HIV-1 Nucleocapsid Proteins as Molecular Chaperones for Tetramolecular Antiparallel G-Quadruplex Formation

Abstract

HIV-1 nucleocapsid proteins (NCps) facilitate remodeling of nucleic acids to fold thermodynamically stable conformations, and thus called nucleic acid chaperones. To date only little is known on the stoichiometry, NCp-NCp interactions, chaperone activity on G-quadruplex formation, and so on. We report here the direct and real-time analysis on such properties of proteolytic intermediate NCp15 and mature NCp7 using DNA origami. The protein particles were found to predominantly exist in monomeric form, while dimeric and multimeric forms were also observed both in free solution and bound to the quadruplex structure. The formation and the dissociation events of the G-quadruplexes were well documented in real-time and the intermediate-like states were also visualized. We anticipate that this pioneering study will strengthen our understanding on the chaperone activity of HIV-1 proteins which in turn will be helpful for the drug design based on G-quadruplex and also for the development of drugs against AIDS.

Direct and Single‐Molecule Visualization of the Solution‐State Structures of G‐Hairpin and G‐Triplex Intermediates

“…Herein we utilize a DNA origami frame24–28 to structurally and stoichiometrically control the DNA sequences (see Supporting Information, Figure S1) so that a particular intermediate can be selectively formed, and used high‐speed atomic force microscopy (HS‐AFM)29–34 to directly visualize the intermediates. For this investigation, we have adopted two types of structures: 1) a tetramolecular antiparallel;28 and 2) (3+1)‐type27 G‐quadruplex structures.…”

Direct and Single‐Molecule Visualization of the Solution‐State Structures of G‐Hairpin and G‐Triplex Intermediates

“…Herein we utilize a DNA origami frame [24][25][26][27][28] to structurally and stoichiometrically control the DNA sequences (see Supporting Information, Figure S1) so that a particular intermediate can be selectively formed, and used high-speed atomic force microscopy (HS-AFM) [29][30][31][32][33][34] to directly visualize the intermediates. For this investigation, we have adopted two types of structures: 1) a tetramolecular antiparallel; [28] and 2) (3+1)-type [27] G-quadruplex structures.…”

The role of RNA G‐quadruplexes in human diseases and therapeutic strategies

“…These GQs in the central region or the 3′‐end of the HIV genome could play a role in the replication of HIV‐1 (Piekna‐Przybylska et al, ). A nucleic acid chaperone Ncp7 can induce tetramolecular antiparallel RNA GQ formation in the Gag gene of HIV‐1 suggesting a possible involvement of this GQ in viral capsid formation (Rajendran et al, ). A PGQS has been identified in the reading frame of the negative regulatory factor (Nef) of HIV‐1.…”