Detection of immobilised murray valley encephalitis virus RNA using oligonucleotide probes with varying degrees of mismatch
Identifieur interne : 004942 ( Main/Exploration ); précédent : 004941; suivant : 004943Detection of immobilised murray valley encephalitis virus RNA using oligonucleotide probes with varying degrees of mismatch
Auteurs : M. J. Howard [Australie] ; R. J. Coelen [Australie] ; J. S. Mackenzie [Australie]Source :
- Journal of Virological Methods [ 0166-0934 ] ; 1991.
English descriptors
- Teeft :
- Base changes, Base mismatches, Base pair mismatches, Base pairs, Contiguous mismatch, Cor1, Dengue type, Duplex, Duplex stability, Encephalitis, Hairpin loop, Hybrid, Hybrid formation, Hybridisation, Hybridisation signal, Hybridisation solution, Hybridisation studies, Lower temperatures, Mismatch, Murray valley encephalitis virus, Nucleic acids, Nucleotide, Nucleotide sequence, Oligodeoxynucleotide probes, Oligonucleotide, Oligonucleotide probe, Oligonucleotide probe cor1, Oligonucleotide probes, Oligonucleotides, Primary sequence, Probe, Room temperature, Same extent, Same number, Sequence information, Such oligonucleotides, Synthetic oligodeoxyribonucleotides, Synthetic oligonucleotide probes, Vero cells, Viral, Virus stocks, Western australia, Yeast trna.
Abstract
Abstract: The design of oligonucleotides used for hybridisation studies often utilises available sequence information of the type strain of a particular virus. If hybridisation studies, using such oligonucleotides, are carried out with field isolates of the same virus, the problem of base pair mismatches and consequent difficulties in detection may arise. This study examined the effect of base pair mismatches on the hybridisation between membrane-bound Murray Valley encephalitis virus (MVE) RNA derived from various strains and deliberately mismatched oligonucleotide probes. Under conditions of very low stringency, probes containing up to 5 mismatches were able to detect MVE RNA, but not yeast RNA. Under washing conditions of increased stringency, hybridisation could be detected between MVE virus RNA and probes with only 3 to 4 mismatches. However, the extent of this interaction was dependent on the number and type of mismatches and their relative sequence position.
Url:
DOI: 10.1016/0166-0934(91)90110-L
Affiliations:
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If hybridisation studies, using such oligonucleotides, are carried out with field isolates of the same virus, the problem of base pair mismatches and consequent difficulties in detection may arise. This study examined the effect of base pair mismatches on the hybridisation between membrane-bound Murray Valley encephalitis virus (MVE) RNA derived from various strains and deliberately mismatched oligonucleotide probes. Under conditions of very low stringency, probes containing up to 5 mismatches were able to detect MVE RNA, but not yeast RNA. Under washing conditions of increased stringency, hybridisation could be detected between MVE virus RNA and probes with only 3 to 4 mismatches. 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