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Nucleic Acids Research, 2001, Vol. 29, No. 22 4751-4759
© 2001 Oxford University Press

Detection of the 5'-cap structure of messenger RNAs with the use of the cap-jumping approach

V. A. Efimov*, O. G. Chakhmakhcheva, J. Archdeacon1, J. M. Fernandez1, O. N. Fedorkin2, Yu. L. Dorokhov2 and J. G. Atabekov2

Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia, 1Active Motif LLC, 5431-C Avenida Encinas, Carlsbad, CA 92008, USA and 2Department of Virology and Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia

An effective procedure for specific determination of the cap structure at the 5'-terminus of mRNA and for isolation of the corresponding full-length cDNA has been developed. The procedure involves covalent attachment of an oligonucleotide template extender to the 5'-cap structure of mRNA followed by RT–PCR using M-MLV SuperScript II reverse transcriptase. In the course of reverse transcription, the enzyme ‘jumps over’ the cap structure and includes the sequence complementary to the oligonucleotide template extender into the 3'-end of the first cDNA strand. The cap-jumping method was successfully tested using some mammalian cellular mRNAs, genomic RNAs of tobacco mosaic virus (TMV) U1 and the recently isolated crucifer-infecting tobamovirus. Moreover, cDNA products corresponding to the genomic tobamovirus RNA were obtained from total RNA extracted from tobacco plants infected by crucifer-infecting tobamovirus or tobacco mosaic virus. Using the cap-jumping method, we have shown for the first time that genomic crucifer-infecting tobamovirus (crTMV) RNA contains a 5'-cap structure. This improved method can be recommended for the construction of full-length and 5'-end enriched cDNA libraries, identification of capped RNAs and determination of their 5'-terminal sequences.

* To whom correspondence should be addressed. Tel: +7 095 3365911; Fax: +7 095 3365911; Email: eva{at}mail.ibch.ru


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