DETECTING DNA

A diphenylamine (DPA) indicator will confirm the presence of DNA. This procedure involves chemical hydrolysis of DNA: when heated (e.g. =95 °C) in acid, the reaction requires a deoxyribose sugar and therefore is specific for DNA. Under these conditions, the 2-deoxyribose is converted to w-hydroxylevulinyl aldehyde, which reacts with the compound, diphenylamine, to produce a blue-colored compound. DNA concentration can be determined measuring the intensity of absorbance of the solution at the 600 nm with a spectrophotometer and comparing to a standard curve of known DNA concentrations.

Measuring the intensity of absorbance of the DNA solution at wavelengths 260 nm and 280 nm is used as a measure of DNA purity. DNA absorbs UV light at 260 and 280 nanometres, and aromatic proteins absorb UV light at 280 nm; a pure sample of DNA has the 260/280 ratio at 1.8 and is relatively free from protein contamination. A DNA preparation that is contaminated with protein will have a 260/280 ratio lower than 1.8.

DNA can be quantified by cutting the DNA with a restriction enzyme, running it on an agarose gel, staining with ethidium bromide or a different stain and comparing the intensity of the DNA with a DNA marker of known concentration.

Using the Southern blot technique this quantified DNA can be isolated and examined further using PCR and RFLP analysis. These procedures allow differentiation of the repeated sequences within the genome. It is these techniques which forensic scientists use for comparison, identification, and analysis.

MITOCHONDRIAL DNA

Mitochondrial DNA (mtDNA) is the DNA located in organelles called mitochondria, structures within eukaryotic cells that convert the energy from food into a form that cells can use. Most other DNA present in eukaryotic organisms is found in the cell nucleus.

Nuclear and mitochondrial DNA are thought to be of separate evolutionary origin, with the mtDNA being derived from the circular genomes of the bacteria that were engulfed by the early ancestors of today's eukaryotic cells. Each mitochondrion is estimated to contain 2-10 mtDNA copies.In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some of them, if not most, are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution. In most multicellular organisms, mtDNA is inherited from the mother (maternally inherited). Mechanisms for this include simple dilution (an egg contains 100,000 to 1,000,000 mtDNA molecules, whereas a sperm contains only 100 to 1000), degradation of sperm mtDNA in the fertilized egg, and, at least in a few organisms, failure of sperm mtDNA to enter the egg. Whatever the mechanism, this single parent (uniparental) pattern of mtDNA inheritance is found in most animals, most plants and in fungi as well. mtDNA is particularly susceptible to reactive oxygen species generated by the respiratory chain due to its close proximity. Though mtDNA is packaged by proteins and harbors significant DNA repair capacity, these protective functions are less robust than those operating on nuclear DNA and therefore thought to contribute to enhanced susceptibility of mtDNA to oxidative damage. Mutations in mtDNA can in some cases cause maternally inherited diseases and some evidence suggests that they might be major contributors to the aging process and age-associated pathologies.

In humans (and probably in metazoans in general), 100-10,000 separate copies of mtDNA are usually present per cell (egg and sperm cells are exceptions). In mammals, each double-stranded circular mtDNA molecule consists of 15,000-17,000 base pairs. The two strands of mtDNA are differentiated by their nucleotide content with the guanine rich strand referred to as the heavy strand, and the cytosine rich strand referred to as the light strand. The heavy strand encodes 28 genes, and the light strand encodes 9 genes for a total of 37 genes. Of the 37 genes, 13 are for proteins (polypeptides), 22 are for transfer RNA (tRNA) and two are for the small and large subunits of ribosomal RNA (rRNA). This pattern is also seen among most metazoans, although in some cases one or more of the 37 genes is absent and the mtDNA size range is greater. Even greater variation in mtDNA gene content and size exists among fungi and plants, although there appears to be a core subset of genes that are present in all eukaryotes (except for the few that have no mitochondria at all). Some plant species have enormous mtDNAs (as many as 2,500,000 base pairs per mtDNA molecule) but, surprisingly, even those huge mtDNAs contain the same number and kinds of genes as related plants with much smaller mtDNAs.

mtDNA is replicated by the DNA polymerase gamma complex which is composed of a 140 kDa catalytic DNA polymerase encoded by the POLG gene and a 55 kDa accessory subunit encoded by the POLG2 gene.

DNA UPTAKE MECHANISM

When DNA uptake and subsequent expression was first demonstrated in vivo in muscle cells, it was thought that these cells were unique in this ability because of their extensive network of T-tubules. Using electron microscopy, it was proposed that DNA uptake was facilitated by caveolae (or, non-clathrin coated pits). However, subsequent research revealed that other cells (such as keratinocytes, fibroblasts and epithelial Langerhans cells) could also internalize DNA. This phenomenon has not been the subject of much research, so the actual mechanism of DNA uptake is not known.

Two theories are currently popular – that in vivo uptake of DNA occurs non-specifically, in a method similar to phago- or pinocytosis, or through specific receptors. These might include a 30kDa surface receptor, or macrophage scavenger receptors. The 30kDa surface receptor binds very specifically to 4500-bp genomic DNA fragments (which are then internalised) and is found on professional APCs and T-cells. Macrophage scavenger receptors bind to a variety of macromolecules, including polyribonucleotides, and are thus also candidates for DNA uptake. Receptor mediated DNA uptake could be facilitated by the presence of polyguanylate sequences. Further research into this mechanism might seem pointless, considering that gene gun delivery systems, cationic liposome packaging, and other delivery methods bypass this entry method, but understanding it might be useful in reducing costs (e.g. by reducing the requirement for cytofectins), which will be important in the food animals industry.

