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dna nanostructure

Rebekah J Karadeema, Maria Stancescu, Tyler P Steidl, Sophia C Bertot, Dmitry M Kolpashchikov
Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is instrumental in healthcare for the detection of genetic and infectious diseases and drug-resistant pathogens. Here we took advantage of the developments in DNA nanotechnology to design a hybridization sensor, named the 'owl sensor', which produces a fluorescence signal only when it complexes with fully complementary DNA or RNA analytes. The novelty of the owl sensor operation is that the selectivity of analyte recognition is, at least in part, determined by the structural rigidity and stability of the entire DNA nanostructure rather than exclusively by the stability of the analyte-probe duplex, as is the case for conventional hybridization probes...
May 21, 2018: Nanoscale
Mohammad Hasanzadeh, Amir Zargami, Hossein Navay Baghban, Ahad Mokhtarzadeh, Nasrin Shadjou, Soltanali Mahboob
The genetic disorder phenylketonuria (PKU) is the inability to metabolize phenylalanine because of a lack of the enzyme phenylalanine hydroxylase. Phenylalanine is used to biochemically form proteins, coded for by DNA. The development of an apta-assay for detection of l-Phenylalanine is presented in this work. A highly specific DNA-aptamer, selected to l-Phenylalanine was immobilized onto a gold nanostructure and electrochemical measurements were performed in a solution containing the phosphate buffer solution with physiological pH...
May 16, 2018: International Journal of Biological Macromolecules
Jianmei Zou, Cheng Jin, Ruowen Wang, Hailan Kuai, Lili Zhang, Xiao-Bing Zhang, Juan Li, Liping Qui, Weihong Tan
Creating new functional building blocks that expand the versatility of nanostructures depends on bottom-up self-assembly of amphiphilic biomolecules. Inspired by the unique physicochemical properties of hydrophobic perfluorocarbons, coupled with the powerful functions of nucleic acids, we herein report the synthesis of a series of diperfluorodecyl-DNA conjugates (PF-DNA) which can efficiently self-assemble into micelles in aqueous solution. Based on the micelle structure, both target binding affinity and enzymatic resistance of the DNA probe can be enhanced...
May 17, 2018: Analytical Chemistry
Kiri Thornalley, Erik Laurini, Sabrina Pricl, David K Smith
A family of four self-assembling lipopeptides containing Ala-Lys peptides attached to a C16 aliphatic chain was synthesised. These compounds form two enantiomeric pairs that bear a diastereomeric relationship to one another (C16-L-Ala-L-Lys/C16-D-Ala-D-Lys) and (C16-D-Ala-L-Lys/C16-L-Ala-D-Lys). These diastereomeric pairs have very different critical micelle concentrations (CMCs), with LL/DD < DL/LD suggesting more effective assembly of the former. The self-assembled multivalent (SAMul) systems bind biological polyanions as result of the cationic lysine groups on their surfaces...
May 15, 2018: Angewandte Chemie
Maartje Bastings, Frances Anastassacos, Nandhini Ponnuswamy, Franziska Leifer, Garry Cuneo, Chenxiang Lin, Donald E Ingber, Ju Hee Ryu, William M Shih
Designer nanoparticles with controlled shape and size are increasingly popular vehicles for therapeutic delivery due to their enhanced cell delivery performance. However, our ability to fashion nanoparticles has offered only limited control over these parameters. Structural DNA nanotechnology has an unparalleled ability to self-assemble three-dimensional nanostructures with near-atomic resolution features and thus, it offers an attractive platform for systematic exploration of the parameter space relevant to nanoparticle uptake by living cells...
May 14, 2018: Nano Letters
Zeming Chen, Fuyao Liu, Yanke Chen, Jun Liu, Xiaoying Wang, Ann T Chen, Gang Deng, Hongyi Zhang, Jie Liu, Zhangyong Hong, Jiangbing Zhou
Due to its simplicity, versatility, and high efficiency, the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technology has emerged as one of the most promising approaches for treatment of a variety of genetic diseases, including human cancers. However, further translation of CRISPR/Cas9 for cancer gene therapy requires development of safe approaches for efficient, highly specific delivery of both Cas9 and single guide RNA to tumors. Here, novel core-shell nanostructure, liposome-templated hydrogel nanoparticles (LHNPs) that are optimized for efficient codelivery of Cas9 protein and nucleic acids is reported...
