What is
NA3DMotif
Contributions
- Analysis of Internal Loops and Bulges: Mr. Teppei Chinone (Sophia University)
- Analysis of Hairpin Loops: Ms. Momo Okada (Sophia University)
- Analysis of G4 DNAs: Ms. Aya Koshizuka (Sophia University)
References
- Molmil (molecular viewer): Bekker GJ, Nakamura H, Kinjo AR. "Molmil: a molecular viewer for the PDB and beyond." Cheminform., 8, 42. (2016). doi: 10.1186/s13321-016-0155-1
- RNAcentral (database): RNAcentral Consortium. "RNAcentral 2021: secondary structure integration, improved sequence search and new member databases." Nucleic Acids Res., 49, D212-D220. (2019). doi: 10.1093/nar/gkaa921
- RNAPDBee (2D drawing): Zok T, Antczak M, Zurkowski M, Popenda M, Blazewicz J, Adamiak RW, Szachniuk M. "RNApdbee 2.0: multifunctional tool for RNA structure annotation." Nucleic Acids Res. 46(W1), W30-W35 (2018). doi: 10.1093/nar/gky314.
- Structure of ribosome (coordinate file): Noeske J, Wasserman MR, Terry DS, Altman RB, Blanchard SC, Cate JH. "High-resolution structure of the Escherichia coli ribosome." Nat. Struct. Mol. Biol., 22, 336-341. (2015). doi: 10.1038/nsmb.2994
Nucleic Acids, such as single-stranded RNAs and repetitive DNAs, are now known to regulate various biological phenomena by partially and transiently folding into complex 3D structures. Recently, the challenge of predicting 3D structures of RNAs from their 1D nucleotide sequences has been advanced, and research into the development of drugs targeting specific nucleic acid structural motifs is also underway.
By the way, have you ever observed structures of nucleic acids with your own eyes?　Please DO NOT rely on artificial intelligence for observation! To truly understand the 3D structures of nucleic acids, it is very important to observe them one by one carefully and deeply with your own eyes.
RNA structural motifs (coming soon...)
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Bulge
A structural motif where one or more unpaired bases appear on only one strand within a double-stranded region, lacking any base-pairing partner on the opposite strand.
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Internal Loop
A structural motif where base mismatches are present on both strands within a double-stranded region, often allowing for non-Watson-Crick base pairing.
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Hairpin Loop
A structural motif where a single strand folds back on itself, forming a double-stranded stem with paired bases and a loop of unpaired bases at the tip.