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dna nanostructure

Minho Kim, Sung Min Ko, Jae-Myoung Kim, Jiwoong Son, Chungyeon Lee, Won-Kyu Rhim, Jwa-Min Nam
Uniformly controlling a large number of metal nanostructures with a plasmonically enhanced signal to generate quantitative optical signals and the widespread use of these structures for surface-enhanced Raman scattering (SERS)-based biosensing and bioimaging applications are of paramount importance but are extremely challenging. Here, we report a highly controllable, facile selective-interdiffusive dealloying chemistry for synthesizing the dealloyed intra-nanogap particles (DIPs) with a ∼2 nm intragap in a high yield (∼95%) without the need for an interlayer...
February 28, 2018: ACS Central Science
Pi Liu, Yan Zhao, Xiaoguo Liu, Jixue Sun, Dede Xu, Yang Li, Qian Li, Lihua Wang, Sichun Yang, Chunhai Fan, Jianping Lin
Shape reconfiguration of membrane protein channels is highly regulated under physiological conditions for gated transportation. Nevertheless, mechanistic understanding of molecular channels remains challenging due to the difficulty in probing gating-associated subtle structural changes. Here we show that charge neutralization can drive shape reconfiguration of a biomimetic 6-helix bundle DNA nanotube (6HB). Specifically, 6HB adopts a compact state when being neutralized by Mg2+; and monovalent ions (Na+) switch it to the expansion state, as revealed by molecular dynamics (MD) simulation, small angle X-ray scattering (SAXS) and Förster resonance energy transfer (FRET) characterization...
March 12, 2018: Angewandte Chemie
Rongrong Huang, Nongyue He, Zhiyang Li
DNA has emerged as a promising biomaterial for assembling a variety of nanostructures based on its programmable base pairing. It also has other remarkable properties including stability, prominent biocompatibility, and can easily be modified with functional groups for further applications. In the past few decades, researchers have established various design rules and assembly technologies to improve the stability and complexity of DNA nanostructures. The detection of cancer-associated biomarkers has significant importance in identifying patients with different clinical stages and also in developing adaptive therapeutic strategies...
March 6, 2018: Biosensors & Bioelectronics
Sai Wang, Yiyang Dong, Xingguo Liang
Although surface plasmon resonance (SPR) technique and aptamer technology shows great potential in analytical and biological chemistry, direct capture and analysis of small molecules using SPR remains tough. Detection sensitivity of aptasensor and recognition ability of aptamer is limited, because direct immobilization of aptamer causes large steric hindrance and strand entanglement. Herein, we chose a typical small molecule-tetracycline (Mw. 444.4 g/mol) as a model, and combined aptamer technology, DNA nanostructure, and commercial Biacore T200 SPR instrument to develop a straightforward format SPR aptasensor...
February 27, 2018: Biosensors & Bioelectronics
Jingjie Tan, Chan Li, Qian Wang, Shuyi Li, Shizhu Chen, Jinchao Zhang, Paul C Wang, Lei Ren, Xing-Jie Liang
Flurbiprofen, a hydrophobic COX inhibitor, was coordinated axially with oxoplatin to form a new conjugate cis, cis, trans-[Pt(IV)(NH3)2Cl2(flurbiprofen)2]. The successful synthsis of this new conjugate was confirmed by 1H, 13C and 195Pt NMR. The potential of this conjugate being reduced to cisplatin and subsequently exerting its DNA cross-linking ability was verified using cyclic voltammetry (CV), HPLC and mass spectrum (MS). This conjugate showed markedly higher cytotoxicity on many cancer cell lines than cisplatin, flurbiprofen and physical mixture (mol ratio, cisplatin: flurbiprofen=1:2) of them...