DNA VACCINATION

DNA vaccination is a technique for protecting an organism against disease by injecting it with genetically engineered DNA to produce an immunological response. Nucleic acid vaccines are still experimental, and have been applied to a number of viral, bacterial and parasitic models of disease, as well as to several tumour models. DNA vaccines have a number of advantages over conventional vaccines, including the ability to induce a wider range of immune response types.

Vaccines are among the greatest achievements of modern medicine – in industrial nations, they have eliminated naturally-occurring cases of smallpox, and nearly eliminated polio, while other diseases, such as typhus, rotavirus, hepatitis A and B and others are well controlled.Conventional vaccines, however, only cover a small number of diseases, and infections that lack effective vaccines kill millions of people every year, with AIDS, hepatitis C and malaria being particularly common.

First generation vaccines are whole-organism vaccines – either live and weakened, or killed forms. Live, attenuated vaccines, such as smallpox and polio vaccines, are able to induce killer T-cell (TC or CTL) responses, helper T-cell (TH) responses and antibody immunity. However, there is a small risk that attenuated forms of a pathogen can revert to a dangerous form, and may still be able to cause disease in immunocompromised people (such as those with AIDS). While killed vaccines do not have this risk, they cannot generate specific killer T cell responses, and may not work at all for some diseases. In order to minimise these risks, so-called second generation vaccines were developed. These are subunit vaccines, consisting of defined protein antigens (such as tetanus or diphtheria toxoid) or recombinant protein components (such as the hepatitis B surface antigen). These, too, are able to generate TH and antibody responses, but not killer T cell responses.

DNA vaccines are third generation vaccines, and are made up of a small, circular piece of bacterial DNA (called a plasmid) that has been genetically engineered to produce one or two specific proteins (antigens) from a micro-organism. The vaccine DNA is injected into the cells of the body, where the "inner machinery" of the host cells "reads" the DNA and converts it into pathogenic proteins. Because these proteins are recognised as foreign, when they are processed by the host cells and displayed on their surface, the immune system is alerted, which then triggers a range of immune responses. These DNA vaccines developed from “failed” gene therapy experiments. The first demonstration of a plasmid-induced immune response was when mice inoculated with a plasmid expressing human growth hormone elicited antibodies instead of altering growth

GENE EXPRESSION

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as rRNA genes or tRNA genes, the product is a functional RNA. The process of gene expression is used by all known life - eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea) and viruses - to generate the macromolecular machinery for life. Several steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation, morphogenesis and the versatility and adaptability of any organism. Gene regulation may also serve as a substrate for evolutionary change, since control of the timing, location, and amount of gene expression can have a profound effect on the functions (actions) of the gene in a cell or in a multicellular organism.

In genetics gene expression is the most fundamental level at which genotype gives rise to the phenotype. The genetic code is "interpreted" by gene expression, and the properties of the expression products give rise to the organism's phenotype.

RECOMBINANT DNA

Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule.

Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together.In terms of genetic modification, recombinant DNA is introduced through the addition of relevant DNA into an existing organismal DNA, such as the plasmids of bacteria, to code for or alter different traits for a specific purpose, such as antibiotic resistance.It differs from genetic recombination in that it does not occur through processes within the cell, but is engineered.A recombinant protein is a protein that is derived from recombinant DNA.

The recombinant DNA technique was first proposed by Peter Lobban, a graduate student, with A. Dale Kaiser at the Stanford University Department of Biochemistry. The technique was then realized by Lobban and Kaiser; Jackson, Symons and Berg; and Stanley Norman Cohen, Chang, Herbert Boyer and Helling, in 1972–74. They published their findings in papers including the 1972 paper "Biochemical Method for Inserting New Genetic Information into DNA of Simian Virus 40: Circular SV40 DNA Molecules Containing Lambda Phage Genes and the Galactose Operon of Escherichia coli", the 1973 paper "Enzymatic end-to-end joining of DNA molecules" and the 1974 paper "Construction of Biologically Functional Bacterial Plasmids in vitro",all of which described techniques to isolate and amplify genes or DNA segments and insert them into another cell with precision, creating a transgenic bacterium. Recombinant DNA technology was made possible by the discovery, isolation and application of restriction endonucleases by Werner Arber, Daniel Nathans, and Hamilton Smith, for which they received the 1978 Nobel Prize in Medicine. Cohen and Boyer applied for a patent on the Process for producing biologically functional molecular chimeras which could not exist in nature in 1974. The patent was granted in 1980

