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Molecular cloning

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genetic change for the whole organism and subsequent generations. This "germ line gene therapy" is considered by many to be unethical in human beings. The second type of gene therapy, "somatic cell gene therapy", is analogous to an organ transplant. In this case, one or more specific tissues are targeted by direct treatment or by removal of the tissue, addition of the therapeutic gene or genes in the laboratory, and return of the treated cells to the patient. Clinical trials of somatic cell gene therapy began in the late 1990s, mostly for the treatment of cancers and blood, liver, and lung disorders.
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trial patients have suffered adverse consequences of the treatment itself, including deaths. In some cases, the adverse effects result from disruption of essential genes within the patient's genome by insertional inactivation. In others, viral vectors used for gene therapy have been contaminated with infectious virus. Nevertheless, gene therapy is still held to be a promising future area of medicine, and is an area where there is a significant level of research and development activity.
587:, an enzyme whose activity results in formation of a blue-colored colony on the culture medium that is used for this work. Insertion of the foreign DNA into the beta-galactosidase coding sequence disables the function of the enzyme so that colonies containing transformed DNA remain colorless (white). Therefore, experimentalists are easily able to identify and conduct further studies on transgenic bacterial clones, while ignoring those that do not contain recombinant DNA. 1932: 90:). This process takes advantage of the fact that a single bacterial cell can be induced to take up and replicate a single recombinant DNA molecule. This single cell can then be expanded exponentially to generate a large number of bacteria, each of which contains copies of the original recombinant molecule. Thus, both the resulting bacterial population, and the recombinant DNA molecule, are commonly referred to as "clones". Strictly speaking, 31: 594:. Libraries may be highly complex (as when cloning complete genomic DNA from an organism) or relatively simple (as when moving a previously cloned DNA fragment into a different plasmid), but it is almost always necessary to examine a number of different clones to be sure that the desired DNA construct is obtained. This may be accomplished through a very wide range of experimental methods, including the use of 1796: 405: 359: 245: 643:, and how that expression is related to other processes in biology, including the metabolic environment, extracellular signals, development, learning, senescence and cell death. Cloned genes can also provide tools to examine the biological function and importance of individual genes, by allowing investigators to 123:, enzymes that could cleave DNA molecules only when specific DNA sequences were encountered. They showed that restriction enzymes cleaved chromosome-length DNA molecules at specific locations, and that specific sections of the larger molecule could be purified by size fractionation. Using a second enzyme, 558:. Cells harboring the plasmid will survive when exposed to the antibiotic, while those that have failed to take up plasmid sequences will die. When mammalian cells (e.g. human or mouse cells) are used, a similar strategy is used, except that the marker gene (in this case typically encoded as part of the 131:. By recombining DNA segments of interest with vector DNA, such as bacteriophage or plasmids, which naturally replicate inside bacteria, large quantities of purified recombinant DNA molecules could be produced in bacterial cultures. The first recombinant DNA molecules were generated and studied in 1972. 663:
Obtaining the molecular clone of a gene can lead to the development of organisms that produce the protein product of the cloned genes, termed a recombinant protein. In practice, it is frequently more difficult to develop an organism that produces an active form of the recombinant protein in desirable
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Whichever method is used, the introduction of recombinant DNA into the chosen host organism is usually a low efficiency process; that is, only a small fraction of the cells will actually take up DNA. Experimental scientists deal with this issue through a step of artificial genetic selection, in which
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Notably, the growing capacity and fidelity of DNA synthesis platforms allows for increasingly intricate designs in molecular engineering. These projects may include very long strands of novel DNA sequence and/or test entire libraries simultaneously, as opposed to of individual sequences. These shifts
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Before actual cloning experiments are performed in the lab, most cloning experiments are planned in a computer, using specialized software. Although the detailed planning of the cloning can be done in any text editor, together with online utilities for e.g. PCR primer design, dedicated software exist
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Molecular cloning has led directly to the elucidation of the complete DNA sequence of the genomes of a very large number of species and to an exploration of genetic diversity within individual species, work that has been done mostly by determining the DNA sequence of large numbers of randomly cloned
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In standard molecular cloning experiments, the cloning of any DNA fragment essentially involves seven steps: (1) Choice of host organism and cloning vector, (2) Preparation of vector DNA, (3) Preparation of DNA to be cloned, (4) Creation of recombinant DNA, (5) Introduction of recombinant DNA into
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Virtually any DNA sequence can be cloned and amplified, but there are some factors that might limit the success of the process. Examples of the DNA sequences that are difficult to clone are inverted repeats, origins of replication, centromeres and telomeres. There is also a lower chance of success
