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PBR322

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A schematic representation of the pBR322 vector with restriction sites indicated in blue.
A schematic representation of the pBR322 vector with restriction sites indicated in blue.

pBR322 is a plasmid and was one of the first widely used E. coli cloning vectors. Created in 1977 in the laboratory of Herbert Boyer at the University of California, San Francisco, it was named after Francisco Bolivar Zapata, the postdoctoral researcher and Raymond L. Rodriguez. The p stands for "plasmid," and BR for "Bolivar" and "Rodriguez."

pBR322 is 4361 base pairs in length[1] and has two antibiotic resistance genes – the gene bla encoding the ampicillin resistance (AmpR) protein, and the gene tetA encoding the tetracycline resistance (TetR) protein. It contains the origin of replication of pMB1, and the rop gene, which encodes a restrictor of plasmid copy number. The plasmid has unique restriction sites for more than forty restriction enzymes. Eleven of these forty sites lie within the TetR gene. There are two sites for restriction enzymes HindIII and ClaI within the promoter of the TetR gene. There are six key restriction sites inside the AmpR gene.The source of these antibiotic resistance genes are from pSC101 for Tetracycline and RSF2124 for Ampicillin.[2]

The circular sequence is numbered such that 0 is the middle of the unique EcoRI site and the count increases through the TetR gene. If we have to remove ampicillin for instance, we must use restriction endonuclease or molecular scissors against PstI and then pBR322 will become anti-resistant to ampicillin .The same process of Insertional Inactivation can be applied to Tetracycline. The AmpR gene is penicillin beta-lactamase. Promoters P1 and P3 are for the beta-lactamase gene. P3 is the natural promoter, and P1 is artificially created by the ligation of two different DNA fragments to create pBR322. P2 is in the same region as P1, but it is on the opposite strand and initiates transcription in the direction of the tetracycline resistance gene.[3]

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Plasmid

Plasmid

A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; however, plasmids are sometimes present in archaea and eukaryotic organisms. In nature, plasmids often carry genes that benefit the survival of the organism and confer selective advantage such as antibiotic resistance. While chromosomes are large and contain all the essential genetic information for living under normal conditions, plasmids are usually very small and contain only additional genes that may be useful in certain situations or conditions. Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation. Synthetic plasmids are available for procurement over the internet.

Cloning

Cloning

Cloning is the process of producing individual organisms with identical or virtually identical DNA, either by natural or artificial means. In nature, some organisms produce clones through asexual reproduction. In the field of biotechnology, cloning is the process of creating cloned organisms (copies) of cells and of DNA fragments.

Herbert Boyer

Herbert Boyer

Herbert Wayne "Herb" Boyer is an American biotechnologist, researcher and entrepreneur in biotechnology. Along with Stanley N. Cohen and Paul Berg he discovered a method to coax bacteria into producing foreign proteins, thereby jump-starting the field of genetic engineering. By 1969, he performed studies on a couple of restriction enzymes of the E.coli bacterium with especially useful properties. He is recipient of the 1990 National Medal of Science, co-recipient of the 1996 Lemelson–MIT Prize, and a co-founder of Genentech. He was professor at the University of California, San Francisco (UCSF) and later served as vice president of Genentech from 1976 until his retirement in 1991.

Gene

Gene

In biology, the word gene can have several different meanings. The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes.

Beta-lactamase

Beta-lactamase

Beta-lactamases, (β-lactamases) are enzymes produced by bacteria that provide multi-resistance to beta-lactam antibiotics such as penicillins, cephalosporins, cephamycins, monobactams and carbapenems (ertapenem), although carbapenems are relatively resistant to beta-lactamase. Beta-lactamase provides antibiotic resistance by breaking the antibiotics' structure. These antibiotics all have a common element in their molecular structure: a four-atom ring known as a beta-lactam (β-lactam) ring. Through hydrolysis, the enzyme lactamase breaks the β-lactam ring open, deactivating the molecule's antibacterial properties.

Ampicillin

Ampicillin

Ampicillin is an antibiotic used to prevent and treat a number of bacterial infections, such as respiratory tract infections, urinary tract infections, meningitis, salmonellosis, and endocarditis. It may also be used to prevent group B streptococcal infection in newborns. It is used by mouth, by injection into a muscle, or intravenously. Common side effects include rash, nausea, and diarrhea. It should not be used in people who are allergic to penicillin. Serious side effects may include Clostridium difficile colitis or anaphylaxis. While usable in those with kidney problems, the dose may need to be decreased. Its use during pregnancy and breastfeeding appears to be generally safe.