DNA ACTIVATION

Most people know that DNA is the 'blueprint of life' and is located in every cell of the body. In addition to each chromosome's 2 strand double helix of DNA, there are an additional 10 etheric strands of DNA available to each human, which have been dormant since the beginning of recorded history. Each additional strand possesses attributes that permit the individual to perform greater human accomplishments. Scientists acknowledge that we currently only use 3% of our current 2 strand DNA. Thus we live in a society where people are sick, unhappy, stressed out, create wars, have difficulty experiencing love, and are totally disconnected with the universe. Most people have to meditate for many years just to have a so-called 'mystical' experience, that's how disconnected we are now. Imagine activating 100% of your 2 strand DNA, PLUS 10 additional strands! You will go from using 10% of your brain to becoming a multi-dimensional being with psychic, telepathic, and manifestation abilities beyond anything you've ever dreamed of. Plus, you will stop the aging process and actually start to rejuvenate to look and feel YOUNGER. This is the Original Divine Blueprint, what man USED to be. It has been written that Jesus had 12 strands of DNA activated. There have been children born throughout the history of humanity to raise the frequency of the planet that have more than 2 strands of DNA active - they are known as Indigo children. These are the incredibly intelligent, loving, and amazing children that are being mistakenly diagnosed as having A.D.D. because they are too smart to pay attention in class. Your DNA is your blueprint of life and is what controls every single function inside each of your cells. If you change your DNA, you really will change your life.

MUTATION

Mutations are changes in the DNA sequence of a cell's genome and are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. They can also be induced by the organism itself, by cellular processes such as hypermutation.

Mutation can result in several different types of change in DNA sequences; these can either have no effect, alter the product of a gene, or prevent the gene from functioning properly or completely. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial. Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as DNA repair to remove mutations.Therefore, the optimal mutation rate for a species is a trade-off between costs of a high mutation rate, such as deleterious mutations, and the metabolic costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes.Viruses that use RNA as their genetic material have rapid mutation rates,which can be an advantage since these viruses will evolve constantly and rapidly, and thus evade the defensive responses of e.g. the human immune system.

GENE TRANSFER

Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved.

Most thinking in genetics has focused upon vertical transfer, but there is a growing awareness that horizontal gene transfer is a highly significant phenomenon, and amongst single-celled organisms perhaps the dominant form of genetic transfer. Artificial horizontal gene transfer is a form of genetic engineering.

MICRO RNA

MicroRNAs (miRNAs) are post-transcriptional regulators that bind to complementary sequences in the three prime untranslated regions (3' UTRs) of target messenger RNA transcripts (mRNAs), usually resulting in gene silencing. miRNAs are short ribonucleic acid (RNA) molecules, on average only 22 nucleotides long. The human genome may encode over 1000 miRNAs, which may target about 60% of mammalian genes and are abundant in many human cell types.Each miRNA may repress hundreds of mRNAs.MiRNAs are well conserved in eukaryotic organisms and are thought to be a vital and evolutionarily ancient component of genetic regulation.

The first miRNAs were characterized in the early 1990s, but miRNAs were not recognized as a distinct class of biologic regulators with conserved functions until the early 2000s. Since then, miRNA research has revealed multiple roles in negative regulation (transcript degradation and sequestering, translational suppression) and possible involvement in positive regulation (transcriptional and translational activation). By affecting gene regulation, miRNAs are likely to be involved in most biologic processes.Different sets of expressed miRNAs are found in different cell types and tissues.

Aberrant expression of miRNAs has been implicated in numerous disease states, and miRNA-based therapies are under investigation

GENE THERAPHY

Gene therapy is the insertion of genes into an individual's cell and biological tissues to treat disease, such as cancer where deleterious mutant alleles are replaced with functional ones. Although the technology is still in its infancy, it has been used with some success. Scientific breakthroughs continue to move gene therapy toward mainstream medicine.

TYPES OF GENE THERAPHY :
1. Germ line gene therapy
2. Somatic gene therapy

In the case of germ line gene therapy, germ cells, i.e., sperm or eggs, are modified by the introduction of functional genes, which are ordinarily integrated into their genomes. Therefore, the change due to therapy would be heritable and would be passed on to later generations. This new approach, theoretically, should be highly effective in counteracting genetic disorders and hereditary diseases. However, many jurisdictions prohibit this for application in human beings, at least for the present, for a variety of technical and ethical reasons.

In the case of somatic gene therapy, the therapeutic genes are transferred into the somatic cells of a patient. Any modifications and effects will be restricted to the individual patient only, and will not be inherited by the patient's offspring or later generations.

RNA VIRUS

An RNA virus is a virus that has RNA (ribonucleic acid) as its genetic material. This nucleic acid is usually single-stranded RNA (ssRNA) but may be double-stranded RNA (dsRNA). The ICTV classifies RNA viruses as those that belong to Group III, Group IV or Group V of the Baltimore classification system of classifying viruses, and does not consider viruses with DNA intermediates as RNA viruses. human diseases caused by RNA viruses include SARS, influenza and hepatitis C.
Another term for RNA viruses that explicitly excludes retroviruses is ribovirus

Double-stranded RNA viruses :

The double-stranded (ds)RNA viruses represent a diverse group of viruses that vary widely in host range (humans, animals, plants, fungi, and bacteria), genome segment number (one to twelve), and virion organization (T-number, capsid layers, or turrets). Members of this group include the rotaviruses, renowned globally as the commonest cause of gastroenteritis in young children, and bluetongue virus , an economically important pathogen of cattle and sheep. In recent years, remarkable progress has been made in determining, at atomic and subnanometeric levels, the structures of a number of key viral proteins and of the virion capsids of several dsRNA viruses, highlighting the significant parallels in the structure and replicative processes of many of these viruses.