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Despite a great deal of publicity and promises, the history of human gene therapy has been characterized by relatively limited success. The effect of introducing a gene into cells often promotes only partial and/or transient relief from the symptoms of the disease being treated. Some gene therapy
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Gene therapy involves supplying a functional gene to cells lacking that function, with the aim of correcting a genetic disorder or acquired disease. Gene therapy can be broadly divided into two categories. The first is alteration of germ cells, that is, sperm or eggs, which results in a permanent
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The DNA mixture, previously manipulated in vitro, is moved back into a living cell, referred to as the host organism. The methods used to get DNA into cells are varied, and the name applied to this step in the molecular cloning process will often depend upon the experimental method that is chosen
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refers to the fact that the method involves the replication of one molecule to produce a population of cells with identical DNA molecules. Molecular cloning generally uses DNA sequences from two different organisms: the species that is the source of the DNA to be cloned, and the species that will
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Prior to the 1970s, the understanding of genetics and molecular biology was severely hampered by an inability to isolate and study individual genes from complex organisms. This changed dramatically with the advent of molecular cloning methods. Microbiologists, seeking to understand the molecular
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Molecular cloning provides scientists with an essentially unlimited quantity of any individual DNA segments derived from any genome. This material can be used for a wide range of purposes, including those in both basic and applied biological science. A few of the more important applications are
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involves the packaging of DNA into virus-derived particles, and using these virus-like particles to introduce the encapsulated DNA into the cell through a process resembling viral infection. Although electroporation and transduction are highly specialized methods, they may be the most efficient
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DNA ligase only recognizes and acts on the ends of linear DNA molecules, usually resulting in a complex mixture of DNA molecules with randomly joined ends. The desired products (vector DNA covalently linked to foreign DNA) will be present, but other sequences (e.g. foreign DNA linked to itself,
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and plasmid vectors are in common use because they are technically sophisticated, versatile, widely available, and offer rapid growth of recombinant organisms with minimal equipment. If the DNA to be cloned is exceptionally large (hundreds of thousands to millions of base pairs), then a
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is chosen that contains appropriate signals for transcription and translation in the desired host organism. Alternatively, if replication of the DNA in different species is desired (for example, transfer of DNA from bacteria to plants), then a multiple host range vector (also termed
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The cloning vector is treated with a restriction endonuclease to cleave the DNA at the site where foreign DNA will be inserted. The restriction enzyme is chosen to generate a configuration at the cleavage site that is compatible with the ends of the foreign DNA (see
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and this restriction enzyme was isolated from E.coli. Most modern vectors contain a variety of convenient cleavage sites that are unique within the vector molecule (so that the vector can only be cleaved at a single site) and are located within a gene (frequently
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Molecular cloning is similar to PCR in that it permits the replication of DNA sequence. The fundamental difference between the two methods is that molecular cloning involves replication of the DNA in a living microorganism, while PCR replicates DNA in an
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to distinguish colonies (clones) of transgenic cells from those that contain the parental vector (i.e. vector DNA with no recombinant sequence inserted). In these vectors, foreign DNA is inserted into a sequence that encodes an essential part of
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In a conventional molecular cloning experiment, the DNA to be cloned is obtained from an organism of interest, then treated with enzymes in the test tube to generate smaller DNA fragments. Subsequently, these fragments are then combined with
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vector DNA linked to itself and higher-order combinations of vector and foreign DNA) are also usually present. This complex mixture is sorted out in subsequent steps of the cloning process, after the DNA mixture is introduced into cells.
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The creation of recombinant DNA is in many ways the simplest step of the molecular cloning process. DNA prepared from the vector and foreign source are simply mixed together at appropriate concentrations and exposed to an enzyme
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The overall goal of molecular cloning is to take a gene of interest from one plasmid and insert it into another plasmid. This is done by performing PCR, digestive reaction, ligation reaction, and transformation.
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quantities than it is to clone the gene. This is because the molecular signals for gene expression are complex and variable, and because protein folding, stability and transport can be very challenging.
