DNA

DNA (Deoxyribonucleic acid) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms (with the exception of RNA viruses). The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life.DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription.

Within cells DNA is organized into long structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

Architecture

DNA is a long polymer made from repeating units called nucleotides. As first discovered by James D. Watson and Francis Crick, the structure of DNA of all species comprises two helical chains each coiled round the same axis, and each with a pitch of 34 Ångströms (3.4 nanometres) and a radius of 10 Ångströms (1.0 nanometres). According to another study, when measured in a particular solution, the DNA chain measured 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit measured 3.3 Å (0.33 nm) long. Although each individual repeating unit is very small, DNA polymers can be very large molecules containing millions of nucleotides. For instance, the largest human chromosome, chromosome number 1, is approximately 220 million base pairs long.

In living organisms DNA does not usually exist as a single molecule, but instead as a pair of molecules that are held tightly together. These two long strands entwine like vines, in the shape of a double helix. The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a nucleobase, which interacts with the other DNA strand in the helix. A nucleobase linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide. Polymers comprising multiple linked nucleotides (as in DNA) are called a polynucleotide.The backbone of the DNA strand is made from alternating phosphate and sugar residues.[10] The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand: the strands are antiparallel. The asymmetric ends of DNA strands are called the 5′ (five prime) and 3′ (three prime) ends, with the 5' end having a terminal phosphate group and the 3' end a terminal hydroxyl group. One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the alternative pentose sugar ribose in RNA.

The DNA double helix is stabilized primarily by two forces: hydrogen bonds between nucleotides and base-stacking interactions among the aromatic nucleobases. In the aqueous environment of the cell, the conjugated π bonds of nucleotide bases align perpendicular to the axis of the DNA molecule, minimizing their interaction with the solvation shell and therefore, the Gibbs free energy. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). These four bases are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.The nucleobases are classified into two types: the purines, A and G, being fused five- and six-membered heterocyclic compounds, and the pyrimidines, the six-membered rings C and T. A fifth pyrimidine nucleobase, uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine. In addition to RNA and DNA a large number of artificial nucleic acid analogues have also been created to study the proprieties of nucleic acids, or for use in biotechnology.

Base pairing

In a DNA double helix, each type of nucleobase on one strand normally interacts with just one type of nucleobase on the other strand. This is called complementary base pairing. Here, purines form hydrogen bonds to pyrimidines, with a bonding only to T, and C bonding only to G. This arrangement of two nucleotides binding together across the double helix is called a base pair. As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature. As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. Indeed, this reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.

The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, left). DNA with high GC-content is more stable than DNA with low GC-content. Although it is often stated that this is due to the added stability of an additional hydrogen bond, this is incorrect. [Citation needed] DNA with high GC-content is more stable due to intra-strand base stacking interactions.As noted above, most DNA molecules are actually two polymer strands, bound together in a helical fashion by noncovalent bonds; this double stranded structure (dsDNA) is maintained largely by the intrastrand base stacking interactions, which are strongest for G,C stacks. The two strands can come apart – a process known as melting – to form two ss DNA molecules. Melting occurs when conditions favor ssDNA; such conditions are high temperature, low salt and high pH (low pH also melts DNA, but since DNA is unstable due to acid depurination, low pH is rarely used). The stability of the dsDNA form depends not only on the GC-content (% G,C basepairs) but also on sequence (since stacking is sequence specific) and also length (longer molecules are more stable). The stability can be measured in various ways; a common way is the "melting temperature", which is the temperature at which 50% of the ds molecules are converted to ss molecules; melting temperature is dependent on ionic strength and the concentration of DNA. As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC-content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands. In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend to have a high AT content, making the strands easier to pull apart.

In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules (ssDNA) have no single common shape, but some conformations are more stable than others.