Origin of replication

Origin of replication

The origin of replication is a particular sequence in a genome at which replication is initiated. Propagation of the genetic material between generations requires timely and accurate duplication of DNA by semiconservative replication prior to cell division to ensure each daughter cell receives the full complement of chromosomes. This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses. Synthesis of daughter strands starts at discrete sites, termed replication origins, and proceeds in a bidirectional manner until all genomic DNA is replicated. Despite the fundamental nature of these events, organisms have evolved surprisingly divergent strategies that control replication onset. Although the specific replication origin organization structure and recognition varies from species to species, some common characteristics are shared.

HindIII

HindIII

HindIII (pronounced "Hin D Three") is a type II site-specific deoxyribonuclease restriction enzyme isolated from Haemophilus influenzae that cleaves the DNA palindromic sequence AAGCTT in the presence of the cofactor Mg2+ via hydrolysis.

Promoter (genetics)

Promoter (genetics)

In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA), or can have a function in and of itself, such as tRNA or rRNA. Promoters are located near the transcription start sites of genes, upstream on the DNA . Promoters can be about 100–1000 base pairs long, the sequence of which is highly dependent on the gene and product of transcription, type or class of RNA polymerase recruited to the site, and species of organism.

EcoRI

EcoRI

EcoRI is a restriction endonuclease enzyme isolated from species E. coli. It is a restriction enzyme that cleaves DNA double helices into fragments at specific sites, and is also a part of the restriction modification system. The Eco part of the enzyme's name originates from the species from which it was isolated - "E" denotes generic name which is "Escherichia" and "co" denotes species name, "coli" - while the R represents the particular strain, in this case RY13, and the I denotes that it was the first enzyme isolated from this strain.

Penicillin

Penicillin

Penicillins are a group of β-lactam antibiotics originally obtained from Penicillium moulds, principally P. chrysogenum and P. rubens. Most penicillins in clinical use are synthesised by P. chrysogenum using deep tank fermentation and then purified. A number of natural penicillins have been discovered, but only two purified compounds are in clinical use: penicillin G and penicillin V. Penicillins were among the first medications to be effective against many bacterial infections caused by staphylococci and streptococci. They are still widely used today for different bacterial infections, though many types of bacteria have developed resistance following extensive use.

DNA ligase

DNA ligase

DNA ligase is a type of enzyme that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms may specifically repair double-strand breaks. Single-strand breaks are repaired by DNA ligase using the complementary strand of the double helix as a template, with DNA ligase creating the final phosphodiester bond to fully repair the DNA.

Background

Early cloning experiments may be conducted using natural plasmids such the ColE1 and pSC101. Each of these plasmids may have its advantages and disadvantages. For example, the ColE1 plasmid and its derivatives have the advantage of higher copy number and allow for chloramphenicol amplification of plasmid to produce a high yield of plasmid, however screening for immunity to colicin E1 is not technically simple.[4] The plasmid pSC101, a natural plasmid from Salmonella panama,[5] confers tetracycline resistance which allows for simpler screening process with antibiotic selection, but it is a low copy number plasmid which does not give a high yield of plasmid. Another plasmid, RSF 2124, which is a derivative of ColE1, confers ampicillin resistance but is larger.

Many other plasmids were artificially constructed to create one that would be ideal for cloning purpose, and pBR322 was found to be most versatile by many and was therefore the one most popularly used.[4] It has two antibiotic resistance genes, as selectable markers, and a number of convenient unique restriction sites that made it suitable as a cloning vector. The plasmid was constructed with genetic material from 3 main sources – the tetracycline resistance gene of pSC101, the ampicillin resistance gene of RSF 2124, and the replication elements of pMB1, a close relative of the ColE1 plasmid.[6][7]

A large number of other plasmids based on pBR322 have since been constructed specifically designed for a wide variety of purposes.[8][9] Examples include the pUC series of plasmids.[10] Most expression vectors for extrachromosomal protein expression and shuttle vectors contain the pBR322 origin of replication, and fragments of pBR322 are very popular in the construction of intraspecies shuttle or binary vectors and vectors for targeted integration and excision of DNA from chromosome.[11]

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ColE1

ColE1

ColE1 is a plasmid found in bacteria. Its name derives from the fact that it carries a gene for colicin E1. It also codes for immunity from this product with the imm gene. In addition, the plasmid has a series of mobility (mob) genes. Its size and the presence of a single EcoRI recognition site caused it to be considered as a vector candidate.

