ENCRAOCHMENT OF NANOTECHNOLOGY IN MATERIAL SCIENCES

ABSTRACT:

Technology & knowledge made our lives to be compact and faster .One of such hot technology, which made our lives to be compact, and fast is “NANOTECHNOLOGY”. It is a versatile one and can relate any one of the existing technologies.

One such field in which nanotechnology can be applied is in creating new materials which are smarter and more interactive using DNA. It is known to all that the DNA found in cells is a double helix consisting of two antiparallel strands held together by specific hydrogen-bonded base pairs; adenine (A) always pairs with thymine (T), and guanine (G) always pairs with cytosine (C). The specificity of this base pairing and the ability to ensure that it occurs in this fashion (and not some other one) is a key to the use of DNA in materials applications.

The goals, which primarily entail the use of DNA and

nanotechnology as a programmable component, but neither crystallography nor nonoelectronics, can rely on DNA alone. For instance, nanoelectric components, such as metallic nanopatricles or carbon nanotubes, will have to be combined with DNA molecules in systems and liquid solutions that are compatible with both the DNA and the other components. A nanotechnological dream machine is one that can replicate. Unlike linear DNS, however, branched DNA does

not lend itself readily to self-replication. By the use of branched DNA instead of linear DNA

This paper deals with the achievements in the structural DNA nanotechnology and the purposes that are being served and where it is going.

Introduction: Since Watson and Crick’s determination of its structure

nearly 50 years ago, DNA has come to fill our lives in many areas, from genetic counseling to forensics, from genomics to gene therapy. These, and other ways in which DNA affects human activities, are related to its function as genetic material, not just our genetic material, but the genetic material of all living organisms. Here, we will ignore DNA’s biological role; rather, we will discuss how the properties that make it so successful in acting as genetic material also make it a convenient and logical molecule to use for constructing new materials on the nanometer scale. The well-known B-DNA double helix is about 20 Å wide, and its helical repeat is 10-10.6 nucleotide pairs for a pitch of 34-36 Å. Thus, constructions made from DNA will have nanoscale features.

The double helical arrangement of the two molecules leads to a linear helix axis, linear not in the geometrical sense of being a straight line, but in the topological sense of being unbranched. Genetic engineers discovered in the 1970s how to splice together pieces of DNA to add new genes to DNA molecules, and synthetic

chemists worked out convenient syntheses for short pieces of DNA (up to ~100-150 units) in the 1980s. Regardless of the impact of these technologies on biological systems, hooking together linear molecules leads only to longer linear molecules, with circles, knots, and catenanes perhaps resulting from time to time.

A nanotechnological dream machine is one that can replicate. Unlike linear DNS, however, branched DNA does not lend itself readily to self-replication. They built an octahedron from one long stand of DNA (about 1,700 bases), using five short “helper” strands to complete the assembly [see illustration below]. Each edge of the octahedron is made of two interlinked DNA double helix. A folded octahedron cannot reproduce, but in the fun folded state, the long strand is readily cloned millions of times by a standard biotechnology process called PCR (polymerase chain reaction). It is still a far cry from the replication achieved by ever living organism, but by the time the Watson-Crick centenary comes around, we should have DNA-based machines that do as well.

The missing element to make natural DNA the basis for interesting nanomaterials is a point where the helix axis can branch. Such DNA branch points are often found in biology they occur as ephemeral structures in cellular DNA metabolism, including the processes of replication and repair, and they are particularly prominent in the Holliday structure4, a four-arm branched intermediate in the process of genetic recombination. It is fairly easy to design sequences of DNA molecules that lead to stable synthetic variants of Holliday junctions, branched molecules with varied numbers of arms5, as well as more complex motifs6; it is also easy to synthesize their constituent strands, and to get them to self assemble into target systems. The use of branched intermediates allows us to

make N-connected objects from DNA, as well as periodic9-11 and periodic arrays. Similarly, branched DNA motifs have been the basis for several nanomechanical devices.

How do we use branched DNA to achieve these goals? A simple four-arm branched junction is shown in Figure below. The design of branched nucleic acid motifs is based on the notion of maximizing the base pairing, regardless of the presence of branch points. The system illustrated in Fig. below .maximizes the base pairing between its four component strands by forming the structure shown. In addition to having strands that are completely paired with one another, it is also possible to have one strand a little longer than its complement, leading to an overhang. This overhang, called a ‘sticky end’, is the way that genetic engineers direct double helices to associate. Likewise, it is possible to direct branched molecules to associate by using sticky ends. This idea is shown in Fig. 1(b). The complementary sticky end pairs {X, X'} and {Y, Y'} are shown to cohere so as to produce a quadrilateral on the right. In addition, there are sticky ends on the outside so that a crystalline array of junctions can be formed. What is shown here is a self assembly process directed by the complementary sequences on the sticky ends? Sticky ends are typically four to eight bases long, and cohere with good fidelity; the ability to direct cohesion through sticky-ended complementarily is straightforward. However, there is a second key feature to sticky-ended

