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DNA nanotechnology

Brunella Pinto, Giulia Rusciano, Stefano D'Errico, Nicola Borbone, Antonio Sasso, Vincenzo Piccialli, Luciano Mayol, Giorgia Oliviero, Gennaro Piccialli
BACKGROUND: G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed. METHODS: The bis-end-linked-(gggt)2 PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS)...
November 29, 2016: Biochimica et Biophysica Acta
A J Cox, H N Bengtson, K H Rohde, D M Kolpashchikov
The Nobel prize in chemistry in 2016 was awarded for 'the design and synthesis of molecular machines'. Here we designed and assembled a molecular machine for the detection of specific RNA molecules. An association of several DNA strands, named multifunctional DNA machine for RNA analysis (MDMR1), was designed to (i) unwind RNA with the help of RNA-binding arms, (ii) selectively recognize a targeted RNA fragment, (iii) attract a signal-producing substrate and (iv) amplify the fluorescent signal by catalysis...
November 25, 2016: Chemical Communications: Chem Comm
Dapeng Li, Wensi Zhang, Xiaoqing Yu, Zhenping Wang, Zhiqiang Su, Gang Wei
Graphene-based materials have attracted increasing attention due to their atomically-thick two-dimensional structures, high conductivity, excellent mechanical properties, and large specific surface areas. The combination of biomolecules with graphene-based materials offers a promising method to fabricate novel graphene-biomolecule hybrid nanomaterials with unique functions in biology, medicine, nanotechnology, and materials science. In this review, we focus on a summarization of the recent studies in functionalizing graphene-based materials using different biomolecules, such as DNA, peptides, proteins, enzymes, carbohydrates, and viruses...
December 1, 2016: Nanoscale
Jinglin Fu, Gabriele Stankeviciute, Sung Won Oh, John Collins, Yinghui Zhong, Ting Zhang
Theranostic medicine has become more promising in cancer treatment, where the cancer diagnosis and chemotherapy are combined for early diagnosis and precise treatment with improved efficacy and reduced side effects. Nanotechnology has played a critical role in developing various nanomaterials with engendered smart functions and targeted delivery. The rapid development of structural DNA nanotechnology has enabled the design and fabrication of complex nanostructures with prescribed 1D, 2D and 3D patterns in vitro and in vivo...
November 22, 2016: Current Topics in Medicinal Chemistry
Jessica A Nash, Tasha L Tucker, William Therriault, Yaroslava G Yingling
The interactions of nanoparticles (NPs) with single stranded nucleic acids (NAs) have important implications in gene delivery, and nanotechnological and biomedical applications. Here, the complexation of cationic ligand functionalized gold nanoparticles with single stranded deoxyribose nucleic acid (DNA) and ribonucleic acid (RNA) are examined using all atom molecular dynamics simulations. The results indicated that complexation depends mostly on charge of nanoparticle, and, to lesser extent, sequence and type of nucleic acid...
November 11, 2016: Biointerphases
Zvi Yaari, Dana da Silva, Assaf Zinger, Evgeniya Goldman, Ashima Kajal, Rafi Tshuva, Efrat Barak, Nitsan Dahan, Dov Hershkovitz, Mor Goldfeder, Janna Shainsky Roitman, Avi Schroeder
Personalized medicine promises to revolutionize cancer therapy by matching the most effective treatment to the individual patient. Using a nanoparticle-based system, we predict the therapeutic potency of anticancer medicines in a personalized manner. We carry out the diagnostic stage through a multidrug screen performed inside the tumour, extracting drug activity information with single cell sensitivity. By using 100 nm liposomes, loaded with various cancer drugs and corresponding synthetic DNA barcodes, we find a correlation between the cell viability and the drug it was exposed to, according to the matching barcodes...
