Instruct: Given a question, retrieve documents that answer the question.
Query: Can DNA be created?
Artificial gene synthesis, sometimes known as DNA printing[1] is a method in synthetic biology that is used to create artificial genes in the laboratory. Based on solid-phase DNA synthesis, it differs from molecular cloning and polymerase chain reaction (PCR) in that it does not have to begin with preexisting DNA sequences. Therefore, it is possible to make a completely synthetic double-stranded DNA molecule with no apparent limits on either nucleotide sequence or size
Bioinstrumentation can be used for genetic testing. This is done with the help of chemistry and medical instruments. Professionals in the field have created tissue analysis instruments, which can compare the DNA of different people. Another example of genetic testing is gel electrophoresis. Gel electrophoresis uses DNA samples, along with biosensors to compare the DNA sequence of individuals. Two other important instruments involved in genomic advances are microarray technology and DNA sequencing. Microarrays reveal the activated and repressed genes of an individual. DNA sequencing uses lasers with different wavelength, to determine the nucleotides present in different DNA strands. Bioinstrumentation has changed the world of genetic testing, and helps scientists understand DNA and the human genome better than ever before. 
Clinical chemotherapeutics can induce enzymatic and non-enzymatic DNA-protein crosslinks. An example of this induction is with platinum derivatives, such as cisplatin and oxaliplatin. They create non-enzymatic DNA-protein crosslinks through non-specific crosslinking of chromatin-interacting proteins to DNA. Crosslinking is also possible in other therapeutic agents by either stabilizing covalent DNA–protein reaction intermediates or by creating a pseudosubstrate, which traps the enzyme on DNA. Camptothecin derivatives, such as irinotecan and topotecan, target and trap specific DNA topoisomerase 1 (TOP1) by intercalating within the enzyme–DNA interface. Because the toxicity of these drugs depends on TOP1 trapping, cellular sensitivity to these compounds depends directly on TOP1 expression levels. As a result, the function of these drugs is to serve as enzyme poisons rather than inhibitors. This can be applied to treat tumor cells by utilizing TOP 2 enzyme poisons.
DNA within our bodies naturally breaks down, replicates itself, and rebuilds itself every time a cell divides. These processes are all controlled and completed by various enzymes. DNA molecules are composed of corresponding base pair nucleotides in a double-helix formation, which makes these processes very efficient, accurate, and predictable. Due to the ease with which DNA molecules can be fashioned, many publications in the academic society are geared towards creating nanostructures using DNA. With a DNA-based nano-device, synthetic proteins could be created, designed to deactivate a nano-device. These synthetic proteins would be injected into the body to break down the DNA and render a nano-device harmless in the event of a malfunction.
One of the important targets for cellular reproduction is thymidylate synthase, which creates thymidine monophosphate (TMP) from deoxyuridine monophosphate (dUMP). By additional phosphorylation reactions, TMP can be used to make thymidine triphosphate (TTP), one of the four nucleotide precursors that are used by DNA polymerases to create DNA. Without the THF required to convert dUMP, there can be no TTP, and DNA synthesis cannot proceed, unless TMP can be produced from another source. The alternative source is the thymidine present in the HAT medium that can be absorbed by the cells and phosphorylated by thymidine kinase (TK) into TMP.
The DNA sequencing is done on a chip that contains many ZMWs. Inside each ZMW, a single active DNA polymerase with a single molecule of single stranded DNA template is immobilized to the bottom through which light can penetrate and create a visualization chamber that allows monitoring of the activity of the DNA polymerase at a single molecule level. The signal from a phospho-linked nucleotide incorporated by the DNA polymerase is detected as the DNA synthesis proceeds which results in the DNA sequencing in real time.
Related to adaptive maternal effects are epigenetic effects. Epigenetics is the study of long lasting changes in gene expression that are produced by modifications to chromatin instead of changes in DNA sequence, as is seen in DNA mutation. This "change" refers to DNA methylation, histone acetylation, or the interaction of non-coding RNAs with DNA. DNA methylation is the addition of methyl groups to the DNA. When DNA is methylated in mammals, the transcription of the gene at that location is turned down or turned off entirely. The induction of DNA methylation is highly influenced by the maternal environment. Some maternal environments can lead to a higher methylation of an offspring's DNA, while others lower methylation.[22] The fact that methylation can be influenced by the maternal environment, makes it similar to adaptive maternal effects. Further similarities are seen by the fact that methylation can often increase the fitness of the offspring. Additionally, epigenetics can refer to histone modifications or non-coding RNAs that create a sort of cellular memory. Cellular memory refers to a cell's ability to pass nongenetic information to its daughter cell during replication. For example, after differentiation, a liver cell performs different functions than a brain cell; cellular memory allows these cells to "remember" what functions they are supposed to perform after replication. Some of these epigenetic changes can be passed down to future generations, while others are reversible within a particular individual's lifetime. This can explain why individuals with identical DNA can differ in their susceptibility to certain chronic diseases.
