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Dimer linkage structure in retroviruses: models that include both duplex and quadruplex domains
M I Zarudnaya1, I M Kolomiets, A L Potyahaylo
1Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv. m.i.zarudna@imbg.org.ua
Ukrains'Kyi Biokhimichnyi Zhurnal (1999 )
|December 13, 2005
Summary
Retrovirus RNA genomes contain a dimer linkage structure (DLS) with duplex and quadruplex domains. This conserved structure is predictable across most human immunodeficiency virus 1 (HIV-1) isolates and Moloney murine sarcoma virus (MuSV).
Area of Science:
- Virology
- Structural Biology
- Molecular Biology
Background:
- Retroviral genomes consist of two non-covalently linked identical RNA molecules.
- The dimer linkage structure (DLS) is a stable contact site near the 5' ends of these RNA molecules.
- The precise molecular interactions within the DLS in mature virions remain largely uncharacterized.
Purpose of the Study:
- To propose and validate models for the dimer linkage structure (DLS) in human immunodeficiency virus 1 (HIV-1) and Moloney murine sarcoma virus (MuSV).
- To investigate the structural domains, including duplex and quadruplex formations, within the DLS.
- To assess the phylogenetic predictability of DLS models across diverse HIV-1 isolates.
Main Methods:
- Comparative analysis of RNA structures based on existing models.
- Phylogenetic analysis of 350 human immunodeficiency virus 1 (HIV-1) isolates from the NCBI database.
- Development of structural models for dimer linkage structures in HIV-1Lai and Moloney murine sarcoma virus (MuSV).
Main Results:
- Similar DLS models, featuring duplex and quadruplex domains, were developed for HIV-1Lai, a North American/European strain, analogous to previous models for HIV-1Mal.
- Duplex domains within the DLS can form through base pair melting/reannealing or recombination, or as kissing loop complexes.
- Quadruplexes identified include both G- and mixed tetrads (e.g., G.C.G.C, A.U.A.U).
- Phylogenetic analysis indicated that these DLS models are predictable for nearly all surveyed HIV-1 isolates.
- A DLS model for Moloney murine sarcoma virus (MuSV) was presented, comprising a palindromic duplex and multiple quadruplexes.
Conclusions:
- The dimer linkage structure (DLS) in human immunodeficiency virus 1 (HIV-1) and Moloney murine sarcoma virus (MuSV) is characterized by a combination of duplex and quadruplex structural domains.
- The proposed DLS models are phylogenetically conserved and predictable across a wide range of human immunodeficiency virus 1 (HIV-1) isolates.
- Understanding the DLS structure provides insights into retroviral genome organization and interactions.
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