GENETIC TESTING

The DNA in an organism's genome can be analyzed to diagnose vulnerabilities to inherited diseases, and can also be used to determine a child's paternity (genetic father) or a person's ancestry. Normally, every person carries two copies of every gene, one inherited from their mother, one inherited from their father. The human genome is believed to contain around 20,000 - 25,000 genes. In addition to studying chromosomes to the level of individual genes, genetic testing in a broader sense includes biochemical tests for the possible presence of genetic diseases, or mutant forms of genes associated with increased risk of developing genetic disorders.

Genetic testing identifies changes in chromosomes, genes, or proteins. of the time, testing is used to find changes that are associated with inherited disorders. The results of a genetic test can confirm or rule out a suspected genetic condition or help determine a person's chance of developing or passing on a genetic disorder. Several hundred genetic tests are currently in use, and more are being developed

NUCLEIC ACID SEQUENCE

The primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms. As nucleic acids, e.g. DNA and RNA, are unbranched polymers, this is equivalent to specifying exact sequence of nucleotides that comprise the whole molecule. This sequence is written as a succession of letters representing a real or hypothetical DNA molecule or strand. By convention, the primary structure of a DNA or RNA molecule is reported from the 5' end to the 3' end.

The sequence has capacity to carry information. When used in reference to biological DNA, which carries the information which directs the functions of living beings, the term genetic sequence is often used. Sequences can be read from the biological raw material through DNA sequencing methods.

Primary structure is sometimes mistakenly termed primary sequence, but there is no such term, as well as no parallel concept of secondary or tertiary sequence.

NOTATION :
While A, T, C, and G represent a particular nucleotide at a position, there are also letters that represent ambiguity. Of all the molecules sampled, there is more than one kind of nucleotide at that position. The rules of the International Union of Pure and Applied Chemistry (IUPAC) are as follows:[1]

* A = adenine
* C = cytosine
* G = guanine
* T = thymine
* R = G A (purine)
* Y = T C (pyrimidine)
* K = G T (keto)
* M = A C (amino)
* S = G C (strong bonds)
* W = A T (weak bonds)
* B = G T C (all but A)
* D = G A T (all but C)
* H = A C T (all but G)
* V = G C A (all but T)
* N = A G C T (any)

These symbols are also valid for RNA, except with U (uracil) replacing T (thymine).

Apart from adenosine (A),
cytidine (C),
guanosine (G),
thymidine (T)
and uridine (U), DNA and RNA also contain bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is 5-methylcytidine (m5C). In RNA, there are many modified bases, including pseudouridine (?), dihydrouridine (D), inosine (I), ribothymidine (rT) and 7-methylguanosine (m7G). Hypoxanthine and xanthine are two of the many bases created through mutagen presence, both of them through deamination (replacement of the amine-group with a carbonyl-group). Hypoxanthine is produced from adenine, xanthine from guanine.Similarly, deamination of cytosine results in uracil.

GENOME SEQUENCING

Full genome sequencing (FGS), also known as whole genome sequencing, complete genome sequencing, or entire genome sequencing, is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and for plants the chloroplast as well. Almost any biological sample—even a very small amount of DNA or ancient DNA—can provide the genetic material necessary for full genome sequencing. Such samples may include saliva, epithelial cells, bone marrow, hair (as long as the hair contains a hair follicle), seeds, plant leaves, or anything else that has DNA-containing cells. Because the sequence data that is produced can be quite large (for example, there are approximately six billion base pairs in each human diploid genome), genomic data is stored electronically and requires a large amount of computing power and storage capacity. Full genome sequencing would have been nearly impossible before the advent of the microprocessor, computers, and the Information Age.

Full genome sequencing should thus not be confused with DNA profiling. The latter only determines the likelihood that genetic material came from a particular individual or group and does not contain additional information on genetic relationships, origin or suspectability on specific diseases. It is also distinct from SNP genotyping which covers less than 0.1% of the genome. Almost all truly complete genomes are of microbes; the term "full genome" is thus sometimes used loosely to mean "greater than 95%". The remainder of this article focuses on nearly complete human genomes.

In general, knowing the complete DNA sequence of an individual's genome does not, on its own, provide useful clinical information, but this may change over time as a large number of scientific studies continue to be published detailing clear associations between specific genetic variants and disease.

The first nearly complete human genomes sequenced were J. Craig Venter's (caucasian at 7.5-fold average coverage) and James Watson's (caucasian male at 7.4-fold)., a Han Chinese (YH at 36-fold) a Yoruban from Nigeria (at 30-fold) female leukemia patient (at 33 and 14-fold coverage for tumor and normal tissues), and Seong-Jin Kim (Korean at 29-fold) . Other full genomes have been sequenced but not published, and as of June 2009, commercialization of full genome sequencing is in an early stage and growing rapidly.

DNA PROFILING

DNA profiling (also called DNA testing, DNA typing, or genetic fingerprinting) is a technique employed by forensic scientists to assist in the identification of individuals on the basis of their respective DNA profiles. DNA profiles are encrypted sets of numbers that reflect a person's DNA makeup, which can also be used as the person's identifier. DNA profiling should not be confused with full genome sequencing. It is used in, for example, parental testing and rape investigation.

Although 99.9% of human DNA sequences are the same in every person, enough of the DNA is different to distinguish one individual from another.DNA profiling uses repetitive ("repeat") sequences that are highly variable, called variable number tandem repeats (VNTR). VNTRs loci are very similar between closely related humans, but so variable that unrelated individuals are extremely unlikely to have the same VNTRs.

