Enzyme-Directed Positioning of Nanoparticles on Large DNA Templates (original) (raw)

Probing DNA assembly into nanoparticles with short DNA

MRS Proceedings, 2012

ABSTRACTDNA is an anionic polyelectrolyte, which occupies a large volume in salt free solution due to the coulomb repulsion between the charged groups. In the presence of high valence cations, DNA condenses into nanoparticles. DNA nanoparticles have generated a lot of interest as a preferred vehicle for delivering therapeutic DNA in gene therapy. The efficiency of gene delivery is determined by stability and compactness of the particles. However not much is known about the organization of DNA within the particles. The large polymer cations condense DNA rapidly, with no distinct intermediate stages that give insight into the arrangement of DNA within the nanoparticle. In our work, we form nanoparticles with short DNA strands to slow down the condensation process. The polymer cation is polyethyleneimine with grafted sugar moieties. Distinct intermediate stages are observed with Atomic Force Microscopy. The assembly occurs via the formation of fiber condensates, which appear to be the ...

Nano-assembly of DNA based electronic devices using atomic force microscopy

2004

DNA electronics circuits require an efficient way to accurately position and individually manipulate DNA molecules. The recent development of Atomic Force Microscopy (AFM) seems to be a promising solution. We have recently developed an AFM based augmented reality system. This new system can provide both real-time force feedback and real-time visual feedback during nanomanipulation. We have shown that nano-imprinting and manipulation of nano-particles and nano-rods can be easily performed under assistance of the augmented reality system. In this research, the system's ability is extended to manipulation of DNA molecules. Using a polynomial fitting method, the deformation of DNA molecules is displayed in real time in the augmented reality system during manipulation. Indeed, DNA molecules adopt many different structures including kinks, bends, bulges and distortions. These different structures and inappropriate physical contacts may result in the controversy of DNA conductivity reported over the last decade. The AFM based nanomanipulation system can be used either as a nanolithography tool to make small gap electrodes or a nanomanipulation tool to elongate, deform and cut DNA molecules. The measurement of the conductivity of DNA molecules in their different shapes and structures is a promising method to find conclusive evidences, which will verify the electrical conductivity of DNA molecules. 0-7803-8463-6

Multimodal Characterization of a Linear DNA-Based Nanostructure

ACS Nano, 2012

9 10 D eveloping methods for patterning 11 discrete particles and molecules at 12 the nanoscale has become an im-13 portant avenue for nanotechnological re-14 search as the limitations and inefficiencies 15 of conventional top-down patterning be-16 come ever more apparent. For such work, 17 investigators are increasingly turning to 18 self-assembly methodologies. While there 19 are many systems that allow for self-assem-20 bly of simple molecular structures, DNA-21 based technologies provide inherent ad-22 vantages due to the precise nature of 23 WatsonÀCrick base pairing and the molec-24 ular-level control one has over base se-25 quence. In the simplest examples, linear 26 DNA constructs have been assembled with 27 a wide variety of particle and molecular 28 attachments including fluorescent dyes, 29 semiconductor quantum dots (QDs), gold 30 nanoparticles (AuNPs), and proteins, clearly 31 demonstrating the potential of DNA functio-32 nalization chemistry for nanoscale control. 1À4 33 Greatly expanding the potential application 34 space, Seeman pioneered methods that use 35 DNA as a self-assembled structural material. 5 36 As he elegantly demonstrated, the use of 37 crossovers, tiles, and junctions permits a wide 38 range of structures to be realized. 6À10 Rothe-39 mund extended this methodology further 40 with DNA origami, 11 an approach for creating 41 arbitrary two-dimensional DNA structures 42 using a long scaffold strand and many smaller 43 staple strands. 12À16 In all implementations, 44 since each base or set of bases within the 45 DNA structure is uniquely addressable, there 46 is potential for a self-assembly approach that 47 allows for arbitrary particle or molecular pla-48 cement with a resolution approaching the 49 base-to-base separation distance of ∼3 Å. 50 In order to reach a full understanding of 51 the accuracy with which such DNA struc-52 tures form and the consequent precision 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 that can be realized in DNA-based pattern-77 ing, it is necessary to examine a variety of 78 assembled structures in intimate detail 79 using a diverse set of techniques. To date, 80 such a study has not been performed, nor is 81 it clear what exactly would constitute a "full" 82 characterization. In molecular biology, X-ray 83 crystallography is the gold standard in di-84 ABSTRACT Designer DNA structures have garnered much interest as a way of assembling novel nanoscale architectures with exquisite control over the positioning of discrete molecules or nanoparticles.

