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Nucleic Acids Research, 1993, Vol. 21, No. 6 1389-1395
© 1993

MOLECULAR BIOLOGY

The secondary structure of the 5'-noncoding region of beet necrotic yellow vein virus RNA 3: evidence for a role in viral RNA replication

David Gilmer, Christine Allmang1, Chantal Ehresmann1, Hubert Guilley, Kenneth Richards*, Gérard Jonard and Bernard Ehresmann1

Institut de Biologie Moléculaire des Plantes du CNRS et de I'Université Louis Pasteur, 12 rue du Général Zimmer, Strasbourg 67084 Cedex, France 1UPR du CNRS No. 9002, Institut de Biologie Moléculaire et Cellulaire 15 rue Descartes, Strasbourg 67084 Cedex, France

*To whom correspondence should be addressed

Received January 4, 1993. Revised February 9, 1993. Accepted February 9, 1993.

Secondary structure-sensitive chemical and enzymatic probes have been used to produce a model for the folding of the first 312 residues of the long 5'-noncodlng region of beet necrotlc yellow vein virus RNA 3. The structure consists of two major domains, one of which Includes long distance base-pairing interactions between two short sequence elements (Box I and Box II) situated between positions 237 and 292 and complementary elements (Box I' and II') near the 5'-terminus. Previous studies have shown that base pairing between these sequence elements (in either the plus-strand or minus-strand RNA) Is important for RNA 3 accumulation during Infection. RNA 3 transcripts were produced containing mutations which preferentially disrupted Box II-II' base pairing in either the plus- or minus-strand. In Infection experiments, transcripts with mutations which disrupted the Box II-II' interaction in the plus-strand structure replicated less efficiently than mutants In which the Box II-II' interaction was disrupted in the minus-strand. These findings Indicate that the complex 5'-proximal plus-strand structure to which the Box II-II' Interaction contributes comprises at least part of the promoter for plus-strand RNA synthesis.


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