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The purified DNA is then treated with a restriction enzyme to generate fragments with ends capable of being linked to those of the vector. If necessary, short double-stranded segments of DNA (
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cells that have not taken up DNA are selectively killed, and only those cells that can actively replicate DNA containing the selectable marker gene encoded by the vector are able to survive.
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Although a very large number of host organisms and molecular cloning vectors are in use, the great majority of molecular cloning experiments begin with a laboratory strain of the bacterium
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bacteria). This will generate a population of organisms in which recombinant DNA molecules are replicated along with the host DNA. Because they contain foreign DNA fragments, these are
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Specialized applications may call for specialized host-vector systems. For example, if the experimentalists wish to harvest a particular protein from the recombinant organism, then an
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is fundamentally the same in all living organisms. Therefore, if any segment of DNA from any organism is inserted into a DNA segment containing the molecular sequences required for
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Whatever combination of host and vector are used, the vector almost always contains four DNA segments that are critically important to its function and experimental utility:
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Once characterized and manipulated to provide signals for appropriate expression, cloned genes may be inserted into organisms, generating transgenic organisms, also termed
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and that these foreign sequences would be carried into bacteria and digested as part of the plasmid. That is, these plasmids could serve as cloning vectors to carry genes.
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introduce complexity that require design to move away from the flat nucleotide-based representation and towards a higher level of abstraction. Examples of such tools are
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Wirth R, Friesenegger A, Fiedler S (Mar 1989). "Transformation of various species of gram-negative bacteria belonging to 11 different genera by electroporation".
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is introduced into the organism from which the replication sequences were obtained, then the foreign DNA will be replicated along with the host cell's DNA in the
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to generate recombinant DNA molecules. The recombinant DNA is then introduced into a host organism (typically an easy-to-grow, benign, laboratory strain of
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For cloning of genomic DNA, the DNA to be cloned is extracted from the organism of interest. Virtually any tissue source can be used (even tissues from
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host organism, (6) Selection of organisms containing recombinant DNA, (7) Screening for clones with desired DNA inserts and biological properties.
433: 383:). Typically, this is done by cleaving the vector DNA and foreign DNA with the same restriction enzyme or restriction endonuclease, for example 1602:"Universal hepatitis B vaccination in Taiwan and the incidence of hepatocellular carcinoma in children. Taiwan Childhood Hepatoma Study Group" 711:), a number of GMOs have been developed for commercial use, ranging from animals and plants that produce pharmaceuticals or other compounds ( 68:
for replication of the recombinant DNA. Molecular cloning methods are central to many contemporary areas of modern biology and medicine.
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Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC (1984). "DNA sequences from the quagga, an extinct member of the horse family".
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enzyme that builds the DNA chain. The mix goes through cycles of heating and cooling to produce large quantities of copied DNA.
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refers to the experimental methods used to assemble them. The idea arose that different DNA sequences could be inserted into a
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uses high voltage electrical pulses to translocate DNA across the cell membrane (and cell wall, if present). In contrast,
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when inserting large-sized DNA sequences. Inserts larger than 10kbp have very limited success, but bacteriophages such as
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When microorganisms are able to take up and replicate DNA from their local environment, the process is termed
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Nathans D, Smith HO (1975). "Restriction endonucleases in the analysis and restructuring of dna molecules".
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is necessary for the vector (and its linked recombinant sequences) to replicate inside the host organism
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The total population of individual clones obtained in a molecular cloning experiment is often termed a
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Boominathan A, Vanhoozer S, Basisty N, Powers K, Crampton AL, Wang X, et al. (November 2016).
1902: 530: 497: 1065: 416:(the building blocks of DNA), primers (short pieces of complementary single stranded DNA) and a 268: 253: 1642: 1210: 515:, and cells that are in a physiological state such that they can take up DNA are said to be 451:(for example, from the mitochondria to the nucleus) or simply for increasing expression via 1806: 1246: 1102: 1019: 960: 516: 393: 569: 8: 1854: 712: 692: 687:), (2) proteins that can be administered to assist in a life-threatening emergency (e.g. 347:
gene that can be used to enable the survival of cells that have taken up vector sequences
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DNA for cloning experiments may also be obtained from RNA using reverse transcriptase (
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provide a means to screen for genes on the basis of the expressed protein's function.
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mechanisms through which bacteria restricted the growth of bacteriophage, isolated
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Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (Sep 1992).
