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Researchers Find Gold Nanoparticles Capable of ‘Unzipping’ DNA

New research from North Carolina State University finds that gold nanoparticles with a slight positive charge work collectively to unravel DNA’s double helix. This finding has ramifications for gene therapy research and the emerging field of DNA-based electronics.

As the nanoparticles cluster together, they pull the strands of DNA apart.

“We began this work with the goal of improving methods of packaging genetic material for use in gene therapy,” says Dr. Anatoli Melechko, an associate professor of materials science and engineering at NC State and co-author of a paper describing the research. Gene therapy is an approach for addressing certain medical conditions by modifying the DNA in relevant cells.

The research team introduced gold nanoparticles, approximately 1.5 nanometers in diameter, into a solution containing double-stranded DNA. The nanoparticles were coated with organic molecules called ligands. Some of the ligands held a positive charge, while others were hydrophobic – meaning they were repelled by water.

Because the gold nanoparticles had a slight positive charge from the ligands, and DNA is always negatively charged, the DNA and nanoparticles were pulled together into complex packages.

“However, we found that the DNA was actually being unzipped by the gold nanoparticles,” Melechko says. The positively-charged ligands on the nanoparticles attached to the DNA as predicted, but the hydrophobic ligands of the nanoparticles became tangled with each other. As this tangling pulled the nanoparticles into clusters, the nanoparticles pulled the DNA apart. Video of how the process works is available here.

“We think gold nanoparticles still hold promise for gene therapy,” says Dr. Yaroslava Yingling, an assistant professor of materials science and engineering at NC State and co-author of the paper. “But it’s clear that we need to tailor the ligands, charge and chemistry of these materials to ensure the DNA’s structural integrity is not compromised.”

The finding is also relevant to research on DNA-based electronics, which hopes to use DNA as a template for creating nanoelectronic circuits. Because some work in that field involves placing metal nanoparticles on DNA, this finding indicates that researchers will have to pay close attention to the characteristics of those nanoparticles – or risk undermining the structural integrity of the DNA.

The paper, “Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation,” was published online June 19 in Advanced Materials. Lead author on the paper is Justin Railsback, a master’s student at NC State. Co-authors include Abhishek Singh and Ryan Pearce, Ph.D. students at NC State; Dr. Ramon Collazo, assistant professor at NC State; Timothy McKnight, of Oak Ridge National Laboratory; and Dr. Zlatko Sitar, Kobe Steel Distinguished Professor of Materials Science and Engineering at NC State. The research was supported by the National Science Foundation.

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Note to Editors: The study abstract follows.

“Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation”

Authors: Justin G. Railsback, Abhishek Singh, Ryan C. Pearce, Ramon Collazo, Zlatko Sitar, Yaroslava G. Yingling and Anatoli V. Melechko, North Carolina State University; Timothy E. McKnight, Oak Ridge National Laboratory

Published: online June 19, 2012 in Advanced Materials

Abstract: The understanding of interactions between double stranded DNA and charged nanoparticles will have a broad bearing on many important applications from drug delivery to DNA-templated metallization. Cationic nanoparticles can bind to DNA, a negatively charged molecule, through a combination of electrostatic attraction, groove binding, and intercalation. Such binding events induce changes in the conformation of a DNA strand. In nature DNA wraps around a cylindrical protein assembly (diameter and height of 6 nm ) with a ~220 positive charge  , creating the complex known as chromatin. The charge of a nanoparticle plays a crucial role in its ability to induce DNA structural changes. If a nanoparticle has a highly positive surface charge density, the DNA is likely to wrap and bend upon binding to the nanoparticle (as in the case of chromatin). On the other hand, if a nanoparticle is weakly charged it will not induce dsDNA compaction.  Consequently, there is a transition zone from extended to compact DNA conformations which depends on chemical nature of the nanoparticle and occurs for polycations with charges between 5 and 10.  While the interactions between highly charged NP and DNA have been extensively studied, the processes occurring within the transition zone are less explored. In this paper, we investigate DNA interactions with weakly charged, ligand functionalized gold nanoparticles (AuNP) and show how binding events with these particles affect the structure of dsDNA. Our chosen AuNP has a 1.4 nm diameter gold core and thiolated alkane ligands bearing primary amines for a total charge of +6 per nanoparticle. The +6 charge permits exploration of DNA-NP molecular interactions in the transition zone. In silico observations showed a reversible and groove specific interaction of AuNPs with DNA and demonstrated that even weakly charged NPs could compromise structural integrity of dsDNA. Electrophoretic mobility indicated the existence of a nanoparticle-modified DNA structure either due to separation into single strands or compaction of DNA. Spectral analysis revealed that the structure of dsDNA with AuNPs is not completely denatured as it has a combination of double and single stranded regions. MD simulations showed that lone AuNPs cannot denature even a dsDNA oligomer, whereas high concentrations of AuNPs can bend and separate DNA strands. Specifically, hydrophobic agglomeration of NPs leads to intercalation of alkane moieties between DNA strands, disrupting Watson-Crick base pairing while charged groups hold and bend the DNA strands. By tuning and balancing charge and hydrophobicity one can envision nanoparticles engineered to evoke a specific structural response from DNA.

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