Since degenerate primers
used in this amplification, more than one fragment is expected to be amplified.
A set of b-tubulin degenerate primers
; forward primer TubF: 5-GGCTTCMRWGTCACCCACTCT-3'; and reverse primer TubR: 5'-CTTGGGGTCGAACATCTGCTG-3, were designed and used in PCR amplification.
RT-PCR that used degenerate primers
against HPeVs, enteroviruses, and rhinoviruses identified 29 HPeVs, 72 enteroviruses, and 26 rhinoviruses, respectively.
RT-PCR amplification of total RNA from the soybean pod borer 3rd instar gut tissues using degenerate primers
(from the regions of conserved amino acids flanking the active site of the His75 and Ser 220 residues) amplified a 400 bp fragment.
Detection and differentiation of whitefly-transmitted geminiviruses in plants and vector insects by the polymerase chain reaction with degenerate primers
(2011) reported that an immune capture reverse transcription (IC-RT)PCR assay employing degenerate primers
for amplifying partial coat protein (CP).
capable of amplifying a homologous fragment in all species were designed using Gene Runner 3.0.5 (Hastings Software Inc.).
The degenerate primers
were designed based on the consensus sequences of the CCR orthologs of Arabidopsis thaliana (NM101463), Raphanus raphanistrum (EV527773), Glycine max (AK286730), Betula luminifera (FJ410450), Capsicum annuum (EU616555), and Brassica rapa (EX046473).
JCVI has an automated degenerate PCR primer design system called JCVI Primer Designer, which is similar to run_tiled_primers in that it designs degenerate primers
to tile across viral genomes .
Identification of begomovirus components by PCR PCR was performed using a pair of degenerate primers
specific to the coat protein region of begomovirus.
DNA from a novel herpesvirus was amplified from lung tissue by polymerase chain reaction by using degenerate primers
derived from conserved avian herpesvirus sequences.
Subsequently, RT-PCR was carried out using the protocol described by Trujillo et al., (10) which includes a set of degenerate primers
(MON 431, 432, 433 and 434) annealing to the 3' end of the ORF1 that corresponds to RNA-polymerase gene.