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Proceedings of the National Academy of Sciences of the United States of America
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Proceedings of the National Academy of Sciences of the United States of America
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Proceedings of the National Academy of Sciences of the United States of America
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Molecular cloning takes advantage of the fact that the chemical structure of
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Lewandowski C, Barsan W (Feb 2001). "Treatment of acute ischemic stroke".
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At the level of individual genes, molecular clones are used to generate
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Molecular Biotechnology: Principles and Applications of Recombinant DNA
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the genes, or make more subtle mutations using regional mutagenesis or
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Screening for clones with desired DNA inserts and biological properties
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gene that can be used to screen for cells containing the foreign DNA
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Pfeifer A, Verma IM (2001). "Gene therapy: promises and problems".
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fragments of the genome, and assembling the overlapping sequences.
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for the purpose. Software for the purpose include for example ApE
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The MJ (Nov 1989). "Human insulin: DNA technology's first drug".
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can be modified to successfully insert a sequence up to 40 kbp.
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and later derivatives including the pGEM vectors) use the
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Diagram of molecular cloning using bacteria and plasmids
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Cohen SN, Chang AC, Boyer HW, Helling RB (Nov 1973).
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When bacterial cells are used as host organisms, the
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to serve as sites where foreign DNA may be introduced
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or cDNA cloning), or in the form of synthetic DNA (
1477: 1209: 758:Recombinant DNA: genes and genomes: a short course 538:Selection of organisms containing vector sequences 487:Introduction of recombinant DNA into host organism 399: 1553: 1190: 1005: 850:(Fifth ed.). Brooks/Cole, Cengage Learning. 1950: 1066:"plasmid / plasmids | Learn Science at Scitable" 799: 774: 746: 667:Many useful proteins are currently available as 550:is usually a gene that confers resistance to an 408:DNA for cloning is most commonly produced using 205:, etc., that is, all the steps described below. 1666: 1664: 1588: 1207: 562:cassette) confers resistance to the antibiotic 554:that would otherwise kill the cells, typically 193:(commercial). These programs allow to simulate 1480:"Haemophilia care then, now and in the future" 1147: 878: 845: 823:Gene cloning and DNA analysis: an introduction 1822: 1647:. Vol. 40. Academic Press. p. 508. 1673:Annual Review of Genomics and Human Genetics 1670: 1661: 1547: 1471: 1336: 1330: 911: 373: 248:Diagram of a commonly used cloning plasmid; 1582: 1520: 1428: 1379: 1230: 1082: 651:. Genes cloned into expression vectors for 466:Creation of recombinant DNA with DNA ligase 1829: 1815: 1006:Jackson DA, Symons RH, Berg P (Oct 1972). 639:that are used for examining how genes are 362:Cleavage of a DNA sequence containing the 338:restriction endonuclease recognition sites 240:Choice of host organism and cloning vector 233:(free for academia) or GeneticConstructor 1728: 1710: 1617: 1495: 1478:Oldenburg J, Dolan G, Lemm G (Jan 2009). 1411: 1385: 1362: 1313: 1173: 1124: 1114: 1041: 1031: 982: 972: 905: 781:Patten CL, Glick BR, Pasternak J (2009). 1913:Restriction fragment length polymorphism 436:) sequences prior to molecular cloning. 403: 357: 243: 212: 86:or genetically modified microorganisms ( 29: 1148:Pingoud A, Jeltsch A (September 2001). 