The DNA profiling technique was first reported in 1984 Sir Alec Jeffreys at the University of Leicester in England, and is now the basis of several national DNA databases. Dr. Alec Jeffrey's genetic fingerprinting was made commercially available in 1987, when a chemical company, ICI, started a blood-testing center in England.

GENES

A gene is a unit of heredity in a living organism. It is normally a stretch of DNA that codes for a type of protein or for an RNA chain that has a function in the organism. All proteins and functional RNA chains are specified by genes. All living things depend on genes. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring. A modern working definition of a gene is "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions ". Colloquial usage of the term gene (e.g. "good genes, "hair color gene") may actually refer to an allele: a gene is the basic instruction, a sequence of nucleic acid (DNA or, in the case of certain viruses RNA), while an allele is one variant of that instruction.

The notion of a gene is evolving with the science of genetics, which began when Gregor Mendel noticed that biological variations are inherited from parent organisms as specific, discrete traits. The biological entity responsible for defining traits was later termed a gene, but the biological basis for inheritance remained unknown until DNA was identified as the genetic material in the 1940s. All organisms have many genes corresponding to many different biological traits, some of which are immediately visible, such as eye color or number of limbs, and some of which are not, such as blood type or increased risk for specific diseases, or the thousands of basic biochemical processes that comprise life.
The chemical structure of a four-base fragment of a DNA double helix.

The vast majority of living organisms encode their genes in long strands of DNA. DNA (deoxyribonucleic acid) consists of a chain made from four types of nucleotide subunits, each composed of: a five-carbon sugar (2'-deoxyribose), a phosphate group, and one of the four bases adenine, cytosine, guanine, and thymine. The most common form of DNA in a cell is in a double helix structure, in which two individual DNA strands twist around each other in a right-handed spiral. In this structure, the base pairing rules specify that guanine pairs with cytosine and adenine pairs with thymine. The base pairing between guanine and cytosine forms three hydrogen bonds, whereas the base pairing between adenine and thymine forms two hydrogen bonds. The two strands in a double helix must therefore be complementary, that is, their bases must align such that the adenines of one strand are paired with the thymines of the other strand, and so on.

Due to the chemical composition of the pentose residues of the bases, DNA strands have directionality. One end of a DNA polymer contains an exposed hydroxyl group on the deoxyribose; this is known as the 3' end of the molecule. The other end contains an exposed phosphate group; this is the 5' end. The directionality of DNA is vitally important to many cellular processes, since double helices are necessarily directional (a strand running 5'-3' pairs with a complementary strand running 3'-5'), and processes such as DNA replication occur in only one direction. All nucleic acid synthesis in a cell occurs in the 5'-3' direction, because new monomers are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile.

The expression of genes encoded in DNA begins by transcribing the gene into RNA, a second type of nucleic acid that is very similar to DNA, but whose monomers contain the sugar ribose rather than deoxyribose. RNA also contains the base uracil in place of thymine. RNA molecules are less stable than DNA and are typically single-stranded. Genes that encode proteins are composed of a series of three-nucleotide sequences called codons, which serve as the words in the genetic language. The genetic code specifies the correspondence during protein translation between codons and amino acids. The genetic code is nearly the same for all known organisms

MOLECULAR GENETICS

Although genes were known to exist on chromosomes, chromosomes are composed of both protein and DNA—scientists did not know which of these is responsible for inheritance. In 1928, Frederick Griffith discovered the phenomenon of transformation (see Griffith's experiment): dead bacteria could transfer genetic material to "transform" other still-living bacteria. Sixteen years later, in 1944, Oswald Theodore Avery, Colin McLeod and Maclyn McCarty identified the molecule responsible for transformation as DNA. The Hershey-Chase experiment in 1952 also showed that DNA (rather than protein) is the genetic material of the viruses that infect bacteria, providing further evidence that DNA is the molecule responsible for inheritance.

James D. Watson and Francis Crick determined the structure of DNA in 1953, using the X-ray crystallography work of Rosalind Franklin and Maurice Wilkins that indicated DNA had a helical structure (i.e., shaped like a corkscrew).Their double-helix model had two strands of DNA with the nucleotides pointing inward, each matching a complementary nucleotide on the other strand to form what looks like rungs on a twisted ladder.This structure showed that genetic information exists in the sequence of nucleotides on each strand of DNA. The structure also suggested a simple method for duplication: if the strands are separated, new partner strands can be reconstructed for each based on the sequence of the old strand.

Although the structure of DNA showed how inheritance works, it was still not known how DNA influences the behavior of cells. In the following years, scientists tried to understand how DNA controls the process of protein production. It was discovered that the cell uses DNA as a template to create matching messenger RNA (a molecule with nucleotides, very similar to DNA). The nucleotide sequence of a messenger RNA is used to create an amino acid sequence in protein; this translation between nucleotide and amino acid sequences is known as the genetic code.

With this molecular understanding of inheritance, an explosion of research became possible. One important development was chain-termination DNA sequencing in 1977 by Frederick Sanger: This technology allows scientists to read the nucleotide sequence of a DNA molecule. In 1983, Kary Banks Mullis developed the polymerase chain reaction, providing a quick way to isolate and amplify a specific section of a DNA from a mixture.Through the pooled efforts of the Human Genome Project and the parallel private effort by Celera Genomics, these and other techniques culminated in the sequencing of the human genome in 2003.

