Unfolding of DNA quadruplexes induced by HIV-1 nucleocapsid protein

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 ΔG of melting for the latter, and with the inverse correlation between nucleic acid stability and the destabilizing activity of NC.

HIV-1 Nucleocapsid Protein Increases Strand Transfer Recombination by Promoting Dimeric G-quartet Formation

“…2C) (15, 27-29). It appears that NC, as reported previously in several other studies, has distinct effects on different forms of G-quartets (43,44). Specifically, the results suggested that NC stabilized the G-quartet dimer but destabilized the G-quartet monomer.…”

“…Interestingly, an apparent divergence of the influence of NC on distinct forms of G-quartets was observed recently. A circular dichroism study demonstrated that NC destabilized DNA monomer quadruplexes formed by the sequence d(GGT TGG TGT GGT TGG) in the presence of K ϩ or Sr 2ϩ , presumably through the unstacking of the G-quartets upon protein binding (43). Significantly, this G-quartet monomer destabilization activity of NC relies on its zinc finger domain but not its basic domain because EDTA-treated NC failed to influence G-quartet folding, whereas truncated NC (11-55) lacking the N-terminal basic domain still maintained the G-quartet destabilization activity (43).…”

“…A circular dichroism study demonstrated that NC destabilized DNA monomer quadruplexes formed by the sequence d(GGT TGG TGT GGT TGG) in the presence of K ϩ or Sr 2ϩ , presumably through the unstacking of the G-quartets upon protein binding (43). Significantly, this G-quartet monomer destabilization activity of NC relies on its zinc finger domain but not its basic domain because EDTA-treated NC failed to influence G-quartet folding, whereas truncated NC (11-55) lacking the N-terminal basic domain still maintained the G-quartet destabilization activity (43). NC has also been shown to exhibit a high binding affinity for but no destabilization effect on the sequence d(TTG GGG GGT ACA GTG CA) derived from the HIV-1 central DNA flap, which folds in vitro into an tetramolecular parallel DNA quadruplex (44).…”

CD and DSC Investigation of Individual and Complex Influence of Meso-Tetra(4-Oxiethylpyridil) Porphyrin (TOEPyP4) and Its Zn-Complex on DNA

“…The water-soluble meso-tetra(4-N-oxyethylpyridil) porpyrin (TOEPyP4) and its Zn-containing analogue was synthesized in ESU according to the method described in work [18], and it was kindly granted by professor S. , where M w is molecular weight, and ε 422 and ε 440 are Sore absorption bands initiated by binding of porphyrin to DNA. All studies were carried out in buffer solution 10 mM NaCl, 1 mM Na-phosphate, and Ph 7.02.…”

Molecular modeling and spectroscopic studies of semustine binding with DNA and its comparison with lomustine–DNA adduct formation

“…Besides this, CD spectra of semustine-DNA complexes illustrate isoelliptic behavior at 231 and 258 nm (isosbestic points shown by red circles in Figure 8). This can be ascribed to semustine induced two-state transition in DNA molecule (Mayer & Drago, 1976;Kankia, Barany, & Musier-Forsyth, 2005), as semustine exerts its anti-cancer mechanism of action in two phase (formation of O6-chloroethyl guanine adducts pursued by the development of dG-dC DNA cross-links). Further, this is in corroboration with the FTIR spectral outcomes that signify an initial interaction of semustine with thymine followed by the formation of dG-dC DNA cross-links.…”