Introduction
Deoxyribonucleic acid or commonly referred to as DNA is an acid that is nucleic within every living organism and forms the very basis of the existence of the organism. The essence of DNA in every living organism and certain viruses is that it forms the basis of the genetic instructions that are essential in the development and functioning of these organisms. In a nutshell therefore the DNA’s main function is to ensure that genetic information existing in each cell is stored and maintained in the long term. It resembles a code or recipe because within its structure are various instructions that are required to many other components of the cell that include such components as RNA molecules and other proteins. Genes in a general sense are the DNA segments that carry the information.
At the center of the DNA makeup are 2 long polymers that are bound via ether bonds to the phosphate groups that are called nucleotides; this forms the structure of the DNA. These 2 polymers run against each other (anti-parallel) within the base of the four types of molecules that comprise each sugar. Information is encoded from the four bases that are laid along the backbone. The general arrangement that is apparent in the amino acids within the proteins is dictated by the genetic code and specifies the order of arrangement. The copying or a process termed as transcription of the DNA extends to the nucleic acid RNA which is used to read the code. Chromosomes are the structures that make up the DNA and are duplicated in a process known as DNA replication. This process takes place before the division of the cells. In most living organisms which are classified as Eukaryotic organisms the DNA is generally stored in the nucleus which is in contrast to organisms that are classified as prokaryotes (bacteria and archaea) where the storage medium is the cell’s cytoplasm (Shen et al). Below is a DNA structure
Nanotechnology
Nanotechnology entails the shrinking of the sizes and properties of various sets of materials with the nano-particles that have and increased sizes in terms of surface areas taking advantage of the ratio in volumes. Their visual properties that including such features as fluorescence, characterize the particle’s diameter. Nano-particles have a great influence on the mechanical properties like elasticity and stiffness of the materials they are introduced to. This is exemplified when nano-particles are used to strengthen the traditional polymers are used as metal alternatives. This leads to a very positive impact of nano-particles on technology and society at large. Such materials that are improved through nano-technology, in a nutshell, have the benefits of weight reduction and the added advantage of improved stability and functionality (Center for Responsible Nanotechnology).
There are many applications of nano-technology and a few of them are going to be discussed. There has been a recent drive towards using DNA molecules for nano-technological applications and extensive research on their potential in the development of novel nano-electronic devices. DNA nanotechnology which is an offshoot of nanotechnology is greatly utilized to create unique DNA structures that can be manipulated. This has possible applications in molecular self-assembly and DNA computing. (Seeman).
The yellow motor compresses DNA coiled lengths into viral capsid to about 6 thousand normal volumes amounting to over x10 pressure
(Image lifted from Carlos Bustamante of Berkeley Lab’s Physical Biosciences Division)
Thus, reviewing the current level of understanding of the behavior of DNA polymers as conducting wires, based on experimental and theoretical investigations of the electronic properties, the emphasis is shifting towards investigations of the DNA electronic structure. Disappointing evidence of negligible conductivity, from both theory and experiment, on double-stranded DNA molecules, has recently been counter-balanced by clear-cut measurements of high currents under controlled experimental conditions that rely on avoiding non-specific molecule-substrate interactions and realizing electrode-molecule covalent binding (Birac et al).
As a parallel effort, scientists are now tracing the route toward the exploration of tailored DNA derivatives that may exhibit enhanced conductivity. The concept of DNA-mediated self-assembly of nanostructures has been extended to metallic nanowires. The rather minute intrinsic conductance of DNA due to its high resistance was an obstacle to the use of its unique self-assembly capabilities in nanoelectronics. The inclusion of metal atoms into the DNA structure has gone a long way in reducing this resistance (Birac et al).
Applications
Braun et al. utilized DNA as a template to grow to conduct silver nanowires. The basic assembly scheme involved the construction of an Ag nano-wire attached to two gold electrodes. Two gold electrodes separated by a defined distance of 12-16 micrometers were deposited onto a glass slide using photolithography. The gold electrodes subsequently were modified with non-complementary hexane disulfide modified oligonucleotides through well-established thiol adsorption chemistry on Au. Subsequently, a fluorescently labeled strand of DNA containing sticky ends that are complementary to the oligonucleotides attached to the electrodes was introduced. Hybridization of the fluorescently tagged DNA molecule to the surface-confined alkylthiololigonucleotides was confirmed by fluorescence microscopy, which showed a fluorescent bridge connecting the two electrodes (Kallenbach & Seeman).
