Mendel-Brno 2000

category image Volume: 17
Issue Number 6, Part 2
June 2000

Structure of a RNA/DNA Hybrid of the Polypurine Tract OF HIV-1

The polypurine tract (PPT)of HIV-1 is a 15 base pair purine tract that serves as the initiation site for synthesis of the second (+) DNA strand, which along with its first strand mate will be incorporated into the host. During transcription in vivothe PPT exists as a RNA/DNA hybrid. It is thought that this hybrid sequence has some unusual structure that causes the RNase H domain of HIV-1 reverse transcriptase to stop degrading the first (-) strand and to initiate second strand synthesis. Our lab has been investigating decamers of the PPT both in DNA/DNA and RNA/DNA hybrid sequences with the goal of eventually crystallizing the entire 15-base pair tract. We had previously reported the structure of the DNA/DNA decamer, C-A-A-A-G-A-A-A-A-G (1), and have now completed the analysis of its RNA/DNA complement at atomic resolution (1.15 Å), with the purine strand RNA and the pyrimidine strand DNA. The strucure has been solved by two methods, molecular replacement and ab initio direct methods using the program "Shake & Bake". A comparison of the DNA/DNA and hybrid structure showed that the hybrid is an A-helix and the DNA/DNA is a B-helix. The interesting features of the RNA/DNA hybrid will be discussed.


(1) Han, G.W., Kopka, M.L., Cascio, D., Grzeskowiak, K., and Dickerson, R.E. J. Mol. Biol. 269:811-826 (1997).

M.L. Kopka, G.W. Han, L. Lavelle, and R.E. Dickerson

Molecular Biology Institute, University of California,
Los Angeles, CA, 90095-1560, USA
kopka @ewald.mbi.ucla.edu