To create sequence logos, related DNA, RNA or protein sequences, or DNA sequences that have common conserved binding sites, are aligned so that the most conserved parts create good alignments. A sequence logo can then be created from the conserved multiple sequence alignment. The sequence logo will show how well residues are conserved at each position: the higher the number of residues, the higher the letters will be, because the better the conservation is at that position. Different residues at the same position are scaled according to their frequency. The height of the entire stack of residues is the information measured in bits. Sequence logos can be used to represent conserved DNA binding sites, where transcription factors bind.
Herbarium specimens of plants are collected for a number of different uses. They can assist in accurate identification and provide a species record for a time and place that can be used in distribution maps. They can also provide biological material for researchers, a reference point to document scientific names and vouchers for research and seed collections. DNA barcoding, a new method of identification of plant vouchers, is being used in herbaria across the world. The Smithsonian National Museum of Natural History creates their barcodes from a short sequence of plant DNA, which can be easily identified from all healthy specimens of the species. This barcode is then printed and placed onto the plant mount. By creating these DNA barcodes, the process of organizing and loaning plant specimens becomes more streamlined and can be mechanized.
High radiation doses can cause DNA damage. If left unrepaired, this damage can create serious and even lethal chromosomal aberrations. Ionizing radiation can produce reactive oxygen species, which are very damaging to DNA.
DNA synthesis is the natural or artificial creation of deoxyribonucleic acid (DNA) molecules. The term DNA synthesis can refer to DNA replication - DNA biosynthesis ("in vivo" DNA amplification), polymerase chain reaction - enzymatic DNA synthesis ("in vitro" DNA amplification) or gene synthesis - physically creating artificial gene sequences.
In nature, DNA molecules are created by all living cells through the process of DNA replication, with replication initiator proteins splitting the cell's DNA and copying each split strand, with the copied strands then joining together with their template strand into a new DNA molecule. Various means exist to artificially stimulate the replication of naturally occurring DNA, or to create artificial gene sequences. The process of DNA replication occurs typically as part of cell division, during interphase.
Longer overhangs are called "cohesive ends" or "sticky ends". They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 5' overhang in one molecule and a complementary 5' overhang in the other. These ends are called cohesive since they are easily joined back together by a ligase. Also, since different restriction endonucleases usually create different overhangs, it is possible to cut a piece of DNA with two different enzymes and then join it with another DNA molecule with ends created by the same enzymes. Since the overhangs have to be complementary in order for the ligase to work, the two molecules can only join in one orientation. This is often highly desirable in molecular biology.
DNA sequencing may be used along with DNA profiling methods for forensic identification and paternity testing. DNA testing has evolved tremendously in the last few decades to ultimately link a DNA print to what is under investigation. The DNA patterns in fingerprint, saliva, hair follicles, etc. uniquely separate each living organism from another. Testing DNA is a technique which can detect specific genomes in a DNA strand to produce a unique and individualized pattern. Every living organism ever created has a one of a kind DNA pattern, which can be determined through DNA testing. It is extremely rare that two people have exactly the same DNA pattern, therefore DNA testing is highly successful.
AP sites are an important feature of the base excision repair pathway. DNA glycosylases first create abasic sites by recognizing and removing modified bases. Many glycosylase variants exist to deal with the multiple ways a base can be damaged. The most common circumstances are base alkylation, oxidation, and the presence of a uracil in the DNA strand. Once an AP site has been successful created, an AP endonuclease catalyzes the breakage of one phosphoester bond, creating a nick in the backbone of the helix. The breakage can be either 3' or 5' of the site, depending on the variant of the enzyme. End processing enzymes then prepare the site for nick for ligation, which is performed by DNA polymerase. The base inserted into the nick is determined by the corresponding base on the opposite strand. The nick is then sealed by DNA ligase.
