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18 pages, 2805 KiB

Open AccessArticle

DNA Nanomachine (DNM) Biplex Assay for Differentiating Bacillus cereus Species

by Muhannad Ateiah, Erik R. Gandalipov, Aleksandr A. Rubel, Maria S. Rubel and Dmitry M. Kolpashchikov

Int. J. Mol. Sci. 2023, 24(5), 4473; https://doi.org/10.3390/ijms24054473 - 24 Feb 2023

Cited by 10 | Viewed by 3463

Abstract

Conventional methods for the detection and differentiation of Bacillus cereus group species have drawbacks mostly due to the complexity of genetic discrimination between the Bacillus cereus species. Here, we describe a simple and straightforward assay based on the detected unamplified bacterial 16S rRNA by DNA nanomachine (DNM). The assay uses a universal fluorescent reporter and four all-DNA binding fragments, three of which are responsible for “opening up” the folded rRNA while the fourth stand is responsible for detecting single nucleotide variation (SNV) with high selectivity. Binding of the DNM to 16S rRNA results in the formation of the 10–23 deoxyribozyme catalytic core that cleaves the fluorescent reporter and produces a signal, which is amplified over time due to catalytic turnover. This developed biplex assay enables the detection of B. thuringiensis 16S rRNA at fluorescein and B. mycoides at Cy5 channels with a limit of detection of 30 × 10³ and 35 × 10³ CFU/mL, respectively, after 1.5 h with a hands-on time of ~10 min. The new assay may simplify the analysis of biological RNA samples and might be useful for environmental monitoring as a simple and inexpensive alternative to amplification-based nucleic acid analysis. The DNM proposed here may become an advantageous tool for detecting SNV in clinically significant DNA or RNA samples and can easily differentiate SNV under broadly variable experimental conditions and without prior amplification. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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12 pages, 10600 KiB

Open AccessArticle

A DNA Finite-State Machine Based on the Programmable Allosteric Strategy of DNAzyme

by Jun Wang, Xiaokang Zhang, Peijun Shi, Ben Cao and Bin Wang

Int. J. Mol. Sci. 2023, 24(4), 3588; https://doi.org/10.3390/ijms24043588 - 10 Feb 2023

Cited by 3 | Viewed by 2580

Abstract

Living organisms can produce corresponding functions by responding to external and internal stimuli, and this irritability plays a pivotal role in nature. Inspired by such natural temporal responses, the development and design of nanodevices with the ability to process time-related information could facilitate the development of molecular information processing systems. Here, we proposed a DNA finite-state machine that can dynamically respond to sequential stimuli signals. To build this state machine, a programmable allosteric strategy of DNAzyme was developed. This strategy performs the programmable control of DNAzyme conformation using a reconfigurable DNA hairpin. Based on this strategy, we first implemented a finite-state machine with two states. Through the modular design of the strategy, we further realized the finite-state machine with five states. The DNA finite-state machine endows molecular information systems with the ability of reversible logic control and order detection, which can be extended to more complex DNA computing and nanomachines to promote the development of dynamic nanotechnology. Full article

(This article belongs to the Section Molecular Nanoscience)

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12 pages, 2416 KiB

Open AccessReview

Structural Changes as a Tool for Affinity Recognition: Conformational Switch Biosensing

by Viviana Scognamiglio and Amina Antonacci

Crystals 2022, 12(9), 1209; https://doi.org/10.3390/cryst12091209 - 27 Aug 2022

Cited by 4 | Viewed by 1791

Abstract

Biosensors draw inspiration from natural chemosensing based on molecular switches between different bond-induced conformational states. Proteins and nucleic acids can be adapted into switch-based biosensors with a wide plethora of different configurations, taking advantage of the variety of transduction systems, from optical to electrochemical or electrochemiluminescence, as well as from nanomaterials for signal augmentation. This review reports the latest trends in conformational switch biosensors reported in the literature in the last 10 years, focusing on the main representative and recent examples of protein-based switching biosensors, DNA nanomachines, and structure-switched aptamers being applied for the detection of a wide range of target analytes with interest in biomedical and agro-environmental sectors. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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10 pages, 1412 KiB

Open AccessArticle

Covalent Positioning of Single DNA Molecules for Nanopatterning

by Eung-Sam Kim, Jung Sook Kim, Nishan Chakrabarty and Chul-Ho Yun

Nanomaterials 2021, 11(7), 1725; https://doi.org/10.3390/nano11071725 - 30 Jun 2021

Viewed by 2285

Abstract

Bottom-up micropatterning or nanopatterning can be viewed as the localization of target molecules to the desired area of a surface. A majority of these processes rely on the physical adsorption of ink-like molecules to the paper-like surface, resulting in unstable immobilization of the target molecules owing to their noncovalent linkage to the surface. Herein, successive single nick-sealing facilitated the covalent immobilization of individual DNA molecules at defined positions on a dendron-coated silicon surface using atomic force microscopy. The covalently-patterned ssDNA was visualized when the streptavidin-coated gold nanoparticles bound to the biotinylated DNA. The successive covalent positioning of the target DNA under ambient conditions may facilitate the bottom-up construction of DNA-based durable nanostructures, nanorobots, or memory system. Full article

(This article belongs to the Special Issue Mechanochemistry and Nanotechnology)

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24 pages, 3601 KiB

Open AccessReview

Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology

by Runjhun Saran, Yong Wang and Isaac T. S. Li

Sensors 2020, 20(24), 7019; https://doi.org/10.3390/s20247019 - 8 Dec 2020

Cited by 26 | Viewed by 8658

Abstract

The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA’s bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA’s rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines. Full article

(This article belongs to the Special Issue DNA-Based Sensors for Single-Molecule Biology)

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9 pages, 1976 KiB

Open AccessArticle

A Nanostructured SERS Switch Based on Molecular Beacon-Controlled Assembly of Gold Nanoparticles

by Yansheng Li, Yaya Cheng, Liping Xu, Hongwu Du, Peixun Zhang, Yongqiang Wen and Xueji Zhang

Nanomaterials 2016, 6(2), 24; https://doi.org/10.3390/nano6020024 - 22 Jan 2016

Cited by 10 | Viewed by 7200

Abstract

In this paper, highly purified and stable gold nanoparticle (AuNP) dimers connected at the two ends of DNA linkage were prepared by a versatile method. A nanostructured, surface-enhanced Raman scattering (SERS) switching sensor system was fabricated based on the controlled organization of gold nanoparticles (AuNPs) by a DNA nanomachine through the controlled formation/deformation of SERS “hotspots”. This strategy not only opens opportunities in the precise engineering of gap distances in gold-gold nanostructures in a highly controllable and reproducible fashion, but also provides a unique ability to research the origin of SERS and sequence-specific DNA detection. Full article

(This article belongs to the Special Issue Nanostructured Biosensors 2016)

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