GENETIC CODE

Genes generally express their functional effect through the production of proteins, which are complex molecules responsible for most functions in the cell. Proteins are chains of amino acids, and the DNA sequence of a gene (through RNA intermediate) is used to produce a specific protein sequence. This process begins with the production of an RNA molecule with a sequence matching the gene's DNA sequence, a process called transcription.

This messenger RNA molecule is then used to produce a corresponding amino acid sequence through a process called translation. Each group of three nucleotides in the sequence, called a codon, corresponds to one of the twenty possible amino acids in protein – this correspondence is called the genetic code. The flow of information is unidirectional: information is transferred from nucleotide sequences into the amino acid sequence of proteins, but it never transfers from protein back into the sequence of DNA—a phenomenon Francis Crick called the central dogma of molecular biology.
The dynamic structure of hemoglobin is responsible for its ability to transport oxygen within mammalian blood.
A single amino acid change causes hemoglobin to form fibers.

The specific sequence of amino acids results in a unique three-dimensional structure for that protein, and the three-dimensional structures of protein are related to their function.Some are simple structural molecules, like the fibers formed by the protein collagen. Proteins can bind to other proteins and simple molecules, sometimes acting as enzymes by facilitating chemical reactions within the bound molecules (without changing the structure of the protein itself). Protein structure is dynamic; the protein hemoglobin bends into slightly different forms as it facilitates the capture, transport, and release of oxygen molecules within mammalian blood.

A single nucleotide difference within DNA can cause a single change in the amino acid sequence of a protein. Because protein structures are the result of their amino acid sequences, some changes can dramatically change the properties of a protein by destabilizing the structure or changing the surface of the protein in a way that changes its interaction with other proteins and molecules. For example, sickle-cell anemia is a human genetic disease that results from a single base difference within the coding region for the ß-globin section of hemoglobin, causing a single amino acid change that changes hemoglobin's physical properties.Sickle-cell versions of hemoglobin stick to themselves, stacking to form fibers that distort the shape of red blood cells carrying the protein. These sickle-shaped cells no longer flow smoothly through blood vessels, having a tendency to clog or degrade, causing the medical problems associated with this disease.

Some genes are transcribed into RNA but are not translated into protein products—these are called non-coding RNA molecules. In some cases, these products fold into structures which are involved in critical cell functions (e.g. ribosomal RNA and transfer RNA). RNA can also have regulatory effect through hybridization interactions with other RNA molecules (e.g. microRNA).

MEDICAL GENETICS RESEARCH

Medical genetics seeks to understand how genetic variation relates to human health and disease.When searching for an unknown gene that may be involved in a disease, researchers commonly use genetic linkage and genetic pedigree charts to find the location on the genome associated with the disease. At the population level, researchers take advantage of Mendelian randomization to look for locations in the genome that are associated with diseases, a technique especially useful for multigenic traits not clearly defined by a single gene. Once a candidate gene is found, further research is often done on the same gene (called an orthologous gene) in model organisms. In addition to studying genetic diseases, the increased availability of genotyping techniques has led to the field of pharmacogenetics—studying how genotype can affect drug responses.

Although it is not usually an inherited disease, cancer is a genetic disease.The process of cancer development in the body is a combination of events. Mutations occasionally occur within cells in the body as they divide. While these mutations will not be inherited by any offspring, they can affect the behavior of cells, sometimes causing them to grow and divide more frequently. There are biological mechanisms that attempt to stop this process; signals are given to inappropriately dividing cells that should trigger cell death, but sometimes additional mutations occur that cause cells to ignore these messages. An internal process of natural selection occurs within the body and eventually mutations accumulate within cells to promote their own growth, creating a cancerous tumor that grows and invades various tissues of the body.

TRANSCRIPTION AND TRANSLATION

A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism. Within a gene, the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences. The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code. The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT).

In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase. This RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids. Since there are 4 bases in 3-letter combinations, there are 64 possible codons (43 combinations). These encode the twenty standard amino acids, giving most amino acids more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAA, TGA and TAG codons.

Genomic DNA is located in the cell nucleus of eukaryotes, as well as small amounts in mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid. The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism. Genes contain an open reading frame that can be transcribed, as well as regulatory sequences such as promoters and enhancers, which control the transcription of the open reading frame.

In many species, only a small fraction of the total sequence of the genome encodes protein. For example, only about 1.5% of the human genome consists of protein-coding exons, with over 50% of human DNA consisting of non-coding repetitive sequences.The reasons for the presence of so much non-coding DNA in eukaryotic genomes and the extraordinary differences in genome size, or C-value, among species represent a long-standing puzzle known as the "C-value enigma."However, DNA sequences that do not code protein may still encode functional non-coding RNA molecules, which are involved in the regulation of gene expression

QUADRUPLEX STRUCTURE

At the ends of the linear chromosomes are specialized regions of DNA called telomeres. The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3' ends of chromosomes.These specialized chromosome caps also help protect the DNA ends, and stop the DNA repair systems in the cell from treating them as damage to be corrected. In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.

These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules. Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable G-quadruplex structure.These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit. structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.

In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops. Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins. At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.

