Base-Tetrad Swapping Results in Dimerization of RNA Quadruplexes: Implications for Formation of the I-Motif RNA Octaplex

Nucleic acids adopt different multistranded helical architectures to perform various biological functions. Here, we report a crystal structure of an RNA quadruplex containing "base-tetrad swapping" and bulged nucleotide at 2.1-Å resolution. The base-tetrad swapping results in a dimer of qu...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 103; no. 9; pp. 3130 - 3134
Main Authors Pan, Baocheng, Shi, Ke, Sundaralingam, Muttaiya
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 28.02.2006
National Acad Sciences
Subjects
Biochemistry
Biological Sciences
Biology
Biophysics
Crystal structure
Crystallography, X-Ray
Crystals
Dimerization
Dimers
DNA
Metal ions
Models, Molecular
Molecules
Nucleic Acid Conformation
Nucleotides
Proteins
Purines - chemistry
Pyrimidines - chemistry
Ribonucleic acid
RNA
RNA - chemistry
RNA - genetics
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Summary:Nucleic acids adopt different multistranded helical architectures to perform various biological functions. Here, we report a crystal structure of an RNA quadruplex containing "base-tetrad swapping" and bulged nucleotide at 2.1-Å resolution. The base-tetrad swapping results in a dimer of quadruplexes with an intercalated octaplex fragment at the 5' end junction. The intercalated base tetrads provide the basic repeat unit for constructing a model of intercalated RNA octaplex. The model we obtained shows fundamentally different characteristics from duplex, triplex, and quadruplex. We also observed two different orientations of bulged uridine residues that are related to the interaction with surroundings. This structural evidence reflects the conformational flexibility of bulged nucleotides in RNA quadruplexes and implies the potential roles of bulged nucleotides as recognition and interaction sites in RNA-protein and RNA-RNA interactions.
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Author contributions: B.P. and M.S. designed research; B.P. and K.S. performed research; B.P., K.S., and M.S. analyzed data; and B.P. wrote the paper.
Edited by Douglas C. Rees, California Institute of Technology, Pasadena, CA, and approved January 3, 2006
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0507730103