Nanotechnology

Nanotechnology has emerged as a growing and rapidly changing field. New generations of nanomaterials will evolve, and with them new and possibly unforeseen environmental issues. It will be crucial that the Agency’s approaches to leveraging the benefits and assessing the impacts of nanomaterials continue to evolve in parallel with the expansion of and advances in these new technologies.Nanotechnology presents potential opportunities to create better materials and products. Already, nanomaterial-containing products are available in U.S. markets including coatings, computers, clothing, cosmetics, sports equipment and medical devices. A survey by EmTech Research of companies working in the field of nanotechnology has identified approximately 80 consumer products, and over 600 raw materials, intermediate components and industrial equipment items that are used by manufacturers.Nanotechnology also has the potential to improve the environment, both through direct applications of nanomaterials to detect, prevent, and remove pollutants, as well as indirectly by using nanotechnology to design cleaner industrial processes and create environmentally responsible products. However, there are unanswered questions about the impacts of nanomaterials and nanoproducts on human health and the environment, and the U.S. Environmental Protection Agency has the obligation to ensure that potential risks are adequately understood to protect human health and the environment. As products made from nanomaterials become more numerous and therefore more prevalent in the environment, EPA is thus considering how to best leverage advances in nanotechnology to enhance environmental protection, as well as how the introduction of nanomaterials into the environment will impact the Agency’s environmental programs, policies, research needs, and approaches to decision making.
A nanometer is one billionth of a meter (10^-9 m)—about one hundred thousand times smaller than the diameter of a human hair, a thousand times smaller than a red blood cell, or about half the size of the diameter of DNA. Figure 1 illustrates the scale of objects in the nanometer range. For the purpose of this document, nanotechnology is defined as: research and technology development at the atomic, molecular, or macromolecular levels using a length scale of approximately one to one hundred nanometers in any dimension; the creation and use of structures, devices and systems that have novel properties and functions because of their small size; and the ability to control or manipulate matter on an atomic scale. This definition is based on part on the definition of nanotechnology used by the National Nanotechnology Initiative (NNI).

Carbon-based materials- The nanomaterials are composed mostly of carbon, most commonly taking the form of a hollow spheres, ellipsoids, or tubes. Spherical and ellipsoidal carbon nanomaterials are referred to as fullerenes, while cylindrical ones are called nanotubes. These particles have many potential applications, including improved films and coatings, stronger and lighter materials, and applications in electronics. Figures 3, 4, and 5 show examples of carbon-based nanomaterials.

Metal-based materials- These nanomaterials include quantum dots, nanogold, nanosilver and metal oxides, such as titanium dioxide. A quantum dot is a closely packed semiconductor crystal comprised of hundreds or thousands of atoms, and whose size is on the order of a few nanometers to a few hundred nanometers. Changing the size of quantum dots changes their optical properties. Figures 6 and 7 show examples of metal-based nanomaterials.

Composites- combine nanoparticles with other nanoparticles or with larger, bulk-type materials. Nanoparticles, such as nanosized clays, are already being added to products ranging from auto parts to packaging materials, to enhance mechanical, thermal, barrier, and flame-retardant properties.The unique properties of these various types of intentionally produced nanomaterials give them novel electrical, catalytic, magnetic, mechanical, thermal, or imaging features that are highly desirable for applications in commercial, medical, military, and environmental sectors. These materials may also find their way into more complex nanostructures and systems.As new uses for materials with these special properties are identified, the number of products containing such nanomaterials and their possible applications continues to grow.

Researcher is with a scanning beam interference lithography (SBIL) machine. This is used to create gratings and grids with structures on the scale of a few nanometres (billionths of a metre). The gratings created on this scale are used in astronomical telescopes such as the orbiting Chandra X-ray telescope and the Solar and Heliospheric Observatory (SOHO) satellite. SBIL uses a laser beam to create the pattern on the target surface. This allows for very precise control over the pattern. The SBIL could have many uses in the future as a source of nanotechnological components for computers and machines.










A research group of Dr. Carroll’s ranges from fundamental investigations of transport phenomena in nano-scale objects (tests of quantum mechanics in exotic topologies) to applications of nano-composite materials in organic devices. The group has active programs in the growth of novel nanostructures, manipulation and characterization of ordered assemblies of nanostructures, and the integration of nanomaterials into both standard device designs and novel quantum effect devices.The creation of novel new nanomaterials is an essential part of the nano-sciences. These materials can have exotic properties not normally found in nature. In fact, properties such as super strength, ultra-high thermal conductivity, and super conductivity have been observed for nano-systems when they are absent for the macro-counterparts of the same element. In our studies, the extra-ordinary properties of assemblies of nano-particles are used to test fundamental physical models, develop new ultra-light, ultra-strong materials systems, and create technology at the smallest length scales.

As an example, the carbon nanotube represents an interesting and complicated topology for the confinement of charge carriers with a diameter of only 1.4 nm and a length of microns. The molecular helicity, or chirality, of the nanotube breaks a fundamental symmetry of the nanotube’s point group. Their studies are examining the relationship of such symmetry breaking and the accumulation of geometrical phase factors (Berry’s phase) in such systems. When defects are added in an ordered fashion, the overall real space topology of the system can become much more interesting. It is hoped that the studies of these fundamental symmetries will set the foundations for the creation of quantum effect computation systems based on macro-molecular objects such as carbon nanotubes.