Cohesion: sticky ends form B-DNA when they bind to each other, so that the local geometry of the cohesive system is known without performing a new experiment (e.g. a crystal structure determination) every time a new sticky end is designed. This feature is central to structural DNA nanotechnology; a number of investigators have used DNA affinity to assemble materials, but those systems have not been characterized by high resolution control of structure. Thus, the use of sticky ends is convenient because the intermolecular structures

formed are predictable, since complementarily is easy to program, and because a great diversity of possible sequences is available.

What purposes would be served by producing DNA-based materials?

We expect these systems can be applied to several practical ends: the initial motivating goal for this research is that spatially periodic networks are crystals. If we can build stick figure crystalline cages on the nanometer scale, they could be used to orient other biological macromolecules as guests inside those cages, thereby rendering their three-dimensional structures amenable to diffraction analysis. This notion is illustrated in Fig. 2(a), which shows magenta DNA ‘box’ hosting macromolecular guests. Similarly, the same types of crystalline arrays could be used to position and orient components of molecular electronic devices with nanometer scale precision20. An example of this type of application is shown in Fig. 2(b).

Two DNA branched junctions have pendent from them a nanowire. When their sticky ends cohere, the nanowires are organized as well. DNA-based nanomechanical devices can lead to nanometer-scale robotics and very smart materials – that respond to specific stimuli by particular spatial transitions. Structural DNA nanotechnology creates motifs that can be useful for DNA-based computation and for the algorithmic assembly of materials.

Algorithmic assembly holds great promise for the highly controlled construction of materials with designed features and sizes in one, two, or three dimensions. There are many advantages to using DNA for these purposes:

1. The key reason has been described above: in the area of intermolecular recognition, DNA is the champion molecule, from the perspective both of predictable affinity and predictable local product structure, with a highly diverse set of sequences available.

2. The field has been accelerated by the presence of convenient automated chemistry, applicable both to ‘vanilla’ DNA and to exotic or conveniently modified bases.

3. The existence of commercially available modifying enzymes, such as ligases (to join cohesive ends ovalently), restriction endonucleases (to cut DNA at specific 4-8 base long sequences), exonucleases (to digest failure products that do not contain cyclic strands), and topoisomerases (to change and analyze the topological linking of DNA strands), has all contributed to the growth of the field.

4. Even when it is base-paired, the sequence of DNA can still be read

from the outside, so points on a construct can be recognized uniquely.

5. DNA is also a stiff molecule; its persistence length is about 500 Å, about 15 double helical turns, under standard conditions, and we work with lengths of double-stranded DNA about two to three turns long. If one were to compare DNA to spaghetti, whose persistence length is about 15 mm, the DNA lengths used correspond to pieces of spaghetti 2-3 mm long, a distance over which its central axis bends very little. Some DNA motifs, such as the DNA double crossover (DX) molecule, are even less flexible.

6. The high functional group density on DNA is also an asset; large DNA tiles

can be dramatized, in principle, down to separations of a single base unit, 3.4 A.

7. Current work with DNA focuses on conventional molecules, particularly because of the enzymes available to troubleshoot experiments. However, the gene therapy enterprise has produced a large number of backbone and base variants that may be better suited to particular applications. For example, peptide nucleic acid (PNA) is an uncharged variant on DNA that may find applications in nanoelectronics, where the charged DNA backbone could be troublesome.

What has structural DNA nanotechnology achieved so far? The first clear success of DNA nanotechnology was the construction of a three-connected DNA molecule whose helix axes were connected like the edges of a stick cube. This object is shown in Fig. 3. It consists of six cyclic single strands of DNA, one for each face of the polyhedron. Each edge consists of two turns of double-helical DNA. The red strand corresponds to the front face; owing to the helical character of DNA, it is linked twice to the green strand on the right, the cyan strand on the top, the magenta strand on the left, and the dark blue strand on the bottom. It is linked only indirectly to the yellow strand at the rear. Individual branched junctions are floppy,

with flexible angles between rigid arms; consequently, only their topology can be designed (or analyzed), not their geometry. In this case, the topology was established by electrophoresis analysis of cubes cleaved by specific restriction end nucleases; every edge contained a unique site for cleavage by a restriction enzyme. The key materials-related area in which structural DNA nanotechnology has been successful has been the production of two-dimensional periodic arrays with defined features. Components with high structural integrity are needed to generate periodic matter, and these have come from DNA molecules containing multiple branch points that link unbent helices. The most prominent of these motifs is the DX motif.

