Analysis of the secondary structure of the poly(C) tract in foot-and-mouth disease virus RNAs

• Published in: Journal of general virology 1985-09, Vol.66 (9), p.1919-1929
• Main Authors: Mellor, E.J.C, Brown, F, Harris, T.J.R
• Format: Article
• Language: English
• Subjects: Animals; Aphthovirus; Aphthovirus - analysis; Biological and medical sciences; Cell Line; Cricetinae; Electrophoresis, Polyacrylamide Gel; foot-and-mouth disease virus; Fundamental and applied biological sciences. Psychology; genome; Kidney; Kinetics; Microbiology; Morphology, structure, chemical composition, physicochemical properties; Nucleic Acid Conformation; Oligoribonucleotides - analysis; Poly C - isolation & purification; Poly C - metabolism; Polyribonucleotides - isolation & purification; Ribonuclease T1; RNA; RNA, Viral - isolation & purification; Sulfites - metabolism; Virology
• ISSN: 0022-1317; 1465-2099
• DOI: 10.1099/0022-1317-66-9-1919

The Animal Virus Research Institute, Pirbright, Woking, Surrey GU24 0NF, U.K. Sodium bisulphite modification of foot-and-mouth disease virus (FMDV) RNA in solution indicates that the majority of the poly(C) tract in the RNA is single-stranded in concordance with previous results with encephalomyocarditis virus RNA. The reaction kinetics are biphasic; 60% of the cytidylic acid in the poly(C) tract reacts like synthetic poly(C), and the remainder with the kinetics of the cytidylic acid in the rest of the RNA. The reactivity of the poly(C) tract with poly(I) indicates that it is looped out and exposed in the RNA. The deamination reaction has also been used to investigate the structure of the replicative form (RF) and replicative intermediate (RI) isolated from infected cells. Analysis by gel electrophoresis of the long RNase A- and T 1 -resistant oligonucleotides of RI suggests that it has five single-stranded poly(C) tracts to every one which is base-paired. Bisulphite reactivity of the poly(C) tract and gel electrophoresis of the ribonuclease-resistant oligonucleotides of RF indicate that the poly(C) is base-paired to a poly(G) tract in this molecule. The presence of a poly(G) tract in RF and RI provides unequivocal evidence that the poly(C) is replicated via poly(G) in the negative strand. Keywords: FMDV RNA, poly(C) tract, RNA secondary structure Present address: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K. Present address: Wellcome Biotechnology Ltd., Ash Road, Pirbright, Woking, Surrey GU24 0NQ, U.K. Present address: Celltech Ltd., 250 Bath Road, Slough, Berks. SL1 4DY, U.K. Received 8 March 1985; accepted 3 June 1985.