Biomaterial Database

HIV-1 genomic RNA U3 region forms a stable quadruplex-hairpin structure. 2021

Chelsea Harpster, and Elaina Boyle, and Karin Musier-Forsyth, and Besik Kankia

Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.

The U3 promoter region of the HIV-1 long terminal repeat (LTR) has previously been shown to fold into a series of dynamic G-quadruplex structures. Among the G-quadruplexes identified in the LTR sequence, LTR-III was shown to be the most stable in vitro. NMR studies of this 28-nucleotide (nt) DNA revealed a unique quadruplex-hairpin structure. Whether the hairpin forms in RNA element is unknown and the role of the hairpin in the structure and stability of quadruplexes has not been characterized. Here, we used optical and thermodynamic studies to address these questions. The wild-type LTR-III RNA formed a monomolecular quadruplex with a parallel topology using only propeller loops, including the hairpin loop element. By comparison to the WT and variant RNAs, LTR-III DNA structures were more heterogeneous and less stable. Increased stability of the RNA suggests that the RNA quadruplex-hairpin structure may be a more attractive therapeutic target than the analogous DNA element.

UI	MeSH Term	Description	Entries
D009690	Nucleic Acid Conformation	The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.	DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D012367	RNA, Viral	Ribonucleic acid that makes up the genetic material of viruses.	Viral RNA
D015497	HIV-1	The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.	Human immunodeficiency virus 1,HIV-I,Human Immunodeficiency Virus Type 1,Immunodeficiency Virus Type 1, Human
D054856	G-Quadruplexes	Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)	DNA G-Quadruplexes,DNA, Quadruplex,G-Quadruplexes, DNA,G-Quadruplexes, RNA,Guanine-Quadruplexes,Guanine-Quartets,Guanine-Tetrads,Quadruplex DNA,RNA, G-Quadruplexes,Tetraplex DNA,DNA G Quadruplexes,DNA, Tetraplex,G Quadruplexes,G Quadruplexes, DNA,G Quadruplexes, RNA,G-Quadruplexes RNA,G-Quadruplexes RNAs,Guanine Quadruplexes,Guanine Quartets,Guanine Tetrads,Guanine-Quartet,Guanine-Tetrad,RNA G-Quadruplexes,RNA, G Quadruplexes,RNAs, G-Quadruplexes
D020537	RNA, Small Nucleolar	Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.	Small Nucleolar RNA,snoRNA