Unfolding of DNA Quadruplexes Induced by HIV-1 Nucleocapsid Protein

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2005 Aug 4

PMID 16077025

Citations 28

Authors

Besik I Kankia

George Barany

Karin Musier-Forsyth

Affiliations

Soon will be listed here.

Abstract

The human immunodeficiency virus type 1 nucleocapsid protein (NC) is a nucleic acid chaperone that catalyzes the rearrangement of nucleic acids into their thermodynamically most stable structures. In the present study, a combination of optical and thermodynamic techniques were used to characterize the influence of NC on the secondary structure, thermal stability and energetics of monomolecular DNA quadruplexes formed by the sequence d(GGTTGGTGTGGTTGG) in the presence of K+ or Sr2+. Circular dichroism studies demonstrate that NC effectively unfolds the quadruplexes. Studies carried out with NC variants suggest that destabilization is mediated by the zinc fingers of NC. Calorimetric studies reveal that NC destabilization is enthalpic in origin, probably owing to unstacking of the G-quartets upon protein binding. In contrast, parallel studies performed on a related DNA duplex reveal that under conditions where NC readily destabilizes and unfolds the quadruplexes, its effect on the DNA duplex is much less pronounced. The differences in NC's ability to destabilize quadruplex versus duplex is in accordance with the higher DeltaG of melting for the latter, and with the inverse correlation between nucleic acid stability and the destabilizing activity of NC.

Citing Articles

The human cellular protein NoL12 is a specific partner of the HIV-1 nucleocapsid protein NCp7.

Zgheib S, Taha N, Zeiger M, Glushonkov O, Lequeu T, Anton H J Virol. 2023; 97(9):e0004023.

PMID: 37695057 PMC: 10537728. DOI: 10.1128/jvi.00040-23.

Recent advances in applying G-quadruplex for SARS-CoV-2 targeting and diagnosis: A review.

Zhai L, Su A, Liu J, Zhao J, Xi X, Hou X Int J Biol Macromol. 2022; 221:1476-1490.

PMID: 36130641 PMC: 9482720. DOI: 10.1016/j.ijbiomac.2022.09.152.

HIV-1 Nucleocapsid Protein Unfolds Stable RNA G-Quadruplexes in the Viral Genome and Is Inhibited by G-Quadruplex Ligands.

Butovskaya E, Solda P, Scalabrin M, Nadai M, Richter S ACS Infect Dis. 2019; 5(12):2127-2135.

PMID: 31646863 PMC: 6909241. DOI: 10.1021/acsinfecdis.9b00272.

CNBP controls transcription by unfolding DNA G-quadruplex structures.

David A, Pipier A, Pascutti F, Binolfi A, Weiner A, Challier E Nucleic Acids Res. 2019; 47(15):7901-7913.

PMID: 31219592 PMC: 6735679. DOI: 10.1093/nar/gkz527.

G-Quadruplex Forming Oligonucleotides as Anti-HIV Agents.

Musumeci D, Riccardi C, Montesarchio D Molecules. 2015; 20(9):17511-32.

PMID: 26402662 PMC: 6332060. DOI: 10.3390/molecules200917511.

References

Kankia B, Marky L . Folding of the thrombin aptamer into a G-quadruplex with Sr(2+): stability, heat, and hydration. J Am Chem Soc. 2001; 123(44):10799-804. DOI: 10.1021/ja010008o. View

Chen F . Sr2+ facilitates intermolecular G-quadruplex formation of telomeric sequences. Biochemistry. 1992; 31(15):3769-76. DOI: 10.1021/bi00130a006. View

Guo J, Wu T, Kane B, Johnson D, Henderson L, Gorelick R . Subtle alterations of the native zinc finger structures have dramatic effects on the nucleic acid chaperone activity of human immunodeficiency virus type 1 nucleocapsid protein. J Virol. 2002; 76(9):4370-8. PMC: 155087. DOI: 10.1128/jvi.76.9.4370-4378.2002. View

Urbaneja M, Wu M, Casas-Finet J, Karpel R . HIV-1 nucleocapsid protein as a nucleic acid chaperone: spectroscopic study of its helix-destabilizing properties, structural binding specificity, and annealing activity. J Mol Biol. 2002; 318(3):749-64. DOI: 10.1016/S0022-2836(02)00043-8. View