November 10, 2016: Nature Communications
Miglė Tomkuvienė, Edita Kriukienė, Saulius Klimašauskas
DNA methyltransferases (MTases) uniquely combine the ability to recognize and covalently modify specific target sequences in DNA using the ubiquitous cofactor S-adenosyl-L-methionine (AdoMet). Although DNA methylation plays important roles in biological signaling, the transferred methyl group is a poor reporter and is highly inert to further biocompatible derivatization. To unlock the biotechnological power of these enzymes, two major types of cofactor AdoMet analogs were developed that permit targeted MTase-directed attachment of larger moieties containing functional or reporter groups onto DNA...
2016: Advances in Experimental Medicine and Biology
Feng Zhou, Haitao Liu
Recent advances in DNA nanotechnology make it possible to fabricate arbitrarily shaped 1D, 2D, and 3D DNA nanostructures through controlled folding and/or hierarchical assembly of up to several thousands of unique sequenced DNA strands. Both individual DNA nanostructures and their assembly can be made with almost arbitrarily shaped patterns at a theoretical resolution down to 2 nm. Furthermore, the deposition of DNA nanostructures on a substrate can be made with precise control of their location and orientation, making them ideal templates for bottom-up nanofabrication...
2017: Methods in Molecular Biology
John Min, William M Shih, Gaëtan Bellot
Thirty percent of the human proteome is composed of membrane proteins that can perform a wide range of cellular functions and communications. They represent the core of modern medicine as the targets of about 50 % of all prescription pharmaceuticals. However, elucidating the structure of membrane proteins has represented a constant challenge, even in the modern era. To date, only a few hundred high-resolution structural models of membrane proteins are available. This chapter describes the emergence of DNA nanotechnology as a powerful tool for the structural characterization of membrane protein using solution-state nuclear magnetic resonance (NMR) spectroscopy...
2017: Methods in Molecular Biology
Steven D Perrault, William M Shih
Structural DNA nanotechnology methods such as DNA origami allow for the synthesis of highly precise nanometer-scale materials (Rothemund, Nature 440:297-302, 2006; Douglas et al., Nature 459:414-418, 2009). These offer compelling advantages for biomedical applications. Such materials can suffer from structural instability in biological environments due to denaturation and nuclease digestion (Hahn et al., ACS Nano 2014; Perrault and Shih, ACS Nano 8:5132-5140, 2014). Encapsulation of DNA nanostructures in a lipid membrane compartmentalizes them from their environment and prevents denaturation and nuclease digestion (Perrault and Shih, ACS Nano 8:5132-5140, 2014)...
2017: Methods in Molecular Biology
Cheng Tian, Chuan Zhang
Tile-based DNA self-assembly is a promising method in DNA nanotechnology and has produced a wide range of nanostructures by using a small set of unique DNA strands. DNA star motif, as one of DNA tiles, has been employed to assemble varieties of symmetric one-, two-, three-dimensional (1, 2, 3D) DNA nanostructures. Herein, we describe the design principles, assembly methods, and characterization methods of 3D DNA nanostructures assembled from the DNA star motifs.
2017: Methods in Molecular Biology
Lei Fu, Heng-Te Ke
Nanotechnology provides various nanomaterials with tremendous functionalities for cancer diagnostics and therapeutics. Recently, theranostics has been developed as an alternative strategy for efficient cancer treatment through combination of imaging diagnosis and therapeutic interventions under the guidance of diagnostic results. Ultrasound (US) imaging shows unique advantages with excellent features of real-time imaging, low cost, high safety and portability, making US contrast agents (UCAs) an ideal platform for construction of cancer theranostic agents...
September 2016: Cancer Biology & Medicine
Hongmei Zheng, Xiang Li, Chuang Chen, Jian Chen, Jinzhong Sun, Si Sun, Liting Jin, Juanjuan Li, Shengrong Sun, Xinhong Wu
BACKGROUND: Topoisomerase 2 alpha (TOP2A) is a key enzyme in DNA replication and a target of various cytotoxic agents including anthracyclines. Previous studies evaluating the predictive and prognostic values of TOP2A in breast cancer are contradictory, likely secondary to the use of both different detection methods and different cutoff thresholds for positive status. Our own studies have previously confirmed the advantages of quantum dot-based nanotechnology for quantitative analysis of biomarkers relative to conventional immunohistochemistry (IHC)...