After a single DNA bridge was observed, the excess hybridization reagents were removed. Silver ions than were deposited onto the DNA through cation exchange with sodium and complexation with the DNA bases. This process was followed by monitoring the quenching of the fluorescent tag on the DNA by the Ag ions. After almost complete quenching of the fluorescence, the silver ion bound to the template DNA was reduced using standard hydroquinone reduction procedures to form small silver aggregates along the backbone of the DNA. A continuous silver wire was then formed by further Ag ion deposition onto the previously constructed silver aggregates followed by reduction (Kallenbach & Seeman).
The wires are comprised of 30-50 nm Ag grains that are contiguous along the DNA backbone. Two terminal electrical measurements subsequently were performed on the Ag wire depicted in the AFM image. When the current-voltage characteristics of the Ag wire were monitored, no current was observed at near-zero bias (10 V in either scan direction), indicating an extremely high resistance. At a higher bias, the wire becomes conductive. Surprisingly, the current-voltage characteristics were dependent on the direction of the scan rate, yielding different I-V curves. Although not well understood, it was postulated that the individual Ag grains that comprise the Ag nanowires may require simultaneous charging, or Ag corrosion may have occurred, resulting in the high resistance observed at a low bias (Birac et al).
By depositing more silver and thereby growing a thicker Ag nano-wire, the no current region was reduced from 10 V to 0.5 V, demonstrating crude control over the electrical properties of these systems. In addition, control experiments where one of the components (DNA or Ag) was removed from the assembly produced no current, establishing that all of the components are necessary to form the conducting Ag nanowires. This work is a proof-of-concept demonstration of how DNA can be used in a new type of chemical lithography to guide the formation of nano-circuitry (Birac et al).
Martin et al. also reported the fabrication of Au and Ag’s wires using the DNA as a template or skeleton. The basic idea behind his work was to fabricate gold or platinum metal wires, functionalize these wires with exchange and formation of complexes between the gold and the DNA bases. Current-voltage characteristics were measured to demonstrate the possible use of these nano-wires. The authors also reported the formation of luminescent self-assembled poly (p-phenylene vinylene) wires for possible optical applications. Their work had a lot of potential and room for further research in the areas of control of the width of the wire, the contact resistances between the gold electrode and the silver wires, and use of other metals and materials (Birac et al).
Just in the recent past, Yan et al. demonstrated the design and construction of a DNA nanostructure that has a square aspect ratio and readily self-assembles into two distinct lattice forms: nano-ribbons and two-dimensional nano-grids. The four-by-four tiles constituted a 4 four-arm DNA junction that has four directional pointers. Such nano-grids contained a hollow that was large and its main purpose was to bind the various other molecular components. For example, the loops within each tile could be customized with suitable functional groups and utilized as a gibbet “for directing periodic assembly of desired molecules” (Birac et al). Systematic protein arrays were attained by outlined self-assembly of streptavidin onto the DNA nano-grids. The authors also used the 4 × 4 tile assemblies as templates to construct a highly conductive, uniform-width silver nano-wire. A two-terminal I-V measurement of the resulting silver nano-wire was conducted at room temperature. “The I-V curve was linear, demonstrating Ohmic behavior in the range of – 0.2 to 0.2 V” (Birac et al). The nano-wire in this case was highly conductive and could be reproduced effortlessly as compared to the double-helix DNA-stenciled silver nanowires (Seeman).
In the Chad Mirkin experiment, direct evidence of a reversible phase transition of DNA-linked colloidal gold assemblies was presented. Electron microscopy and optical absorption spectroscopy are the main 2 processes that are utilized to check and monitor the phase in the colloidal gold transition. The DNA interaction made up a larger aspect of its behavior. What was used were some DNA-laden colloidal gold that was in single strands which were interconnected via an extra linker to form an assembly. As can be observed from the experiment conducted, the sharp melting is the characteristic outcome that is in direct contrast to the free DNA. The assemblies’ structure was non-crystalline, which was adding up to the theoretical predictions made. Visual spectra and curves that were melting curves were ample evidence of the gelation of the system. The “phase transition and separation” are perfect examples of absorption solvent that is dilute in nature (Seeman).
