CODEHOP-mediated PCR – A powerful technique for the identification and characterization of viral genomes

Table 5 CODEHOP and gene-specific primers developed for cloning the divergent region B within the RFHV genome

Primer	Gene Target	Bias²		Sense	5'>3' Sequence (degenerate codons are in lower case)³
		3' Core	5' Clamp
CODEHOP ¹
RHFGA (48)	TS⁴gene	All cellular and viral TS	KSHV⁵	+	CCTGTTTACGGTTTCcartggagrcayttygg
DMGLB (32)	TS gene	All cellular and viral TS	KSHV	-	GGCAATGTTAAAAGGAACTccnarncccatrtc
RFHVMn-specific ⁶
PolF1LR	DNA polymerase	NA⁷	NA	+	CCACCGTCCCAGACCAACGAAAGCGCCAGA
TSR1LR	TS gene	NA	NA	+	GTCTGCCTGGAATCCCGTGGATATACCAAA

¹ CODEHOP, consensus-degenerate hybrid oligonucleotide primers. The degree of degeneracy, ie the number of individual primers in the pool, is given in parentheses.
² Bias indicates the reliance on a specified subset of sequences for determination of the 3' degenerate core or 5' consensus clamp.
³ See legend to Table 1 for the IUB code.
⁴ TS, thymidylate synthase.
⁵ Clamp region derived from the KSHV viral TS gene [11]
⁶ Primer sequence derived from the RFHVMn sequence obtained by the CODEHOP technique
⁷ NA, not applicable – these are gene-specific primer

ISSN: 1743-422X