December 8, 2017: Advanced Functional Materials
Katharina Brassat, Saminathan Ramakrishnan, Julius Bürger, Marcel Hanke, Mahnaz Doostdar, Jörg K N Lindner, Guido Grundmeier, Adrian Keller
DNA origami nanostructures are versatile substrates for the controlled arrangement of molecular capture sites with nanometer precision and thus have many promising applications in single-molecule bioanalysis. Here, we investigate the adsorption of DNA origami nanostructures in nanohole arrays which represent an important class of biosensors and may benefit from the incorporation of DNA origami-based molecular probes. Nanoholes with well-defined diameter that enable the adsorption of single DNA origami triangles are fabricated in Au films on Si wafers by nanosphere lithography...
May 13, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Xiaoyan Li, Gang Peng, Feng Cui, Qianying Qiu, Xiaojun Chen, He Huang
An ultrasensitive electrochemical genosensor has been fabricated for the double determination of two different specific sequences deduced from the maternally expressed gene3 (MEG3) lncRNA (long noncoding RNA), which was demonstrated by coupling RNase A-aided target recycling with DNA supersandwich-induced signal enhancement, based on a composite interface of graphene-like tungsten disulfide/dendritic gold nanostructures (WS2 /DGN). Firstly, duple target sequences of T1 and T2 were captured by the primer probes of P1 /P2 functionalized Fe3 O4 @C magnetic nanoparticles, via the DNA/RNA hybridization between T1 /T2 and P1 /P2 ...
May 2, 2018: Biosensors & Bioelectronics
Elisa Scatena, Sara Pascale, Cristina Cairone, Filippo Fabbri, Costantino Del Gaudio
Aptamers, synthetic single-stranded DNA or RNA molecules, can be regarded as a valuable improvement to develop novel ad hoc sensors to diagnose several clinical pathologies. Their intrinsic potential is related to the high specificity and sensitivity to the selected target biomarkers, being capable of detecting very low concentrations and thus allowing an early diagnosis of a possible disease. This kind of probe can be usefully integrated into a number of different devices in order to provide a reliable acquisition of the analyte and properly elaborate the related signal...
2018: BioMed Research International
Yingxu Shang, Jia Shi, Huan Liu, Xinfeng Liu, Zhen-Gang Wang, Baoquan Ding
We present a SERS-active gold nanostructure with built-in electromagnetic hotspots formed by densely packed gold nanoparticles on a gold nanorod. Cy3 labeled stimuli-responsive DNA motifs were introduced to the SERS-active nanostructure. The SERS signals can be switched ON and OFF reversibly in response to external stimuli (pH, metal ions or organic molecules).
May 11, 2018: Nanoscale
Sang Won Jung, Han Seul Kim, Art E Cho, Yong-Hoon Kim
Controlling the dynamics of DNA translocation is a central issue in the emerging nanopore-based DNA sequencing. To address the potential of heteroatom doping of carbon nanostructures to achieve this goal, herein we carry out atomistic molecular dynamics simulations for single-stranded DNAs translocating between two pristine or doped carbon nanotube (CNT) electrodes. Specifically, we consider the substitutional nitrogen doping of capped CNT (capCNT) electrodes and perform two types of molecular dynamics simulations for the entrapped and translocating single-stranded DNAs...
May 9, 2018: ACS Applied Materials & Interfaces
Gang Peng, Xiaoyan Li, Feng Cui, Qianying Qiu, Xiaojun Chen, He Huang
In the food safety evaluation, aflatoxin B1 (AFB1) is an important indicator. In this work, we developed an AFB1 electrochemical aptasensor based on tetrahedral DNA nanostructures (TDNs) immobilized three dimensionally ordered macroporous MoS2-AuNPs hybrid (3DOM MoS2-AuNPs) recognition interface and horseradish peroxidase (HRP) functionalized magnetic signal amplifier. To greatly enhance the recognition efficiency, sensitivity and stability of the aptasensor, the AFB1 aptamer-incorporated TDNs were ingeniously combined with the 3DOM MoS2-AuNPs film for the construction of the sensing interface...
May 7, 2018: ACS Applied Materials & Interfaces
Erik E Augspurger, Muhit Rana, Mehmet Veysel Yigit
Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. DNA-based technologies' recent prominence in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions and solvent types...