A variety of cleavage agents can be chosen. a desirable agent is one that is sequence neutral, easy to use, and is easy to control. Unfortunately no available agents meet all of these standards, so an appropriate agent can be chosen, depending on your DNA sequence and ligand of interest. The following cleavage agents are described in detail:
DNase I is a large protein that functions as a double-strand endonuclease. It binds the minor groove of DNA and cleaves the phosphodiester backbone. It is a good cleavage agent for footprinting because its size makes it easily physically hindered. Thus is more likely to have its action blocked by a bound protein on a DNA sequence. In addition, the DNase I enzyme is easily controlled by adding EDTA to stop the reaction. There are however some limitations in using DNase I. The enzyme does not cut DNA randomly; its activity is affected by local DNA structure and sequence and therefore results in an uneven ladder. This can limit the precision of predicting a protein’s binding site on the DNA molecule.
Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe with HO to form free hydroxyl molecules. These hydroxyl molecules react with the DNA backbone, resulting in a break. Due to their small size, the resulting DNA footprint has high resolution. Unlike DNase I they have no sequence dependence and result in a much more evenly distributed ladder. The negative aspect of using hydroxyl radicals is that they are more time consuming to use, due to a slower reaction and digestion time.
Ultraviolet irradiation can be used to excite nucleic acids and create photoreactions, which results in damaged bases in the DNA strand. Photoreactions can include: single strand breaks, interactions between or within DNA strands, reactions with solvents, or crosslinks with proteins. The workflow for this method has an additional step, once both your protected and unprotected DNA have been treated, there is subsequent primer extension of the cleaved products. The extension will terminate upon reaching a damaged base, and thus when the PCR products are run side-by-side on a gel; the protected sample will show an additional band where the DNA was crosslinked with a bound protein. Advantages of using UV are that it reacts very quickly and can therefore capture interactions that are only momentary. Additionally it can be applied to "in vivo" experiments, because UV can penetrate cell membranes. A disadvantage is that the gel can be difficult to interpret, as the bound protein does not protect the DNA, it merely alters the photoreactions in the vicinity.
Nicked DNA can be the result of DNA damage or purposeful and carefully regulated biomolecular reactions carried out in the cell. DNA can be nicked by physical shearing, over-drying or enzymes. Excessive rough handling happening in pipetting or vortexing creates the physical stress that can lead to breaks and nicks in DNA. Overdrying of DNA can also break the phosphodiester bond in DNA and result in nicks. Enzyme Nicking endonucleases can assist with this process. A single-stranded break (nick) in DNA can be formed by the hydrolysis and subsequent removal of a phosphate group within the helical backbone. This leads to a different DNA conformation, where a hydrogen bond forms in place of the missing piece of the DNA backbone in order to preserve the structure.
DNA polymerases are a family of enzymes that carry out all forms of DNA replication. DNA polymerases in general cannot initiate synthesis of new strands, but can only extend an existing DNA or RNA strand paired with a template strand. To begin synthesis, a short fragment of RNA, called a primer, must be created and paired with the template DNA strand.
The diagram shows the effects of nicks on intersecting DNA forms. Nicking can be used to alleviate the energy created by intersecting states. By creating nicks, the DNA forms a circular shape.
The DNA sequences used in the construction of recombinant DNA molecules can originate from any species. For example, plant DNA may be joined to bacterial DNA, or human DNA may be joined with fungal DNA. In addition, DNA sequences that do not occur anywhere in nature may be created by the chemical synthesis of DNA, and incorporated into recombinant molecules. Using recombinant DNA technology and synthetic DNA, literally any DNA sequence may be created and introduced into any of a very wide range of living organisms.
DNA damage is an abnormal alteration in the structure of DNA that cannot, itself, be replicated when DNA replicates. In contrast, a mutation is a change in the nucleic acid sequence that can be replicated; hence, a mutation can be inherited from one generation to the next. Damage can occur from chemical addition (adduct), or structural disruption to a base of DNA (creating an abnormal nucleotide or nucleotide fragment), or a break in one or both DNA strands. When DNA containing damage is replicated, an incorrect base may be inserted in the new complementary strand as it is being synthesized (see ). The incorrect insertion in the new strand will occur opposite the damaged site in the template strand, and this incorrect insertion can become a mutation (i.e. a changed base pair) in the next round of replication. Furthermore, double-strand breaks in DNA may be repaired by an inaccurate repair process, non-homologous end joining, which produces mutations. Mutations can ordinarily be avoided if accurate DNA repair systems recognize DNA damage and repair it prior to completion of the next round of replication. At least 169 enzymes are either directly employed in DNA repair or influence DNA repair processes. Of these, 83 are directly employed in the 5 types of DNA repair processes indicated in the chart shown in the article DNA repair.
