Structural requirement for the two-step dimerization of human immunodeficiency virus type 1 genome

1 January 2000

journal article
research article
Published by Cold Spring Harbor Laboratory in RNA

Vol. 6 (1) , 96-102
https://doi.org/10.1017/s1355838200991635

Abstract

Generation of RNA dimeric form of the human immunodeficiency virus type 1 (HIV-1) genome is crucial for viral replication. The dimerization initiation site (DIS) has been identified as a primary sequence that can form a stem-loop structure with a self-complementary sequence in the loop and a bulge in the stem. It has been reported that HIV-1 RNA fragments containing the DIS form two types of dimers, loose dimers and tight dimers. The loose dimers are spontaneously generated at the physiological temperature and converted into tight dimers by the addition of nucleocapsid protein NCp7. To know the biochemical process in this two-step dimerization reaction, we chemically synthesized a 39-mer RNA covering the entire DIS sequence and also a 23-mer RNA covering the self-complementary loop and its flanking stem within the DIS. Electrophoretic dimerization assays demonstrated that the 39-mer RNA reproduced the two-step dimerization process, whereas the 23-mer RNA immediately formed the tight dimer. Furthermore, deletion of the bulge from the 39-mer RNA prevented the NCp7-assisted tight-dimer formation. Therefore, the whole DIS sequence is necessary and sufficient for the two-step dimerization. Our data suggested that the bulge region regulates the stability of the stem and guides the DIS to the two-step dimerization process.

Keywords

This publication has 25 references indexed in Scilit:

Variant Effects of Non-Native Kissing-Loop Hairpin Palindromes on HIV Replication and HIV RNA Dimerization: Role of Stem−Loop B in HIV Replication and HIV RNA Dimerization
Biochemistry, 1998
Mapping the RNA binding sites for human immunodeficiency virus type-1 Gag and NC proteins within the complete HIV-1 and -2 untranslated leader regions
Nucleic Acids Research, 1998
Solution studies of the dimerization initiation site of HIV-1 genomic RNA
Nucleic Acids Research, 1998
Structure of the dimer a initiation complex of HIV-1 genomic RNA
Nature Structural & Molecular Biology, 1998
The Annealing of tRNA3Lys to Human Immunodeficiency Virus Type 1 Primer Binding Site Is Critically Dependent on the NCp7 Zinc Fingers Structure
Published by Elsevier ,1998
Structure of the HIV-1 Nucleocapsid Protein Bound to the SL3 Ψ-RNA Recognition Element
Science, 1998
Non-canonical interactions in a kissing loop complex: the dimerization initiation site of HIV-1 genomic RNA
Journal of Molecular Biology, 1997
Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro.
Proceedings of the National Academy of Sciences, 1994
Viral RNA annealing activities of human immunodeficiency virus type 1 nucleocapsid protein require only peptide domains outside the zinc fingers.
Proceedings of the National Academy of Sciences, 1992
Improved Estimation of Secondary Structure in Ribonucleic Acids
Nature New Biology, 1973