698: 627:Genome organization and gene expression 574:Modern bacterial cloning vectors (e.g. 14: 1951: 1640: 1212:Molecular cloning: a laboratory manual 755: 259:are present, conferring resistance to 1810: 1529:American Journal of Hospital Pharmacy 820: 1337:Plotkin JB, Kudla G (January 2011). 41:is a set of experimental methods in 1606:The New England Journal of Medicine 1526: 926:10.1146/annurev.bi.44.070175.001421 27:Set of methods in molecular biology 24: 1703: 659:Production of recombinant proteins 25: 1980: 1759: 719:, and fluorescent tropical fish ( 1931: 1930: 1794: 1497:10.1111/j.1365-2516.2008.01946.x 1437:Molecular & General Genetics 825:. Cambridge, MA: Blackwell Pub. 534:methods to move DNA into cells. 165:solution, free of living cells. 1634: 1281: 1208:Russell DW, Sambrook J (2001). 1141: 879:Garrett RH, Grisham CM (2010). 846:Garrett RH, Grisham CM (2013). 785:. Washington, D.C.: ASM Press. 760:. San Francisco: W.H. Freeman. 726: 717:herbicide-resistant crop plants 617: 400:Preparation of DNA to be cloned 300:bacterial artificial chromosome 94:refers to DNA molecules, while 1711:Matsumura I (September 2015). 1058: 999: 940: 872: 839: 705:genetically modified organisms 683:, used to treat some forms of 49:molecules and to direct their 13: 1: 1685:10.1146/annurev.genom.2.1.177 914:Annual Review of Biochemistry 739: 608:restriction fragment analysis 412:. Template DNA is mixed with 183:(open source), Serial Cloner 1969:Molecular biology techniques 1785:Resources in other libraries 1556:Annals of Emergency Medicine 689:tissue plasminogen activator 7: 1619:10.1056/NEJM199706263362602 596:nucleic acid hybridizations 580:blue-white screening system 322:into a specialized vector. 304:yeast artificial chromosome 134: 10: 1985: 1404:10.1093/genetics/136.2.423 723:) for home entertainment. 180:(open source), DNAStrider 113: 45:that are used to assemble 18:Recombinant DNA technology 1926: 1893: 1880:Site-directed mutagenesis 1845: 1780:Resources in your library 649:site-directed mutagenesis 604:polymerase chain reaction 445:artificial gene synthesis 430:Polymerase chain reaction 374:Preparation of vector DNA 345:selectable genetic marker 121:restriction endonucleases 1386:Lederberg J (Feb 1994). 1343:Nature Reviews. Genetics 306:vector is often chosen. 208: 1568:10.1067/mem.2001.111573 1116:10.1073/pnas.89.18.8794 1033:10.1073/pnas.69.10.2904 974:10.1073/pnas.70.11.3240 172:cloning and simulations 1840:: key methods of study 1294:Nucleic Acids Research 1166:10.1093/nar/29.18.3705 1154:Nucleic Acids Research 421: 370: 291:plasmid cloning vector 276: 271:that the host uses to 236:(free for academics). 218: 57:. The use of the word 35: 1535:(11 Suppl 2): S9-11. 407: 361: 269:origin of replication 254:antibiotic resistance 247: 216: 33: 1803:at Wikimedia Commons 699:Transgenic organisms 669:recombinant products 394:alkaline phosphatase 186:(gratis), Collagene 147:, and the resulting 64:serve as the living 1959:Genetics techniques 1855:Gel electrophoresis 1251:1984Natur.312..282H 1107:1992PNAS...89.8794S 1024:1972PNAS...69.2904J 965:1973PNAS...70.3240C 693:hepatitis B vaccine 336:one or more unique 199:restriction digests 189:(open source), and 1964:Molecular genetics 1875:Restriction digest 1838:Molecular genetics 1641:August JT (1997). 1449:10.1007/BF00332248 1306:10.1093/nar/gkw756 756:Watson JD (2007). 679:, and recombinant 653:functional cloning 585:beta-galactosidase 453:codon optimization 422: 390:beta-galactosidase 371: 331:replication origin 277: 219: 36: 1946: 1945: 1860:Molecular cloning 1801:Molecular cloning 1799:Media related to 1771:Molecular cloning 1766:Library resources 1730:10.2144/000114324 1654:978-0-08-058132-3 1300:(19): 9342–9357. 1245:(5991): 282–284. 1223:978-0-87969-576-7 1160:(18): 3705–3727. 890:978-0-495-10935-8 857:978-1-133-10629-6 832:978-1-4051-1121-8 792:978-1-55581-498-4 767:978-0-7167-2866-5 623:summarized here. 548:selectable marker 441:complementary DNA 311:expression vector 96:molecular cloning 43:molecular biology 39:Molecular cloning 16:(Redirected from 1976: 1934: 1933: 1870:Promoter bashing 1831: 1824: 1817: 1808: 1807: 1798: 1754: 1752: 1750: 1741:. 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Index

Recombinant DNA technology

molecular biology
recombinant DNA
replication
host organisms
cloning
host
vector DNA
E. coli
transgenic
GMOs
plasmid
bacteriophage λ
restriction endonucleases
DNA ligase
recombinant DNA
DNA
DNA replication
recombinant DNA
transgenic
in vitro




SnapGene
PCR reactions
restriction digests
ligations

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