Molecular nanotechnology

Molecular nanotechnology, sometimes called molecular manufacturing, describes engineered nanosystems (nanoscale machines) operating on the molecular scale. Molecular nanotechnology is especially associated with the molecular assembler, a machine that can produce a desired structure or device atom-by-atom using the principles of mechanosynthesis. Manufacturing in the context of productive nanosystems is not related to, and should be clearly distinguished from, the conventional technologies used to manufacture nanomaterials such as carbon nanotubes and nanoparticles.When the term "nanotechnology" was independently coined and popularized by Eric Drexler (who at the time was unaware of an earlier usage by Norio Taniguchi) it referred to a future manufacturing technology based on molecular machine systems. The premise was that molecular scale biological analogies of traditional machine components demonstrated molecular machines were possible: by the countless examples found in biology, it is known that sophisticated, stochastically optimised biological machines can be produced.

It is hoped that developments in nanotechnology will make possible their construction by some other means, perhaps using biomimetic principles. However, Drexler and other researchers have proposed that advanced nanotechnology, although perhaps initially implemented by biomimetic means, ultimately could be based on mechanical engineering principles, namely, a manufacturing technology based on the mechanical functionality of these components (such as gears, bearings, motors, and structural members) that would enable programmable, positional assembly to atomic specification. The physics and engineering performance of exemplar designs were analyzed in Drexler's book Nanosystems.In general it is very difficult to assemble devices on the atomic scale, as all one has to position atoms on other atoms of comparable size and stickiness. Another view, put forth by Carlo Montemagno, is that future nanosystems will be hybrids of silicon technology and biological molecular machines. Yet another view, put forward by the late Richard Smalley, is that mechanosynthesis is impossible due to the difficulties in mechanically manipulating individual molecules.

This led to an exchange of letters in the ACS publication Chemical & Engineering News in 2003.Though biology clearly demonstrates that molecular machine systems are possible, non-biological molecular machines are today only in their infancy. Leaders in research on non-biological molecular machines are Dr. Alex Zettl and his colleagues at Lawrence Berkeley Laboratories and UC Berkeley. They have constructed at least three distinct molecular devices whose motion is controlled from the desktop with changing voltage: a nanotube nanomotor, a molecular actuator, and a nanoelectromechanical relaxation oscillator.

Tools and techniques

There are several important modern developments. The atomic force microscope (AFM) and the Scanning Tunneling Microscope (STM) are two early versions of scanning probes that launched nanotechnology. There are other types of scanning probe microscopy, all flowing from the ideas of the scanning confocal microscope developed by Marvin Minsky in 1961 and the scanning acoustic microscope (SAM) developed by Calvin Quate and coworkers in the 1970s, that made it possible to see structures at the nanoscale. The tip of a scanning probe can also be used to manipulate nanostructures (a process called positional assembly). Feature-oriented scanning-positioning methodology suggested by Rostislav Lapshin appears to be a promising way to implement these nanomanipulations in automatic mode. However, this is still a slow process because of low scanning velocity of the microscope. Various techniques of nanolithography such as optical lithography, X-ray lithography dip pen nanolithography, electron beam lithography or nanoimprint lithography were also developed. Lithography is a top-down fabrication technique where a bulk material is reduced in size to nanoscale pattern.

Another group of nanotechnological techniques include those used for fabrication of nanotubes and nanowires, those used in semiconductor fabrication such as deep ultraviolet lithography, electron beam lithography, focused ion beam machining, nanoimprint lithography, atomic layer deposition, and molecular vapor deposition, and further including molecular self-assembly techniques such as those employing di-block copolymers. However, all of these techniques preceded the nanotech era, and are extensions in the development of scientific advancements rather than techniques which were devised with the sole purpose of creating nanotechnology and which were results of nanotechnology research.The top-down approach anticipates nanodevices that must be built piece by piece in stages, much as manufactured items are made. Scanning probe microscopy is an important technique both for characterization and synthesis of nanomaterials. Atomic force microscopes and scanning tunneling microscopes can be used to look at surfaces and to move atoms around. By designing different tips for these microscopes, they can be used for carving out structures on surfaces and to help guide self-assembling structures. By using, for example, feature-oriented scanning-positioning approach, atoms can be moved around on a surface with scanning probe microscopy techniques. At present, it is expensive and time-consuming for mass production but very suitable for laboratory experimentation.

In contrast, bottom-up techniques build or grow larger structures atom by atom or molecule by molecule. These techniques include chemical synthesis, self-assembly and positional assembly. Dual polarisation interferometry is one tool suitable for characterisation of self-assembled thin films. Another variation of the bottom-up approach is molecular beam epitaxy or MBE. Researchers at Bell Telephone Laboratories like John R. Arthur. Alfred Y. Cho and Art C. Gossard developed and implemented MBE as a research tool in the late 1960s and 1970s. Samples made by MBE were key to the discovery of the fractional quantum Hall effect for which the 1998 Nobel Prize in Physics was awarded. MBE allows scientists to lay down atomically precise layers of atoms and, in the process, build up complex structures. Important for research on semiconductors, MBE is also widely used to make samples and devices for the newly emerging field of spintronics.