PSC101

PSC101

pSC101 is a DNA plasmid that is used as a cloning vector in genetic cloning experiments. pSC101 was the first cloning vector, used in 1973 by Herbert Boyer and Stanley Norman Cohen. Using this plasmid they have demonstrated that a gene from a frog could be transferred into bacterial cells and then expressed by the bacterial cells. The plasmid is a natural plasmid from Salmonella typhimurium.

Chloramphenicol

Chloramphenicol

Chloramphenicol is an antibiotic useful for the treatment of a number of bacterial infections. This includes use as an eye ointment to treat conjunctivitis. By mouth or by injection into a vein, it is used to treat meningitis, plague, cholera, and typhoid fever. Its use by mouth or by injection is only recommended when safer antibiotics cannot be used. Monitoring both blood levels of the medication and blood cell levels every two days is recommended during treatment.

Colicin

Colicin

A colicin is a type of bacteriocin produced by and toxic to some strains of Escherichia coli. Colicins are released into the environment to reduce competition from other bacterial strains. Colicins bind to outer membrane receptors, using them to translocate to the cytoplasm or cytoplasmic membrane, where they exert their cytotoxic effect, including depolarisation of the cytoplasmic membrane, DNase activity, RNase activity, or inhibition of murein synthesis.

Tetracycline

Tetracycline

Tetracycline, sold under various brand names, is an oral antibiotic in the tetracyclines family of medications, used to treat a number of infections, including acne, cholera, brucellosis, plague, malaria, and syphilis.

Cloning vector

Cloning vector

A cloning vector is a small piece of DNA that can be stably maintained in an organism, and into which a foreign DNA fragment can be inserted for cloning purposes. The cloning vector may be DNA taken from a virus, the cell of a higher organism, or it may be the plasmid of a bacterium. The vector contains features that allow for the convenient insertion of a DNA fragment into the vector or its removal from the vector, for example through the presence of restriction sites. The vector and the foreign DNA may be treated with a restriction enzyme that cuts the DNA, and DNA fragments thus generated contain either blunt ends or overhangs known as sticky ends, and vector DNA and foreign DNA with compatible ends can then be joined by molecular ligation. After a DNA fragment has been cloned into a cloning vector, it may be further subcloned into another vector designed for more specific use.

Origin of replication

Origin of replication

The origin of replication is a particular sequence in a genome at which replication is initiated. Propagation of the genetic material between generations requires timely and accurate duplication of DNA by semiconservative replication prior to cell division to ensure each daughter cell receives the full complement of chromosomes. This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses. Synthesis of daughter strands starts at discrete sites, termed replication origins, and proceeds in a bidirectional manner until all genomic DNA is replicated. Despite the fundamental nature of these events, organisms have evolved surprisingly divergent strategies that control replication onset. Although the specific replication origin organization structure and recognition varies from species to species, some common characteristics are shared.

PUC19

PUC19

pUC19 is one of a series of plasmid cloning vectors created by Joachim Messing and co-workers. The designation "pUC" is derived from the classical "p" prefix and the abbreviation for the University of California, where early work on the plasmid series had been conducted. It is a circular double stranded DNA and has 2686 base pairs. pUC19 is one of the most widely used vector molecules as the recombinants, or the cells into which foreign DNA has been introduced, can be easily distinguished from the non-recombinants based on color differences of colonies on growth media. pUC18 is similar to pUC19, but the MCS region is reversed.

Expression vector

Expression vector

An expression vector, otherwise known as an expression construct, is usually a plasmid or virus designed for gene expression in cells. The vector is used to introduce a specific gene into a target cell, and can commandeer the cell's mechanism for protein synthesis to produce the protein encoded by the gene. Expression vectors are the basic tools in biotechnology for the production of proteins.

Shuttle vector

Shuttle vector

A shuttle vector is a vector constructed so that it can propagate in two different host species. Therefore, DNA inserted into a shuttle vector can be tested or manipulated in two different cell types. The main advantage of these vectors is they can be manipulated in E. coli, then used in a system which is more difficult or slower to use.

DNA sequence

The sequence in pBR322 is[3]

