TABLE 1.

ZF sequences assembled to regulate the HIV LTR; the predicted 18-bp DNA-binding sites are indicated

TFSZF	ZF helix						Predicted target sitec
	F6	F5	F4	F3	F2	F1	Half site 1-half site 2
PBS1a	QRANLRA	RGGWLQA	QRHSLTE	QSGDLRR	RSDVLVR	RSDDLVR	5′-AAA TCT CTA—GCA GTG GCG-3′
PBS1ab	RSDVLVR	RSDHLTT	QRANLRA	QSGDLRR	RSDVLVR	RSDDLVR	5′-GTG TGG AAA atctcta GCA GTG GCG-3′
PBS2	QSGDLRR	RSDVLVR	RSDDLVR	HTGHLLE	QSSNLVR	RADNLTE	5′-GCA GTG GCG—CCC GAA CAG-3′
PBS3	RSDHLTT	HTGHLLE	RNDTLTE	DSGNLRV	RSDHLTN	DPGNLVR	5′-TGG CGC CCG—AAC AGG GAC-3′

^aZF helices are positioned in the antiparallel orientation (COOH-F6 to F1-NH2) relative to the DNA target sequence. Amino acid positions −1 to +6 of each DNA recognition sequence are shown. Web-based software is available for automated zinc finger protein design (http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php).

^bPBS1a is composed of two three-finger ZFs separated by a long flexible linker (Gly₃SerGly₄). F3 to F1 bind to the second half site, GCA GTG GCG, and F6 to F4 bind to the first half site, GTG TGG AAA. The intervening nonbound DNA sequence is indicated by lowercase letters.

^cPredicted target DNA sequences are presented in the 5′ to 3′ orientation.