GENETIC CHANGE

During the process of DNA replication, errors occasionally occur in the polymerization of the second strand. These errors, called mutations, can have an impact on the phenotype of an organism, especially if they occur within the protein coding sequence of a gene. Error rates are usually very low—1 error in every 10–100 million bases—due to the "proofreading" ability of DNA polymerases.(Without proofreading error rates are a thousand-fold higher; because many viruses rely on DNA and RNA polymerases that lack proofreading ability, they experience higher mutation rates.) Processes that increase the rate of changes in DNA are called mutagenic: mutagenic chemicals promote errors in DNA replication, often by interfering with the structure of base-pairing, while UV radiation induces mutations by causing damage to the DNA structure. Chemical damage to DNA occurs naturally as well, and cells use DNA repair mechanisms to repair mismatches and breaks in DNA—nevertheless, the repair sometimes fails to return the DNA to its original sequence.
In organisms that use chromosomal crossover to exchange DNA and recombine genes, errors in alignment during meiosis can also cause mutations. Errors in crossover are especially likely when similar sequences cause partner chromosomes to adopt a mistaken alignment; this makes some regions in genomes more prone to mutating in this way. These errors create large structural changes in DNA sequence—duplications, inversions or deletions of entire regions, or the accidental exchanging of whole parts between different chromosomes (called translocation).

INTERACTIONS OF MULTIPLE GENES

Organisms have thousands of genes, and in sexually reproducing organisms assortment of these genes are generally independent of each other. This means that the inheritance of an allele for yellow or green pea color is unrelated to the inheritance of alleles for white or purple flowers. This phenomenon, known as "Mendel's second law" or the "Law of independent assortment", means that the alleles of different genes get shuffled between parents to form offspring with many different combinations.(Some genes do not assort independently, demonstrating genetic linkage, a topic discussed later in this article.)
Often different genes can interact in a way that influences the same trait. In the Blue-eyed Mary (Omphalodes verna), for example, there exists a gene with alleles that determine the color of flowers: blue or magenta. Another gene, however, controls whether the flowers have color at all or are white. When a plant has two copies of this white allele, its flowers are white—regardless of whether the first gene has blue or magenta alleles. This interaction between genes is called epistasis, with the second gene epistatic to the first.
Many traits are not discrete features (e.g. purple or white flowers) but are instead continuous features (e.g. human height and skin color). These complex traits are the product of many genes. The influence of these genes is mediated, to varying degrees, by the environment an organism has experienced. The degree to which an organism's genes contribute to a complex trait is called heritability. Measurement of the heritability of a trait is relative—in a more variable environment, the environment has a bigger influence on the total variation of the trait. For example, human height is a complex trait with a heritability of 89% in the United States. In Nigeria, however, where people experience a more variable access to good nutrition and health care, height has a heritability of only 62%

NON CODING DNA

In genetics, noncoding DNA describes components of an organism's DNA sequences that do not encode for protein sequences. In many eukaryotes, a large percentage of an organism's total genome size is noncoding DNA, although the amount of noncoding DNA, and the proportion of coding versus noncoding DNA varies greatly between species.
Much of this DNA has no known biological function and is sometimes referred to as "junk DNA". However, many types of noncoding DNA sequences do have known biological functions, including the transcriptional and translational regulation of protein-coding sequences. Other noncoding sequences have likely but as-yet undetermined function, an inference from high levels of homology and conservation seen in sequences that do not encode proteins but appear to be under heavy selective pressure.

DNA NANOTECNOLOGY

The concept of DNA nanotechnology was invented by Nadrian Seeman in early 1980s.A crystallographer, Seeman was frustrated with the haphazardness and guesswork involved with crystallizing certain molecules. In fall 1980, while at a campus pub, Seeman was inspired by the M. C. Escher woodcut Depth to realize that a three-dimensional DNA lattice could be used to orient target molecules, simplifying their crystallographic study. In 1991, Seeman's laboratory published the synthesis of a cube made of DNA, the first three-dimensional nanoscale object, for which he received the 1995 Feynman Prize in Nanotechnology, which was followed by a DNA truncated octahedron. However, it soon became clear that these objects were not rigid enough to form three-dimensional lattices.
Seeman developed the more rigid "DX" motif, and in collaboration with Erik Winfree, in 1998 published the creation of two-dimensional lattices of DX tiles. These tile-based structures had the advantage that they provided the capability to implement DNA computing, which was demonstrated by Winfree and Paul Rothemund in 2004, and for which they shared the 2006 Feynman Prize in Nanotechnology.
The field has continued to branch out. The first DNA nanomachine—a motif which changes its structure in response to an input—was demonstrated in 1999. Nanoarchitecture, first proposed by Seeman in 1987, was beginning to be demonstrated by 2006. Also in 2006, Rothemund first demonstrated the new DNA origami technique for easily and robustly creating folded DNA molecules of any shape. In 2009, Seeman published the synthesis of a three-dimensional lattice, nearly thirty years after he had set out to do so.

DENTAL TREATMENT COULD ADVANCE WITH GENETICS DISCOVERY

Researchers have identified the gene that ultimately controls the production of tooth enamel, a significant advance that could some day lead to the repair of damaged enamel, a new concept in cavity prevention, and restoration or even the production of replacement teeth.

