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J. Biol. Chem., Vol. 276, Issue 35, 32575-32584, August 31, 2001

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Three-dimensional Interaction of Phi29 pRNA Dimer Probed by Chemical Modification Interference, Cryo-AFM, and Cross-linking^*

Yahya Mat-Arip^§¶, Kyle Garver^¶, Chaoping Chen^§§, Sitong Sheng, Zhifeng Shao, and Peixuan Guo^**

From the  Department of Pathobiology, Purdue University, West Lafayette, Indiana 47907 and the  Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908

Six pRNAs (p for packaging) of bacterial virus phi29 form a hexamer complex that is an essential component of the viral DNA translocating motor. Dimers, the building block of pRNA hexamer, assemble in the order of dimer  tetramer  hexamer. The two-dimensional structure of the pRNA monomer has been investigated extensively; however, the three-dimensional structure concerning the distance constraints of the three stems and loops are unknown. In this report, we probed the three-dimensional structure of pRNA monomer and dimer by photo affinity cross-linking with azidophenacyl. Bases 75-81 of the left stem were found to be oriented toward the head loop and proximate to bases 26-31 in a parallel orientation. Chemical modification interference indicates the involvement of bases 45-71 and 82-91 in dimer formation. Dimer was formed via hand-in-hand contact, a novel RNA dimerization that in some aspects is similar to the kissing loops of the human immunodeficiency virus. The covalently linked dimers were found to be biologically active. Both the native dimer and the covalently linked dimer were found by cryo-atomic force microscopy to be similar in global conformation and size.

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