Table 1.

Evolutionary conservation of the intramolecular triple helix

No affect on triple helix formation (618 of 715 = 86.4%)

Consensus sequence, 106

Changes do not affect the ability to form potential triplex, 512

Single changes to the ends of strands that minimally impact on  triplex formation (36 of 715 = 5%)

Bottom of strand 1/strand 2 base pairing region, 6

Bottom or top of strand 2/strand 3 base pairing region, 30

Two simultaneous changes only at nucleotides 46 and 52, 5

Internal changes that disrupt strand 1/strand 2 base pairing region, 1

One or more internal mismatches in strand 2/strand 3 base pairing  region, 55 (7.7%)

Of 20,946 reported HIV-1 sequences in the NCBI sequence database, 715 contained the sequence TTTTTTA plus at least 45 nucleotides. A global alignment of these sequences was produced using clustal w 1.7 (36), and the resulting output file was analyzed for the impact of each variant on intramolecular triplex structure formation.