2016: International Journal of Nanomedicine
Zhe Han, Qi Yan, Wei Ge, Zhi-Guo Liu, Sangiliyandi Gurunathan, Massimo De Felici, Wei Shen, Xi-Feng Zhang
BACKGROUND: Nanoscience and nanotechnology are developing rapidly, and the applications of nanoparticles (NPs) have been found in several fields. At present, NPs are widely used in traditional consumer and industrial products, however, the properties and safety of NPs are still unclear and there are concerns about their potential environmental and health effects. The aim of the present study was to investigate the potential toxicity of ZnO NPs on testicular cells using both in vitro and in vivo systems in a mouse experimental model...
2016: International Journal of Nanomedicine
Saminathan Ramakrishnan, Sivaraman Subramaniam, Adrian Francis Stewart, Guido Grundmeier, Adrian Keller
DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas...
October 25, 2016: ACS Applied Materials & Interfaces
Huijie Zhang, Xiao-Dong Gao
Synthetic oligodeoxynucleotides containing immunostimulatory CpG motif mimic bacterial DNA and are potent activator of innate and adaptive immune responses. Therefore, CpG ODNs have significant potentials as immunotherapeutic agent for treatment of infectious diseases, allergy and cancer. Many clinical trials involving CpG ODNs either used alone or as adjuvant have been initiated. However, delivery of CpG ODNs to target sites still remains a great challenge due to their extreme susceptibility to nuclease degradation in serum and poor cellular uptake...
January 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
I Caglar Tanrikulu, Audrey Forticaux, Song Jin, Ronald T Raines
Sticky-ended DNA duplexes can associate spontaneously into long double helices; however, such self-assembly is much less developed with proteins. Collagen is the most prevalent component of the extracellular matrix and a common clinical biomaterial. As for natural DNA, the ~10(3)-residue triple helices (~300 nm) of natural collagen are recalcitrant to chemical synthesis. Here we show how the self-assembly of short collagen-mimetic peptides (CMPs) can enable the fabrication of synthetic collagen triple helices that are nearly a micrometre in length...
November 2016: Nature Chemistry
Petr Stadlbauer, Liuba Mazzanti, Tristan Cragnolini, David J Wales, Philippe Derreumaux, Samuela Pasquali, Jiri Sponer
G-quadruplexes are the most important non-canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradicting models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach the thermodynamics equilibrium...
October 21, 2016: Journal of Chemical Theory and Computation
Pandeeswar Makam, Satyaprasad P Senanayak, Thimmaiah Govindaraju
Reliable and ultrasensitive detection of mercury ions is of paramount importance for toxicology assessment, environmental protection and human health. Herein, we present a novel optoelectronic approach based on nanoachitectonics of small molecule templated DNA system that consists of an adenine (A) conjugated small organic semiconductor (BNA) and deoxyribo-oligothymidine (dTn). This mutually templated dynamic chiral co-assembly system (BNAn-dTn) with tunable chiroptical, morphological and electrical properties is tapped in to enable ultra-sensitive and selective detection of inorganic and organometallic mercury in water...
October 18, 2016: ACS Applied Materials & Interfaces
Jaimie Marie Stewart, Mathias Viard, Hari K K Subramanian, Brandon K Roark, Kirill A Afonin, Elisa Franco
RNA is a natural multifunctional polymer, and is an essential component in both complex pathways and structures within the cellular environment. For this reason, artificial self-assembling RNA nanostructures are emerging as a powerful tool with broad applications in drug delivery and metabolic pathway regulation. To date, coordinated delivery of functional molecules via programmable RNA assemblies has been primarily done using nanosize RNA scaffolds. However, larger scaffolds could expand existing capabilities for spatial arrangement of ligands, and enable the controlled delivery of highly concentrated molecular loads...
October 14, 2016: Nanoscale
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