8. Nanomaterials in the Assembly of Electrochemical DNA Sensors

Nanoanalytics, 2018

The development of electrochemical DNA sensors and aptasensors based on nanoparticles different in nature, size, shape, and preparation protocols has been considered with particular emphasis to the mechanism of their influence on signal readout and way of implementation in the biosensor assembly. Most attention is paid to application of Au nanoparticles and carbonaceous nanomaterials though the examples of other applications and hybrid nanomaterials are given. The analytical performance of DNA sensors and aptasensors utilizing nanomaterials is classified in accordance with their targets and role of nanoparticles in sensitivity and selectivity of the response. The trends of future progress in the biochemical applications of nanomaterials are discussed.

DNA-Templated Assembly of a Protein-Functionalized Nanogap Electrode

Advanced Materials, 2004

Reported is the DNA-templated assembly of a protein-functionalized 10 nm gap electrode from suitably modified gold nanoparticles on a silicon wafer substrate. Also reported is that the above protein-functionalized electrode is recognized and bound selectively by a suitably modified gold nanoparticle that is localized in the 10 nm gap. Clearly, a range of suitably modified nanoparticles and biomolecules could similarly be localized in the above gap.

Control of Steric Hindrance on Restriction Enzyme Reactions with Surface-Bound DNA Nanostructures

Nano Letters, 2008

To understand better enzyme/DNA interactions and to design innovative detectors based on DNA nanoarrays, we need to study the effect of nanometric confinement on the biochemical activity of the DNA molecules. We focus on the study of the restriction enzyme reactions (Dpnll) within DNA nanostructures on flat gold films by atomic force microscopy (AFM). Typically we work with a few patches of DNA self assembled monolayers (SAMs) that are hundred nm in size and are lithographically fabricated within alkylthiol SAMs by AFM nanografting. We start by nanografting a few patches of a single-stranded DNA (ssDNA) molecule of 44 base pairs (bps) with a 4 bps recognition sequence (specific for Dpnll) in the middle. Afterwards, reaction-ready DNA nanopatches are obtained by hybridization with a complementary 44bps ssDNA sequence. The enzymatic reactions were carried out over nanopatches with different density. By carrying out AFM height measurements, we are able to show that the capability of the Dpnll enzyme to reach and react at the recognition site is easily varied by controlling the DNA packing in the nanostructures. We have found strong evidence that inside our ordered DNA nanostructures the enzyme (that works as a dimer) can operate down to the limit in which the space between adjacent DNA molecules is equal to the size of the DNA/enzyme complex. Similar experiments were carried out with a DNA sequence without the recognition site, clearly finding that in that case the enzymatic reaction did not lead to digestion of the molecules. These findings suggest that it is possible to tune the efficiency of an enzymatic reaction on a surface by controlling the steric hindrance inside the DNA nanopatches without vary any further physical or chemical variable. These findings are opening the door to novel applications in both the fields of biosensing and fundamental biophysics.

Synthesis and AFM visualization of DNA nanostructures

Thin Solid Films, 2004

We propose a novel bottom-up approach for the fabrication of various desired nanostructures, based on self-assembly of oligonucleotides governed by Watson-Crick base pairing. Using this approach, we designed Y-shaped, closed Y-shaped, H-shaped, and hexagonal structures with oligonucleotides. These structures were autonomously fabricated simply by mixing equimolar solutions of oligonucleotides and performing hybridization. After synthesis of the nanostructures, we confirmed their validity by agarose gel electrophoresis and atomic force microscope (AFM) visualization. We detected bands of the desired molecular sizes in the gel electrophoresis and observed the desired structures by AFM analysis. We concluded that the synthesized structures were consistent with our intended design and that AFM visualization is a very useful tool for the observation of nanostructures.

ChemInform Abstract: DNA Nanoarchitectures: Steps Towards Biological Applications

ChemInform, 2014

DNA's remarkable molecular recognition properties, flexibility and structural features make it one of the most promising scaffolds to design a variety of nanostructures. During the past decades, two major methods have been developed for the construction of DNA nanomaterials in a programmable way, both generating nanostructures in one, two and three dimensions: the tile-based assembly process, which provides a useful tool to construct large and simple structures, and the DNA origami method, suitable for the production of smaller, more sophisticated and well defined structures. Proteins, nanoparticles and other functional elements have been specifically positioned into designed patterns on these structures. They can also act as templates to study chemical reactions, help in the structural determination of proteins and be used as platform for genomic and drug delivery applications. In this review we examine recent progresses towards the potential use of DNA nanostructures for molecular and cellular biology.