Figure 14

Alignment of CODEHOPs with the nucleotide sequences of the "DMGL" motif in several herpesvirus TS genes. A) Nucleotide sequences encoding the "DMGL" motif in several rhadinoviruses. B) Complementary sequences of CODEHOP PCR primers derived from the "DMGL" motif. The sequence of the complementary strand of the primer is shown to identify the coding sequence. The actual PCR primer is the complement of the sequence. DMGLB was biased towards KSHV-like sequences by using the codons from the KSHV TS gene in the 5' clamp region of the primer with KSHV-specific nucleotides highlighted (3' region of the complementary coding strand shown). DMGLXB was predicted from the amino acid sequence block of the conserved "DMGL" motif using the CODEHOP software and utilizes the most common human codons for the amino acids in the 5' clamp region, and is unbiased in design. The underlined sequence in the 5' clamp region can form a stem-loop structure, shown in C. The CODEHOP PCR primer, DMGLX1B, is a revised version of DMGLXB to eliminate base pairing in the stem-loop structure by changing the highlighted cytosine (C) in Fig. 13-C. to an adenosine (A), boxed in Fig. 13-B.