Newly synthesized DNA, otherwise known as Okazaki fragments, are bound by DNA ligase, which forms a new strand of DNA. There are two strands that are created when DNA is synthesized. The leading strand is continuously synthesized and is elongated during this process to expose the template that is used for the lagging strand (Okazaki fragments). During the process of DNA replication, DNA and RNA primers are removed from the lagging strand of DNA to allow Okazaki fragments to bind to. Since this process is so common, Okazaki maturation will take place around a million times during one completion of DNA replication. For Okazaki maturation to occur, RNA primers must create segments on the fragments to be ligated. This is used as a building block for the synthesis of DNA in the lagging strand. On the template strand, polymerase will synthesize in the opposite direction from the replication fork. Once the template becomes discontinuous, it will create an Okazaki fragment. Defects in the maturation of Okazaki fragments can potentially cause strands in the DNA to break and cause different forms of chromosome abnormality. These mutations in the chromosomes can affect the appearance, the number of sets, or the number of individual chromosomes. Since chromosomes are fixed for each specific species, it can also change the DNA and cause defects in the genepool of that species.
Genetic engineering, also called genetic modification or genetic manipulation, is the direct manipulation of an organism's genes using biotechnology. It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms. New DNA is obtained by either isolating and copying the genetic material of interest using recombinant DNA methods or by artificially synthesising the DNA. A construct is usually created and used to insert this DNA into the host organism. The first recombinant DNA molecule was made by Paul Berg in 1972 by combining DNA from the monkey virus SV40 with the lambda virus. As well as inserting genes, the process can be used to remove, or "knock out", genes. The new DNA can be inserted randomly, or targeted to a specific part of the genome.
Transformation is the direct alteration of a cells genetic components by passing the genetic material through the cell membrane. About 1% of bacteria are naturally able to take up foreign DNA, but this ability can be induced in other bacteria. Stressing the bacteria with a heat shock or electroporation can make the cell membrane permeable to DNA that may then incorporate into the genome or exist as extrachromosomal DNA. Typically the cells are incubated in a solution containing divalent cations (often calcium chloride) under cold conditions, before being exposed to a heat pulse (heat shock). Calcium chloride partially disrupts the cell membrane, which allows the recombinant DNA to enter the host cell. It is suggested that exposing the cells to divalent cations in cold condition may change or weaken the cell surface structure, making it more permeable to DNA. The heat-pulse is thought to create a thermal imbalance across the cell membrane, which forces the DNA to enter the cells through either cell pores or the damaged cell wall. Electroporation is another method of promoting competence. In this method the cells are briefly shocked with an electric field of 10-20 kV/cm, which is thought to create holes in the cell membrane through which the plasmid DNA may enter. After the electric shock, the holes are rapidly closed by the cell's membrane-repair mechanisms. Up-taken DNA can either integrate with the bacterials genome or, more commonly, exist as extrachromosomal DNA.
The absence of the 3'-hydroxyl group means that, after being added by a DNA polymerase to a growing nucleotide chain, no further nucleotides can be added as no phosphodiester bond can be created based on the fact that deoxyribonucleoside triphosphates (which are the building blocks of DNA) allow DNA chain synthesis to occur through a condensation reaction between the 5' phosphate (following the cleavage of pyrophospate) of the current nucleotide with the 3' hydroxyl group of the previous nucleotide. The dideoxyribonucleotides do not have a 3' hydroxyl group, hence no further chain elongation can occur once this dideoxynucleotide is on the chain. This can lead to the termination of the DNA sequence. Thus, these molecules form the basis of the dideoxy chain-termination method of DNA sequencing, which was developed by Frederick Sanger in 1977.
The use of ligation enzymes allows DNA fragments to be connected. By binding ("ligating") fragments of DNA together from different sources, researchers can create recombinant DNA, the DNA often associated with genetically modified organisms. Recombinant DNA is commonly used in the context of plasmids: short circular DNA molecules with a few genes on them. In the process known as molecular cloning, researchers can amplify the DNA fragments by inserting plasmids into bacteria and then culturing them on plates of agar (to isolate clones of bacteria cells—"cloning" can also refer to the various means of creating cloned ("clonal") organisms).