March 9, 2018: Molecular Pharmaceutics
Chun Feng, Zhaobo He, Bo Cai, Jianhong Peng, Jieping Song, Xuechen Yu, Yue Sun, Jing Yuan, Xingzhong Zhao, Yuanzhen Zhang
Detection of detached fetal nucleated red blood cells (fNRBCs) in the maternal peripheral blood may serve as a prospective testing method competing with the cell-free DNA, in non-invasive prenatal testing (NIPT). Methods: Herein, we introduce a facile and effective lab-on-a-chip method of fNRBCs detection using a capture-releasing material that is composed of biotin-doped polypyrrole nanoparticles. To enhance local topographic interactions between the nano-components and fNRBC, a specific antibody, CD147, coated on the nanostructured substrate led to the isolation of fNRBCs from maternal peripheral blood...
2018: Theranostics
Erin E Bedford, Souhir Boujday, Claire-Marie Pradier, Frank X Gu
Combined separation and detection of biomolecules has the potential to speed up and improve the sensitivity of disease detection, environmental testing, and biomolecular analysis. In this work, we synthesized magnetic particles coated with spiky nanostructured gold shells and used them to magnetically separate out and detect oligonucleotides using SERS. The distance dependence of the SERS signal was then harnessed to detect DNA hybridization using a Raman label bound to a hairpin probe. The distance of the Raman label from the surface increased upon complementary DNA hybridization, leading to a decrease in signal intensity...
May 15, 2018: Talanta
Jonathan R Burns, Stefan Howorka
DNA nanopores are a recent class of bilayer-puncturing nanodevices that can help advance biosensing, synthetic biology, and nanofluidics. Here, we create archetypal lipid-anchored DNA nanopores and characterize them with a nanoprobe-based approach to gain essential information about their interactions with bilayers. The strategy determines the molecular accessibility of DNA pores with a nuclease and can thus distinguish between the nanopores' membrane-adhering and membrane-spanning states. The analysis reveals, for example, that pores interact with bilayers in two steps whereby fast initial membrane tethering is followed by slower reorientation to the puncturing state...
March 1, 2018: ACS Nano
Dekai Ye, Xiaolei Zuo, Chunhai Fan
Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly...
February 28, 2018: Annual Review of Analytical Chemistry
X Xie, X Shao, W Ma, D Zhao, S Shi, Q Li, Y Lin
Paclitaxel (PTX) is an effective drug against diseases such as lung cancer, ovarian cancer, and breast cancer. However, multidrug resistance limits the clinical applications of this drug. Tetrahedral DNA nanostructures (TDNs) offer great promise as a drug delivery candidate. In our study, we prepared TDNs that were subsequently loaded with PTX (PTX/TDNs). The cytotoxicity of PTX/TDNs and PTX alone on non-small cell lung cancer (NSCLC) cells (A549) and the PTX-resistant cell line (A549/T) was determined using a cell count kit-8 (CCK-8) assay...
February 27, 2018: Nanoscale
Elena Piacenza, Alessandro Presentato, Raymond J Turner
In the last 15 years, the exploitation of biological systems (i.e. plants, bacteria, mycelial fungi, yeasts, and algae) to produce metal(loid) (Me)-based nanomaterials has been evaluated as eco-friendly and a cost-effective alternative to the chemical synthesis processes. Although the biological mechanisms of biogenic Me-nanomaterial (Bio-Me-nanomaterials) production are not yet completely elucidated, a key advantage of such bio-nanostructures over those chemically synthesized is related to their natural thermodynamic stability, with several studies ascribed to the presence of an organic layer surrounding these Bio-Me-nanostructures...
February 25, 2018: Critical Reviews in Biotechnology
Manil Kukkar, Girish C Mohanta, Satish K Tuteja, Parveen Kumar, Akhshay Singh Bhadwal, Pallabi Samaddar, Ki-Hyun Kim, Akash Deep
The development of nucleic acid-based portable platforms for the real-time analysis of diseases has attracted considerable scientific and commercial interest. Recently, 2D layered molybdenum sulfide (2D MoS2 from here on) nanosheets have shown great potential for the development of next-generation platforms for efficient signal transduction. Through combination with DNA as a biorecognition medium, MoS2 nanostructures have opened new opportunities to design and construct highly sensitive, specific, and commercially viable sensing devices...