More recent work of the Mirkin group concerned the generation of binary networks. For example, two types of gold clusters were modified with 12-mer oligonucleotides and were assembled using a complementary 24-mer oligonucleotide linker. Due to the specificity of Watson-crick base pairing; only heterodimeric composites with alternating particle sizes are formed. In the case of an excess of one particle, satellite-like aggregate structures are generated and characterized by TEM. Further studies of DNA-Linked gold nano-particle assemblies concerned the influence of the DNA spacer length on the optical and electrical as well as the melting properties of these networks (Seeman).
The experiments provided evidence that the linker length kinetically controlled the size of the aggregates and that the optical properties of the nanoparticle assemblies are governed by aggregate size. DNA that is short and double-stranded and consisting of a thiol-group was used for the assembly of the nano-gold particle. It was only in the high concentration of Sodium chloride (NaCl) that the web increased. In the case of single-stranded DNA, what is observable is that the DNA is incomplete attachment with the gold surface and in a span of one hour can be separated we see that the DNA is completely attached to the gold surface and can be detached within one hour until it is fully erected. High concentrations of MgCl2 allowed no growth of particle webs. In this situation there is no noticeable difference between the single and double-stranded DNA. Absorption spectroscopy was used to conduct these investigations (Shen et al).
Summary
DNA melting and hybridization is a biological process that plays a pivotal role in contemporary applications in biotechnology. DNA that is only limited to the surface, displays certain unique characteristics compared to the free solutions. At the same time, the DNA-capped gold nano-particles system also shows certain unique transitions and introduces quite some complex fluids. The DNA arrangement determines the linkage via direct complementary DNA sequences “via a ‘linker’ DNA, whose sequence is complementary to the sequence attached to the gold nano-particles. Different melting transitions for these two distinct systems were observed” (Shen et al).
The emerging fields of nanoscience and nano-engineering are contributing greatly towards the development of the understanding of physical matter control and manipulation.. Today, nano-phase engineering finds its use in many areas of structural and functional materials (both inorganic and organic). This leads to the enhancement of other electronic functions. The amalgamation of nano-phase or cluster-assembled materials is primarily founded on the establishment of minute separated clusters that are joined into certain bulk-like material or as a thin film or into solid matrixes, in an orderly manner or not (Shen et al).
DNA progressions steer the assemblage of similar inorganic nano-particle into differentiated crystalline forms. The various findings thus clearly “demonstrate that synthetically programmable colloidal crystallization is possible and that a single-component system can be directed to form different structures. The structural properties of DNA-linked gold nano-particle materials were examined using synchrotron small-angle X-ray scattering” (Seeman).
Works Cited
- Center for Responsible Nanotechnology: The Meaning of Nanotechnology: Web.
- DNA Web.
- J.J. Birac, W.B. Sherman, J. Kopatsch, P.E. Constantinou and N.C. Seeman, Gideon, AProgram for Design in Structural DNA Nanotechnology, J. Mol. Graphics & Modeling 25, 470-480 (2006).
- N.C. Seeman, In the Nick of Space: Generalized Nucleic Acid Complementarity and the Development of DNA Nanotechnology, Synlett (2000), 1536-1548
- N.R. Kallenbach, R.-I. Ma and N.C. Seeman, An Immobile Nucleic Acid Junction Constructed from Oligonucleotides. (1983) Nature 305, 829-831.
- N.C. Seeman, DNA Engineering and its Application to Nanotechnology, Trends in Biotechnology (1999)17, 437-443.
- N.C. Seeman: Key Experimental Approaches in DNA Nanotechnology, Current Protocols in Nucleic Acid Chemistry, Unit 12.1, John Wiley & Sons, New York (2002). 25-67
- Z. Shen, H. Yan, T. Wang and N.C. Seeman: Paranemic Crossover DNA: A Generalized Holliday Structure with Applications in Nanotechnology J. Am. Chem. Soc. (2004) 126, 1666-1674