TABLE 1.

Modified PCR primers for amplification of hypermutated sequences

Primer	Function	Modification	Sequence type amplified	Location in HXB2	Sequence (5′–3′)a
DP10	1st round, forward	None	Normal	2198–2223	GAA CTC CCT CTC AGA AGC AGG AGC CG
DP10hyp	1st round, forward	Shortened, G+A mixed bases introduced	Normal and hypermutant	2198–2223	AA CTC CCT CTC ARA AGC ARR A
DP10hypa	1st round, forward	Shortened, G-to-A replacements made	Hypermutant	2198–2223	AA CTC CCT CTC AAA AGC AAA A
DP11	1st round, reverse	None	Normal	2598–2572	CCA TTCCTG GCT TTA ATT TTA CTG GTA
DP11hyp	1st round, reverse	Shortened, C+T mixed bases introduced	Normal and hypermutant	2598–2572	CCA TTY YTG GCT TTA ATT TTA CTG
DP11hypa	1st round, reverse	Shortened, C to T replacements made	Hypermutant	2598–2572	CCA TTT TTG GCT TTA ATT TTA CTG
DP16	2nd round, forward	None	Normal and hypermutant	2253–2274	CCT CAA ATC ACT CTT TGG CAA C
DP17	2nd round, reverse	None	Normal and hypermutant	2549–2529	AAA ATT TAA AGT GCA GCC AAT

^aPrimer sequences DP10, DP11, DP16, and DP17 have been published previously (28, 52a). They amplify a 297-bp segment of the HIV-1 genome encoding the protease gene, as indicated by their location in the reference sequence HXB2 (GenBank accession number AF033819). Sequences susceptible to hypermutation (GA or GG in forward primers and TC or CC in reverse primers, respectively) are underlined. Some of these sequences were modified (indicated by boldface), either by incorporation of G+A (R) or C+T mixtures (Y), or by G-to-A or C-to-T mutation. Modified primers were also shortened to bring potential mismatches with normal sequences nearer to their 3′ ends and further destabilize their interaction with normal sequences.