May 7, 2018: ACS Sensors
Avigail Stern, Gennady Eidelshtein, Roman Zhuravel, Gideon I Livshits, Dvir Rotem, Alexander Kotlyar, Danny Porath
Over the past decades, DNA, the carrier of genetic information, has been used by researchers as a structural template material. Watson-Crick base pairing enables the formation of complex 2D and 3D structures from DNA through self-assembly. Various methods have been developed to functionalize these structures for numerous utilities. Metallization of DNA has attracted much attention as a means of forming conductive nanostructures. Nevertheless, most of the metallized DNA wires reported so far suffer from irregularity and lack of end-to-end electrical connectivity...
May 4, 2018: Advanced Materials
Shulian Bai, Bangtian Xu, Yongcan Guo, Juhui Qiu, Wen Yu, Guoming Xie
While detection of microRNA with or without signal amplification is highly informative, nanosensors with high specificity for cell-specific RNA detection are rare. Methods: In this study, a tetrahedral DNA nanostructure (TDN) with a specific function was combined with gold nanoparticles (Au-NP) possessing fluorescence quenching effects and a large surface area to fabricate a fluorescence resonance energy transfer based nanosensor (Au-TDNN). The presence of miR-21 (target) can separate the fluorescent dye-labeled detection probe on Au-TDNNs from Au-NPs, which separates the donor and acceptor, thus inducing an intensive fluorescence signal...
2018: Theranostics
Samuel W Schaffter, Leopold N Green, Joanna Schneider, Hari K K Subramanian, Rebecca Schulman, Elisa Franco
The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes...
April 30, 2018: Nucleic Acids Research
Melánia Babincová, Hana Vrbovská, Paul Sourivong, Peter Babinec, Štefan Durdík
BACKGROUND/AIM: Malignant gliomas remain refractory to several therapeutic approaches and the requirement for novel treatment modalities is critical to combat this disease. Etoposide is a topoisomerase-II inhibitor, which promotes DNA damage and apoptosis of cancer cells. In this study, we prepared albumin with embedded magnetic nanoparticles and etoposide for in vitro evaluation of combined hyperthermia and chemotherapy. MATERIAL AND METHODS: Magnetic nanoparticles were prepared by a modified co-precipitation method in the presence of human serum albumin and etoposide...
May 2018: Anticancer Research
Jianbing Liu, Linlin Song, Shaoli Liu, Qiao Jiang, Qing Liu, Na Li, Zhen-Gang Wang, Baoquan Ding
The efficient delivery of a therapeutic gene into target tissues has remained a major obstacle in realizing a viable gene-based medicine. Herein, we introduce a facile and universal strategy to construct a DNA nanostructure-based co-delivery system containing a linear tumor therapeutic gene (p53) and a chemotherapeutic drug (doxorubicin, DOX) for combined therapy of multi-drug resistant tumor (MCF-7R). This novel co-delivery system, which is structurally similar to a kite, is rationally designed to contain multiple functional groups for the targeted delivery and controlled release of the therapeutic cargoes...
April 30, 2018: Nano Letters
Bin Guo, Bo Wen, Wei Cheng, Xiaoyan Zhou, Xiaolei Duan, Min Zhao, Qianfeng Xia, Shijia Ding
In this research, an enzyme-free and label-free surface plasmon resonance (SPR) biosensing strategy has been developed for ultrasensitive detection of fusion gene based on the heterogeneous target-triggered DNA self-assembly aptamer-based hydrogel with streptavidin (SA) encapsulation. In the presence of target, the capture probes (Cp) immobilized on the chip surface can capture the PML/RARα, forming a Cp-PML/RARα duplex. After that, the aptamer-based network hydrogel nanostructure is formed on the gold surface via target-triggered self-assembly of X shaped polymers...
April 14, 2018: Biosensors & Bioelectronics
Congcong Bu, Lixuan Mu, XIngxing Cao, Min Chen, Guangwei She, Wensheng Shi
Linking the fluorescent silver nanoclusters (AgNCs) and guanine-rich(G-rich)DNA chains by the thermal sensitive DNA stem-loop at teminal 5' and 3', DNA nanostructure-based fluorescence thermometers were fabricated. The variations of the temperature alter the distance between AgNCs and G-rich DNA chain, which could affect the interaction between them. As a result, the intensity of fluorescence emission from AgNCs at 636 nm can be sensitively modulated. It was found that such red emission is more sensitive to the temperature comparing with its intrinsic green emission at 543 nm, and sensitivity of -3...
April 27, 2018: Nanotechnology
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