BIOMAT Database Logo BIOMAT Database Logo

Identification of potyviruses using the polymerase chain reaction with degenerate primers. 1991

S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Department of Biochemistry, Leiden University, The Netherlands.

Local areas of conserved amino acid sequence in the replicase and coat proteins of potyviruses were used to select nucleotide sequences for use in the construction of sets of degenerate oligonucleotide primers for amplification of DNA fragments on potyvirus-specific templates in a combined assay of reverse transcription and the polymerase chain reaction (RT-PCR). Sequences selected for the construction of degenerate primers included the coat protein gene sequence of tulip breaking virus from lily, which is reported in this paper. It is shown that the degenerate primers support potyvirus-specific amplification, but do not support amplification on carlavirus and potexvirus templates. A panel consisting of definite and prospective members of the potyvirus group occurring in bulbous crops was subjected to the degenerate primer RT-PCR assay; amplified fragments were used in cross-hybridization experiments and restriction fragment length polymorphism analysis to detect relationships among these potyviruses. A partially characterized virus isolated from Gloriosa rothschildiana was positively identified as a potyvirus by specific amplification and subsequent sequence analysis of an amplified DNA fragment.

UI MeSH Term Description Entries
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D009693 Nucleic Acid Hybridization Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503) Genomic Hybridization,Acid Hybridization, Nucleic,Acid Hybridizations, Nucleic,Genomic Hybridizations,Hybridization, Genomic,Hybridization, Nucleic Acid,Hybridizations, Genomic,Hybridizations, Nucleic Acid,Nucleic Acid Hybridizations
D010942 Plant Viruses Viruses parasitic on plants. Phytophagineae,Plant Virus,Virus, Plant,Viruses, Plant
D012150 Polymorphism, Restriction Fragment Length Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment. RFLP,Restriction Fragment Length Polymorphism,RFLPs,Restriction Fragment Length Polymorphisms
D002213 Capsid The outer protein protective shell of a virus, which protects the viral nucleic acid. Capsids are composed of repeating units (capsomers or capsomeres) of CAPSID PROTEINS which when assembled together form either an icosahedral or helical shape. Procapsid,Prohead,Capsids,Procapsids,Proheads
D003001 Cloning, Molecular The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells. Molecular Cloning
D004279 DNA, Viral Deoxyribonucleic acid that makes up the genetic material of viruses. Viral DNA
D004587 Electrophoresis, Agar Gel Electrophoresis in which agar or agarose gel is used as the diffusion medium. Electrophoresis, Agarose Gel,Agar Gel Electrophoresis,Agarose Gel Electrophoresis,Gel Electrophoresis, Agar,Gel Electrophoresis, Agarose
D005784 Gene Amplification A selective increase in the number of copies of a gene coding for a specific protein without a proportional increase in other genes. It occurs naturally via the excision of a copy of the repeating sequence from the chromosome and its extrachromosomal replication in a plasmid, or via the production of an RNA transcript of the entire repeating sequence of ribosomal RNA followed by the reverse transcription of the molecule to produce an additional copy of the original DNA sequence. Laboratory techniques have been introduced for inducing disproportional replication by unequal crossing over, uptake of DNA from lysed cells, or generation of extrachromosomal sequences from rolling circle replication. Amplification, Gene
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein

Related Publications

S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Polymerase chain reaction cloning with degenerate primers: homology-based identification of adhesion molecules.
January 1994, Methods in enzymology,
S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Cloning gene family members using the polymerase chain reaction with degenerate oligonucleotide primers.
January 1997, Methods in molecular biology (Clifton, N.J.),
S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Highly degenerate, inosine-containing primers specifically amplify rare cDNA using the polymerase chain reaction.
November 1988, Nucleic acids research,
S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Polymerase chain reaction with degenerate oligonucleotide primers to clone gene family members.
January 1996, Methods in molecular biology (Clifton, N.J.),
S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Generation of polymerase chain reaction-specific probes for library screening using single degenerate primers.
March 1995, Genetic analysis : biomolecular engineering,
S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Detection of bovine viral diarrhea virus, using degenerate oligonucleotide primers and the polymerase chain reaction.
August 1991, American journal of veterinary research,
S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Sampling P450 diversity by cloning polymerase chain reaction products obtained with degenerate primers.
January 1996, Methods in enzymology,
S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Detection of genital human papillomaviruses by polymerase chain reaction amplification with degenerate nested primers.
March 1991, Journal of medical virology,
S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Identification of mosquito bloodmeals using polymerase chain reaction (PCR) with order-specific primers.
March 2003, Journal of medical entomology,
S A Langeveld, and J M Dore, and J Memelink, and A F Derks, and C I van der Vlugt, and C J Asjes, and J F Bol
Leishmania (Viannia) braziliensis: New primers for identification using polymerase chain reaction.
December 2008, Experimental parasitology,
Copied contents to your clipboard!