The gene, called Ctip2, is a "transcription factor" that was already known to have several functions - in immune response, and the development of skin and the nervous system. Scientists can now add tooth development to that list.
The findings were just published in the Proceedings of the National Academy of Sciences.
"It's not unusual for a gene to have multiple functions, but before this we didn't know what regulated the production of tooth enamel," said Chrissa Kioussi, an assistant professor in the College of Pharmacy at Oregon State University. "This is the first transcription factor ever found to control the formation and maturation of ameloblasts, which are the cells that secrete enamel."
The researchers used a laboratory mouse model in this study in which this gene has been "knocked out" and its protein is missing. Such mice lack basic biological systems and cannot live after birth, but allow scientists to study what is there, and what's missing.
In this case, the mice had rudimentary teeth ready to erupt, but they lacked a proper enamel coating, and never would have been functional.
"Enamel is one of the hardest coatings found in nature, it evolved to give carnivores the tough and long-lasting teeth they needed to survive," Kioussi said.
With an understanding of its genetic underpinning, Kioussi said, it may be possible to use tooth stem cells to stimulate the growth of new enamel. Some groups are already having success growing the inner portions of teeth in laboratory animal experiments, but those teeth have no hard coatings – the scientists lacked the genetic material that makes enamel.
"A lot of work would still be needed to bring this to human applications, but it should work," Kioussi said. "It could be really cool, a whole new approach to dental health."
Many people have problems with eroded tooth enamel, including people who smoke, drink and especially some who use illegal drugs such as methamphetamine. And most cavities start as a hole in tooth enamel that allows decay to begin.
This research was supported by the National Institutes of Health and the OSU College of Pharmacy. The study was a collaboration of scientists from the OSU College of Pharmacy, College of Science and College of Engineering, and the Institut de Genetique et de Biologie Moleculaire et Cellulaire in France

DNA DOUBLE HELIX

The DNA Double Helix is one of the greatest scientific discoveries of all time. First described by James Watson and Francis Crick in 1953, DNA is the famous molecule of genetics that establishes each organism's physical characteristics. It wasn't until mid-2001, that the Human Genome Project and Celera Genomics jointly presented the true nature and complexity of the digital code inherent in DNA. We now understand that each human DNA molecule is comprised of chemical bases arranged in approximately 3 billion precise sequences. Even the DNA molecule for the single-celled bacterium, E. coli, contains enough information to fill all the books in any of the world's largest libraries.

DNA Double Helix: The "Basics"
DNA (deoxyribonucleic acid) is a double-stranded molecule that is twisted into a helix like a spiral staircase. Each strand is comprised of a sugar-phosphate backbone and numerous base chemicals attached in pairs. The four bases that make up the stairs in the spiraling staircase are adenine (A), thymine (T), cytosine (C) and guanine (G). These stairs act as the "letters" in the genetic alphabet, combining into complex sequences to form the words, sentences and paragraphs that act as instructions to guide the formation and functioning of the host cell. Maybe even more appropriately, the A, T, C and G in the genetic code of the DNA molecule can be compared to the "0" and "1" in the binary code of computer software. Like software to a computer, the DNA code is a genetic language that communicates information to the organic cell.

The DNA code, like a floppy disk of binary code, is quite simple in its basic paired structure. However, it's the sequencing and functioning of that code that's enormously complex. Through recent technologies like x-ray crystallography, we now know that the cell is not a "blob of protoplasm", but rather a microscopic marvel that is more complex than the space shuttle. The cell is very complicated, using vast numbers of phenomenally precise DNA instructions to control its every function.

Although DNA code is remarkably complex, it's the information translation system connected to that code that really baffles science. Like any language, letters and words mean nothing outside the language convention used to give those letters and words meaning. This is modern information theory at its core. A simple binary example of information theory is the "Midnight Ride of Paul Revere." In that famous story, Mr. Revere asks a friend to put one light in the window of the North Church if the British came by land, and two lights if they came by sea. Without a shared language convention between Paul Revere and his friend, that simple communication effort would mean nothing. Well, take that simple example and multiply by a factor containing many zeros.

We now know that the DNA molecule is an intricate message system. To claim that DNA arose by random material forces is to say that information can arise by random material forces. Many scientists argue that the chemical building blocks of the DNA molecule can be explained by natural evolutionary processes. However, they must realize that the material base of a message is completely independent of the information transmitted. Thus, the chemical building blocks have nothing to do with the origin of the complex message. As a simple illustration, the information content of the clause "nature was designed" has nothing to do with the writing material used, whether ink, paint, chalk or crayon. In fact, the clause can be written in binary code, Morse code or smoke signals, but the message remains the same, independent of the medium. There is obviously no relationship between the information and the material base used to transmit it. Some current theories argue that self-organizing properties within the base chemicals themselves created the information in the first DNA molecule. Others argue that external self-organizing forces created the first DNA molecule. However, all of these theories must hold to the illogical conclusion that the material used to transmit the information also produced the information itself. Contrary to the current theories of evolutionary scientists, the information contained within the genetic code must be entirely independent of the chemical makeup of the DNA molecule.

DNA Double Helix: Its Existence Alone Defeats any Theory of Evolution
The scientific reality of the DNA double helix can single-handedly defeat any theory that assumes life arose from non-life through materialistic forces. Evolution theory has convinced many people that the design in our world is merely "apparent" -- just the result of random, natural processes. However, with the discovery, mapping and sequencing of the DNA molecule, we now understand that organic life is based on vastly complex information code, and such information cannot be created or interpreted without a Master Designer at the cosmic keyboard.