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PCR with degenerate primers for RT of LINE elements and the following cloning and sequencing of randomly selected colonies yielded three clones, namely Aesp24 (460 nt), Aesp25 (384 nt), and Aesp26 (710 nt), comprising similar sequences to non-LTR LINE-like elements and short fragments similar to Ty3-gypsy Fatima (Supplementary Table S1, Figure S1).
Following preliminary observations that the sensitivity and efficiency of amplification with the primers from [21] were not homogeneous for different flaviviruses, we decided to design a modified set of degenerate primers. Using VisualOligoDeg we selected primers for a modified RT-qPCR for Flavivirus detection and quantification.
1, were used to design degenerate primers. Forward (for) and reverse (rev) primers were used to amplify genomic DNA fragments 300-500 base pairs in length.
Degenerate Oligonucleotide-primed PCR: General Amplification of target DNA by a single degenerate primer. Genome 13: 718725 Yamagishi M.
In this regard, development of degenerate primers would be a valuable tool in identifying the other populations of B.
To isolate the 5' eDNA fragment of the isolated NII561-2000, the eDNA fragment containing part of the 5' untranslated region (UTR) and capsid precursor protein VP0 was amplified by PCR from the cDNA prepared from the NII561-2000 virus with degenerate primers corresponding to this region.
To amplify the major portion of Spbtry1, the following degenerate primers were designed according to the amino acid residues flanking the His and Ser of the serine proteases SP-F and SP-R active site (Table 1) (Waniek et al.
The degenerate primers CLCV1/CLCV2 and specific primers (PadCPPVXF/PadCPPVXR) were used for detection of ToLCNDV (Table I).
Although MY09/11 degenerate primers are routinely and largely used to detect mucosal HPV (Alpha species), especially from genital mucosa, the FAP 59/64 system has been applied in the detection of cutaneous HPV (Beta and Gamma species) and has been used to improve detection of oral HPV (12) The combination of these systems tracks a broad range of types, even types not yet identified.