February 15, 2018: Biosensors & Bioelectronics
Stephanie J Heerema, Leonardo Vicarelli, Sergii Pud, Raymond N Schouten, Henny W Zandbergen, Cees Dekker
Many theoretical studies predict that DNA sequencing should be feasible by monitoring the transverse current through a graphene nanoribbon while a DNA molecule translocates through a nanopore in that ribbon. Such a readout would benefit from the special transport properties of graphene, provide ultimate spatial resolution because of the single-atom layer thickness of graphene, and facilitate high-bandwidth measurements. Previous experimental attempts to measure such transverse inplane signals were however dominated by a trivial capacitive response...
February 23, 2018: ACS Nano
Graeme A King, Andreas S Biebricher, Iddo Heller, Erwin Peterman, Gijs Wuite
The ability to measure mechanics and forces in biological nanostructures, such as DNA, proteins and cells, is of great importance as a means to analyze biomolecular systems. However, current force detection methods often require specialized instrumentation. Here, we present a novel and versatile method to quantify tension in molecular systems locally and in real time using intercalated DNA fluorescence. This approach can report forces over a range of ~1-65 pN with a resolution of 1-3 pN, using commercially available intercalating dyes and a general-purpose fluorescence microscope...
February 23, 2018: Nano Letters
Qinqin Hu, Hua Li, Lihua Wang, Hongzhou Gu, Chunhai Fan
Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function...
February 21, 2018: Chemical Reviews
Nabanita Saikia, Floyd Johnson, Kevin Waters, Ravi Pandey
Molecular self-assembly of cytosine (Cn) bases on graphene was investigated using molecular dynamics methods. For free-standing Cn bases, simulation conditions (gas vs. aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process...
February 20, 2018: Nanotechnology
Mi Zhou, Nan-Xin Liu, Si-Rong Shi, Yong Li, Qi Zhang, Quan-Quan Ma, Tao-Ran Tian, Wen-Juan Ma, Xiao-Xiao Cai, Yun-Feng Lin
Dental pulp stem cells (DPSCs) derived from the human dental pulp tissue have multiple differentiation capabilities, such as osteo/odontogenic differentiation. Therefore, DPSCs are deemed as ideal stem cell sources for tissue regeneration. As new nanomaterials based on DNA, tetrahedral DNA nanostructures (TDNs) have tremendous potential for biomedical applications. Here, the authors aimed to explore the part played by TDNs in proliferation and osteo/odontogenic differentiation of DPSCs, and attempted to investigate if these cellular responses could be driven by activating the canonical Notch signaling pathway...
February 16, 2018: Nanomedicine: Nanotechnology, Biology, and Medicine
Nayan P Agarwal, Michael Matthies, Bastian Joffroy, Thorsten L Schmidt
The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer. For this purpose, four different wireframe DNA origami structures were designed to have single-stranded gap regions...
February 16, 2018: ACS Nano
Jian Chen, Jun-Feng Wang, Xue-Zhong Wu, Zhen Rong, Pei-Tao Dong, Rui Xiao
We developed a high-performance surface-enhanced Raman scattering (SERS) sensing platform that can be used for specific and sensitive DNA detection. The SERS platform combines the advantages of Au film over nanosphere (AuFON) substrate and Ag@PATP@SiO2 SERS tag. SERS tag-on-AuFON is a sensing system that operates by the self-assembly of SERS tag onto an AuFON substrate in the presence of target DNAs. The SERS signals can be dramatically enhanced by the formation of "hot spots" in the interstices between the assembled nanostructures, as confirmed by finite-difference time-domain (FDTD) simulation...
June 1, 2018: Journal of Nanoscience and Nanotechnology
Xiao Wang, Chen Li, Dong Niu, Ruojie Sha, Nadrian C Seeman, James W Canary
An electro-optical modulator was constructed using a DNA nanostructure scaffold with oligomers of poly(phenylene vinylene) and polyaniline. A molecular device containing one each of the functional molecules was assembled in a DNA origami. The constructs formed an "X" shape and were visualized by AFM. In response to redox reconfiguration, the device reversibly altered fluorescence signal output. This molecular self-assembly strategy provides opportunities to make unique material composites that are difficult to achieve by blending...
February 12, 2018: Nano Letters
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