Fig. 4(a) illustrates two different lattices constructed from designed DX components9. At the top is a DX molecule, labeled A, and a second DX molecule, labeled B*. B*, contains an extra short DNA double helix protruding from the plane of the two helix axes. The dimensions of the two molecules are about 4 x 16 nm in this

projection. Thus, the feature contained in B* should lead to stripes separated by ~32 nm, as shown in the atomic force micrograph (AFM) on the right. As a control, an ABCD* array was assembled containing stripes separated by the expected ~64 nm.

Another example is shown in Fig. 5, which contains a motif known as a DNA triple crossover (TX). Analogous to the DX molecule, three helices are linked to each other, twice each, in an arrangement as coplanar as possible. Two TX molecules (or tiles), A and B, are shown on the upper left. Below them is a lattice formed by connecting them top to bottom, so that there are helix-wide gaps in the array. The gaps can be filled with a double helix, D. A TX molecule can also fill them, if it is rotated three helical positions, to be about 102° from its original position, roughly perpendicular to the AB array. This molecule is shown as C, and its rotated version is shown as C'. The ABC'D array can be seen at the bottom of Fig. 5. On the right is an AFM image showing features that result from the C' molecule extending out of the AB plane. We have also demonstrated that we can build two-dimensional arrays containing cavities with tunable dimensions from parallelograms made from branched junctions10. A periodic self-assemblies corresponding to logical computations have also been produced. The other area to which structural DNA nanotechnology is making a contribution is a nanomechanical device, with ultimate applications in nanorobotics and smart materials. The first such device contained two DX molecules separated by a DNA shaft containing a segment that can be converted to left-handed Z-DNA when Co (NH3)6Cl3 is added to the solution. The rotary motion had a maximum displacement of 60 Å, and was demonstrated by fluorescence resonance energy transfer (FRET). To produce effective nanorobotics,

devices must be embedded in an array matrix and they must molecule to the solution.

So there developed a new device using a principle originated by Yurke et al. The machine cycle of this device is shown in Fig. 6. The device is based on a motif called PX; in which strands crossing over at all possible places join two helices. A related motif, JX2, is similar, except that it lacks two crossovers in the middle. Note that the ends of PX molecule, on the left of Fig. 6, and those of the JX2 molecule, on the right, are the same on the top (A and B), but rotated 180° on the bottom (C and D). The green strands in the PX molecule have small (horizontal) extensions on them. When the complete complement, including the extensions, is added to the PX molecule, the green strands are removed from the PX molecule (process I), to leave the intermediate at the top. When the purple strands are added to the intermediate (process II), the JX2 molecule is formed, rotating the bottom of the molecule. Processes III and IV restore the original PX conformation. The operation of this device has been demonstrated by electrophoresis and AFM. Changing the sequences of the green strands, the purple strands, and the sections of the device to which they bind can develop a variety of sequence-specific devices.

Where is structural DNA nanotechnology going?

The achievement of several key near-term goals will move structural DNA nanotechnology to practical applications. First among these goals is the extension of array-making capabilities from two to three dimensions, particularly with high order. Likewise, heterologous molecules must be incorporated into DNA arrays, so that the goals of

orienting biological macromolecules for diffraction purposes and of organizing nanoelectronic circuits may be met. DNANanorobotics awaits the incorporation of the PX-JX2 device into arrays. Algorithmic assembly in two and three dimensions will lead ultimately to very smart materials, particularly if combined with nanodevices. The incorporation of functionality (e.g. aptamers, enzymes, or ribosome) will lead to active materials. Techniques must be developed to interface with top-down methods and the macroscopic world to bring nanoelectronics to reality. Combinatorial approaches need to be developed to achieve diversity and programmability of materials. The development of self replicating systems using branched DNA appears today to be somewhat oblique, but it nevertheless represents an exciting challenge that will significantly economize on the preparation of these systems and enhance their evolvability. Ultimately, structural DNA nanotechnology must advance from the biokleptic to the biomimetic, not just using the central molecules of life, but also improving on them, without losing the inherent power they possess

CONCLUSION: Achieving these goals primarily entails the use of DNA as a

programmable component, but neither crystallography nor nonoelectronics can rely on DNA alone. For instance, nanoelectric components, such as metallic nanopatricles or carbon nanotubes, will have to be combined with DNA molecules in systems and liquid solutions that are compatible with both the DNA and the other components. Given the diverse chemical nature of these molecules, achieving this will not be simple. In addition, even if the nanoelectronics can be constructed by DNA self-assembly the nanomachines ultimately need to interact with the macroscopic world in a manner that is more sophisticated then the addition and removal

of set strands from a solution. This challenge is likely to be formidable.

REFERENCES: 1. Scientific American-June 2004.2. www.nanotech.com3. www.nanodna.com