A-DNA from calf thymus (#1 in the list). The dsRNA, as its dsDNA counterpart, has a helical twist of 32.7° and a helical rise of 2.548 Å. Relevant to the above citation, here the propeller twist angle of each base pair is –10.5°, a negative value similar to that observed in high-resolution x-ray crystal structures. Furthermore, you can easily verify the three numbers with the following commands:

fiber -r -seq=AUAAAAAACUAA wt-12nt.pdb
find_pair wt-12nt.pdb stdout | analyze stdin

In summary, it is very easy to generate canonical RNA structures with the revised fiber command. Through its integrated analysis routine, 3DNA can also be used to check structural features of the resultant RNA models. Moreover, as mentioned in the opening post What can 3DNA do for RNA structures? on the forum, 3DNA has much to offer in the filed of RNA structural bioinformatics.





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