Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads.
Loop-loop tertiary interactions play a key role in the folding and catalytic activity of natural hammerhead ribozymes. Using a combination of NMR spectroscopy, site-directed mutagenesis and kinetic and infectivity analyses, we have examined the structure and function of loops 1 and 2 of the (+) and (-) hammerheads of chrysanthemum chlorotic mottle viroid RNA. In both hammerheads, loop 1 is a heptanucleotide hairpin loop containing an exposed U at its 5' side and an extrahelical U at its 3'-side critical for the catalytic activity of the ribozyme in vitro and for viroid infectivity in vivo, whereas loop 2 has a key opened A at its 3'-side. These structural features promote a specific loop-loop interaction motif across the major groove. The essential features of this tertiary structure element, base pairing between the 5' U of loop 1 and the 3' A of loop 2, and interaction of the extrahelical pyrimidine of loop 1 with loop 2, are likely shared by a significant fraction of natural hammerheads.
Dufour
David
D
Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, 46012 Valencia, Spain.
de la Peña
Marcos
M
Gago
Selma
S
Flores
Ricardo
R
Gallego
José
J
D001483:Base Sequence; D017124:Conserved Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D010942:Plant Viruses / Q000201:enzymology*; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship; D014498:Uracil / Q000737:chemistry; D014772:Viroids / Q000201:enzymology* / Q000502:physiology
D016337:RNA, Catalytic; C427204:hammerhead ribozyme; D014498:Uracil