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Nucleic Acids Research, 1989, Vol. 17, No. 8 3275-3288
© 1989

MOLECULAR BIOLOGY

Sequence divergence and open regions of RNA secondary structures in the envelope regions of the 17 human immunodeficiency virus isolates

Shu-Yun Le1,3, Jih-H. Chen2, Devjani Chatterjee1 and Jacob V. Maizel1

1Laboratory of Mathematical Biology, Division of Cancer Biology and Diagnosis, National Cancer Institute National Institutes of Health, Bldg 469, Rm, 151, Frederick, MD 21701, USA 2Advanced Scientific Computer Laboratory, Program Resources, Inc. NCI/FCRF, Frederick, MD 21701, USA 3Shanghai Institute of Biochemistry Chinese Academy of Sciences, Shanghai 200031, China

Received August 26, 1988. Revised March 8, 1989. Accepted March 8, 1989.

Genetic variation during the course of infection of an individual is a remarkable feature of the acquired immune deficiency syndrome(AIDS) disease. This variation has been studied for the envelope protein encoding regions of seventeen different sequences from various isolates of human immunodeficiency virus (HIV) using multiple sequence comparison and calculation of variability. The open regions with little intramolecular base pairing in these envelope sequences are predicted by a recently developed statistical method. The minimum length L for a run of hypervariable sites, conserved sites, or open regions that gives significance at the 1%(or 0.1%) level is then determined by a scan statistical method. The results show that significant clusters of open regions predicted at the RNA level correlate with significant clusters of hypervariable sites in the HIV envelope gene. Those significant genomic variations in HIVs seem to be manifested mainly in the extracellular portion of the envelope protein. Twelve potential antigenic determinants are predicted using an antigenic index method. Interestingly, the majority of the significant hypervariable regions in the exterior envelope protein (gp120) were predicted potential epitopes.


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