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Open AccessArticle

DNA Unwinding Driven by Gold Nanoparticles

by Liat Katrivas, Galina M. Proshkina, Sergey M. Deyev and Alexander B. Kotlyar

Nanomaterials 2025, 15(24), 1872; https://doi.org/10.3390/nano15241872 - 13 Dec 2025

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We demonstrate that gold nanoparticles (AuNPs) are capable of unwinding double-stranded (ds) DNA. Upon unwinding, the exposed nucleobases of the separated strands adsorb onto the nanoparticle surface, resulting in the coating of the particles. The unwinding process was characterized by Atomic Force Microscopy (AFM) and absorption spectroscopy. Our results show that AuNPs initially bind to single-stranded overhangs at the duplex termini, forming dsDNA–nanoparticle dumbbells. This binding event subsequently initiates the separation of the DNA strands. As the unwinding proceeds, the nanoparticles become progressively wrapped by the unwound DNA strands, which leads to a gradual reduction in the interparticle distance within the dumbbells. This process is driven by the strong affinity of nucleobases for the gold surface. The efficiency of DNA unwinding was found to depend strongly on both nanoparticle size and temperature. These findings provide new insights into DNA-nanoparticle interactions and may facilitate the rational design of DNA–AuNP hybrid nanostructures such as dumbbell-shaped conjugates for applications in DNA-based nanoelectronics, biosensing, and self-assembled nanomaterials. Full article

(This article belongs to the Special Issue Nanosomes in Precision Nanomedicine (Second Edition))

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15 pages, 2122 KB

Open AccessArticle

DNA–Gold Nanoparticle Dumbbells: Synthesis and Nanoscale Characterization

by Esraa Hijaze, Liat Katrivas, Zakhar Reveguk, Shachar Richter and Alexander B. Kotlyar

Nanomaterials 2025, 15(20), 1583; https://doi.org/10.3390/nano15201583 - 17 Oct 2025

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Abstract

We report an efficient, high-yield method for synthesizing dumbbell-shaped conjugates composed of gold nanoparticles (AuNPs) connected by double-stranded (ds) DNA. The dsDNA, bearing terminal thiol groups, was covalently attached to two AuNPs to form uniform constructs comprising either 15 nm or 25 nm particles bridged by 38 base pairs (bp) or 100 bp dsDNA. The dumbbells were purified by gel electrophoresis and exhibited high stability, remaining intact for several days in pure water or buffers at ambient temperature. Deposition onto solid substrates followed by drying, however, led to their partial structural collapse. TEM imaging showed that deposition on carbon grids typically yielded dumbbell structures with interparticle gaps of only 1–2 nm, suggesting that the dsDNA bridge contracts during deposition and drying. However, deposition on polylysine-coated mica for AFM imaging preserved the native geometry, with the gaps consistent with the expected DNA length. Our results reveal that deposition significantly affects the structure and integrity of dsDNA bridges in dumbbell constructs, highlighting the importance of appropriate substrate and surface coating selection for reliable characterization of DNA properties in dried dumbbells. Full article

(This article belongs to the Section Biology and Medicines)

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10 pages, 2395 KB

Open AccessCommunication

Fluorescence DNA Switch for Highly Sensitive Detection of miRNA Amplified by Duplex-Specific Nuclease

by Xiaoqiang Li, Zhenzhen Guo, Gangyin Luo and Peng Miao

Sensors 2022, 22(9), 3252; https://doi.org/10.3390/s22093252 - 23 Apr 2022

Cited by 3 | Viewed by 3101

Abstract

DNA is a type of promising material for the construction of sensors owing to its sequence programmability to control the formation of certain structures. MicroRNA (miRNA) can be applied as promising biomarkers for the diagnosis of a range of diseases. Herein, a novel fluorescent sensing strategy for miRNA is proposed combining duplex-specific nuclease (DSN)-mediated amplification and dumbbell DNA structural switch. Gold nanoparticles (AuNPs) are employed, which provide a 3D reaction interface. They also act as effective fluorescence quenchers. The proposed sensor exhibits high sensitivity (sub-femtomolar level) with a wide dynamic range. In addition, excellent selectivity to distinguish homology sequences is achieved. It also performs satisfactorily in biological samples. Overall, this fluorescent sensor provides a powerful tool for the analysis of miRNA levels and can be applied for related biological studies and clinical diagnosis. Full article

(This article belongs to the Collection Recent Advances in Fluorescent Sensors)

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8 pages, 1679 KB

Open AccessFeature PaperArticle

Preparation, Characterization and Manipulation of Conjugates between Gold Nanoparticles and DNA

by Gennady Eidelshtein, Moran Fattal, Gavriel Avishai, Benjamin Kempinski, Clelia Giannini and Alexander Kotlyar

Nanomaterials 2016, 6(9), 167; https://doi.org/10.3390/nano6090167 - 8 Sep 2016

Cited by 4 | Viewed by 7202

Abstract

Here we described the preparation and characterization by atomic force microscopy of dumbbell-shaped conjugates between 450 bp double-stranded DNA polymer, poly(dG)-poly(dC), and 5 nm gold nanoparticles (GNPs). We have demonstrated that the size of the nanoparticles in the conjugates can be increased in [...] Read more.

(This article belongs to the Special Issue DNA-Based Nanotechnology)

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