Williams M, Gorelick R, Musier-Forsyth K . Specific zinc-finger architecture required for HIV-1 nucleocapsid protein's nucleic acid chaperone function. Proc Natl Acad Sci U S A. 2002; 99(13):8614-9. PMC: 124332. DOI: 10.1073/pnas.132128999. View

Lyonnais S, Hounsou C, Teulade-Fichou M, Jeusset J, Le Cam E, Mirambeau G . G-quartets assembly within a G-rich DNA flap. A possible event at the center of the HIV-1 genome. Nucleic Acids Res. 2002; 30(23):5276-83. PMC: 137959. DOI: 10.1093/nar/gkf644. View

Beltz H, Azoulay J, Bernacchi S, Clamme J, Ficheux D, Roques B . Impact of the terminal bulges of HIV-1 cTAR DNA on its stability and the destabilizing activity of the nucleocapsid protein NCp7. J Mol Biol. 2003; 328(1):95-108. DOI: 10.1016/s0022-2836(03)00244-4. View

Heath M, Derebail S, Gorelick R, DeStefano J . Differing roles of the N- and C-terminal zinc fingers in human immunodeficiency virus nucleocapsid protein-enhanced nucleic acid annealing. J Biol Chem. 2003; 278(33):30755-63. DOI: 10.1074/jbc.M303819200. View

Lyonnais S, Gorelick R, Mergny J, Le Cam E, Mirambeau G . G-quartets direct assembly of HIV-1 nucleocapsid protein along single-stranded DNA. Nucleic Acids Res. 2003; 31(19):5754-63. PMC: 206446. DOI: 10.1093/nar/gkg716. View

10.

Hargittai M, Gorelick R, Rouzina I, Musier-Forsyth K . Mechanistic insights into the kinetics of HIV-1 nucleocapsid protein-facilitated tRNA annealing to the primer binding site. J Mol Biol. 2004; 337(4):951-68. DOI: 10.1016/j.jmb.2004.01.054. View

11.

Bampi C, Jacquenet S, Lener D, Decimo D, Darlix J . The chaperoning and assistance roles of the HIV-1 nucleocapsid protein in proviral DNA synthesis and maintenance. Curr HIV Res. 2004; 2(1):79-92. DOI: 10.2174/1570162043485022. View

12.

Beltz H, Piemont E, Schaub E, Ficheux D, Roques B, Darlix J . Role of the structure of the top half of HIV-1 cTAR DNA on the nucleic acid destabilizing activity of the nucleocapsid protein NCp7. J Mol Biol. 2004; 338(4):711-23. DOI: 10.1016/j.jmb.2004.03.019. View

13.

Mao X, Marky L, Gmeiner W . NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+. J Biomol Struct Dyn. 2004; 22(1):25-33. DOI: 10.1080/07391102.2004.10506977. View

14.

Cosa G, Harbron E, Zeng Y, Liu H, OConnor D, Eta-Hosokawa C . Secondary structure and secondary structure dynamics of DNA hairpins complexed with HIV-1 NC protein. Biophys J. 2004; 87(4):2759-67. PMC: 1304694. DOI: 10.1529/biophysj.104.043083. View

15.

DSouza V, Summers M . Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus. Nature. 2004; 431(7008):586-90. DOI: 10.1038/nature02944. View

16.

Lumry R, Rajender S . Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: a ubiquitous property of water. Biopolymers. 1970; 9(10):1125-227. DOI: 10.1002/bip.1970.360091002. View

17.

Henderson L, Copeland T, Sowder R, Smythers G, Oroszlan S . Primary structure of the low molecular weight nucleic acid-binding proteins of murine leukemia viruses. J Biol Chem. 1981; 256(16):8400-6. View

18.

Covey S . Amino acid sequence homology in gag region of reverse transcribing elements and the coat protein gene of cauliflower mosaic virus. Nucleic Acids Res. 1986; 14(2):623-33. PMC: 339453. DOI: 10.1093/nar/14.2.623. View

19.

Berg J . Potential metal-binding domains in nucleic acid binding proteins. Science. 1986; 232(4749):485-7. DOI: 10.1126/science.2421409. View

20.

Marky L, Breslauer K . Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers. 1987; 26(9):1601-20. DOI: 10.1002/bip.360260911. View