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Nucleic Acids Research Advance Access originally published online on October 21, 2008
Nucleic Acids Research 2008 36(20):6620-6632; doi:10.1093/nar/gkn669
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Nucleic Acids Research, 2008, Vol. 36, No. 20 6620-6632
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Novel mechanism of hexamer ring assembly in protein/RNA interactions revealed by single molecule imaging

Feng Xiao, Hui Zhang and Peixuan Guo*

Department of Biomedical Engineering, College of Engineering/College of Medicine, University of Cincinnati, Cincinnati, OH 45221, USA

*To whom correspondence should be addressed. Tel: +1 513 558 0041; Fax: +1 513 558 6079; Email: guopn{at}ucmail.uc.edu

Received June 26, 2008. Revised September 22, 2008. Accepted September 22, 2008.

Many nucleic acid-binding proteins and the AAA+ family form hexameric rings, but the mechanism of hexamer assembly is unclear. It is generally believed that the specificity in protein/RNA interaction relies on molecular contact through a surface charge or 3D structure matching via conformational capture or induced fit. The pRNA of bacteriophage phi29 DNA-packaging motor also forms a ring, but whether the pRNA ring is a hexamer or a pentamer is under debate. Here, single molecule studies elucidated a mechanism suggesting the specificity and affinity in protein/RNA interaction relies on pRNA static ring formation. A combined pRNA ring-forming group was very specific for motor binding, but the isolated individual members of the ring-forming group bind to the motor nonspecifically. pRNA did not form a ring prior to motor binding. Only those RNAs that formed a static ring, via the interlocking loops, stayed on the motor. Single interlocking loop interruption resulted in pRNA detachment. Extension or reduction of the ring circumference failed in motor binding. This new mechanism was tested by redesigning two artificial RNAs that formed hexamer and packaged DNA. The results confirmed the stoichiometry of pRNA on the motor was the common multiple of two and three, thus, a hexamer.


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