Following an approach used to specifically identify polioviruses and enterovirus 71, we have developed reverse transcriptase (RT) PCR primers containing mixed-base residues or deoxyinosine at positions of codon degeneracy. These primers permit specific RT-PCR amplification of echovirus 30 (E30) sequences by targeting sites that encode conserved amino acid motifs within the major capsid protein,...

Designing degenerate PCR primers for templates of unknown nucleotide sequence may be a very difficult task. In this paper, we present a new method to design degenerate primers, implemented in family-specific degenerate primer design (FAS-DPD) computer software, for which the starting point is a multiple alignment of related amino acids or nucleotide sequences. To assess their efficiency, four d...

This protocol describes a method for the microdissection of Drosophila polytene chromosomes. The microdissected DNA can be amplified by degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) and then used to prepare probes for fluorescent in situ hybridization (FISH).

Almond (Prunus dulcis L.) is one of the most important nut crops in Iran. Most almond cultivars and genotypes are self-incompatible. However, research on S-alleles indicates that it is very efficient in cultivar selection. Selfincompatibility in almond is gametophytic and controlled by a single S-locus with multiple codominant alleles. In this study, compatibility relationships among cultivars,...

We investigated if any change in spatial resolution of comparative genomic hybridization analysis could be detected when using DNA amplified by degenerate oligonucleotide primed PCR (DOP-PCR) as opposed to the use of unamplified DNA. Five DNA samples from B-cell leukemias with small 11q deletions were amplified by DOP-PCR and analysed by means of high resolution comparative genomic hybridizatio...

We have generated a 3' cDNA pool from the RNA of only 1000 or fewer cells by reverse transcription (RT) from an extended oligo(dT) primer with a 3' degenerate base and a second strand primer with four degenerate 3' bases, followed by PCR. Reproducible differential displays (DD) can be made from this essentially inexhaustible source of DNA. The method produced DD patterns that are comparable but...

The movement protein genes from several isolates of ArMV and GFLV of different geographical origins were amplified by RT/PCR using degenerate primers, cloned and sequenced. A single pair of degenerate primers was designed from these sequences to allow the simultaneous amplification of parts of the movement protein genes of ArMV and GFLV. Their use in an immunocapture-RT/PCR for the detection of...

We have cloned and sequenced a cDNA for a histone H2A from parsley (Petroselinum crispum). A library of parsley cDNA in lambda gtll was probed with a cloned fragment originally generated by polymerase chain reaction (PCR). The DNA amplified by PCR was a cDNA preparation made using the downstream PCR oligo primer with a total RNA preparation from parsley cell culture. The PCR upstream primer (a ...