pBR322
       1 ttctcatgtt tgacagctta tcatcgataa gctttaatgc ggtagtttat cacagttaaa
      61 ttgctaacgc agtcaggcac cgtgtatgaa atctaacaat gcgctcatcg tcatcctcgg
     121 caccgtcacc ctggatgctg taggcatagg cttggttatg ccggtactgc cgggcctctt
     181 gcgggatatc gtccattccg acagcatcgc cagtcactat ggcgtgctgc tagcgctata
     241 tgcgttgatg caatttctat gcgcacccgt tctcggagca ctgtccgacc gctttggccg
     301 ccgcccagtc ctgctcgctt cgctacttgg agccactatc gactacgcga tcatggcgac
     361 cacacccgtc ctgtggatcc tctacgccgg acgcatcgtg gccggcatca ccggcgccac
     421 aggtgcggtt gctggcgcct atatcgccga catcaccgat ggggaagatc gggctcgcca
     481 cttcgggctc atgagcgctt gtttcggcgt gggtatggtg gcaggccccg tggccggggg
     541 actgttgggc gccatctcct tgcatgcacc attccttgcg gcggcggtgc tcaacggcct
     601 caacctacta ctgggctgct tcctaatgca ggagtcgcat aagggagagc gtcgaccgat
     661 gcccttgaga gccttcaacc cagtcagctc cttccggtgg gcgcggggca tgactatcgt
     721 cgccgcactt atgactgtct tctttatcat gcaactcgta ggacaggtgc cggcagcgct
     781 ctgggtcatt ttcggcgagg accgctttcg ctggagcgcg acgatgatcg gcctgtcgct
     841 tgcggtattc ggaatcttgc acgccctcgc tcaagccttc gtcactggtc ccgccaccaa
     901 acgtttcggc gagaagcagg ccattatcgc cggcatggcg gccgacgcgc tgggctacgt
     961 cttgctggcg ttcgcgacgc gaggctggat ggccttcccc attatgattc ttctcgcttc
    1021 cggcggcatc gggatgcccg cgttgcaggc catgctgtcc aggcaggtag atgacgacca
    1081 tcagggacag cttcaaggat cgctcgcggc tcttaccagc ctaacttcga tcactggacc
    1141 gctgatcgtc acggcgattt atgccgcctc ggcgagcaca tggaacgggt tggcatggat
    1201 tgtaggcgcc gccctatacc ttgtctgcct ccccgcgttg cgtcgcggtg catggagccg
    1261 ggccacctcg acctgaatgg aagccggcgg cacctcgcta acggattcac cactccaaga
    1321 attggagcca atcaattctt gcggagaact gtgaatgcgc aaaccaaccc ttggcagaac
    1381 atatccatcg cgtccgccat ctccagcagc cgcacgcggc gcatctcggg cagcgttggg
    1441 tcctggccac gggtgcgcat gatcgtgctc ctgtcgttga ggacccggct aggctggcgg
    1501 ggttgcctta ctggttagca gaatgaatca ccgatacgcg agcgaacgtg aagcgactgc
    1561 tgctgcaaaa cgtctgcgac ctgagcaaca acatgaatgg tcttcggttt ccgtgtttcg
    1621 taaagtctgg aaacgcggaa gtcagcgccc tgcaccatta tgttccggat ctgcatcgca
    1681 ggatgctgct ggctaccctg tggaacacct acatctgtat taacgaagcg ctggcattga
    1741 ccctgagtga tttttctctg gtcccgccgc atccataccg ccagttgttt accctcacaa
    1801 cgttccagta accgggcatg ttcatcatca gtaacccgta tcgtgagcat cctctctcgt
    1861 ttcatcggta tcattacccc catgaacaga aatccccctt acacggaggc atcagtgacc
    1921 aaacaggaaa aaaccgccct taacatggcc cgctttatca gaagccagac attaacgctt
    1981 ctggagaaac tcaacgagct ggacgcggat gaacaggcag acatctgtga atcgcttcac
    2041 gaccacgctg atgagcttta ccgcagctgc ctcgcgcgtt tcggtgatga cggtgaaaac
    2101 ctctgacaca tgcagctccc ggagacggtc acagcttgtc tgtaagcgga tgccgggagc
    2161 agacaagccc gtcagggcgc gtcagcgggt gttggcgggt gtcggggcgc agccatgacc
    2221 cagtcacgta gcgatagcgg agtgtatact ggcttaacta tgcggcatca gagcagattg
    2281 tactgagagt gcaccatatg cggtgtgaaa taccgcacag atgcgtaagg agaaaatacc
    2341 gcatcaggcg ctcttccgct tcctcgctca ctgactcgct gcgctcggtc gttcggctgc
    2401 ggcgagcggt atcagctcac tcaaaggcgg taatacggtt atccacagaa tcaggggata
    2461 acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc caggaaccgt aaaaaggccg
    2521 cgttgctggc gtttttccat aggctccgcc cccctgacga gcatcacaaa aatcgacgct
    2581 caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt ccccctggaa
    2641 gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg tccgcctttc
    2701 tcccttcggg aagcgtggcg ctttctcata gctcacgctg taggtatctc agttcggtgt
    2761 aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg
    2821 ccttatccgg taactatcgt cttgagtcca acccggtaag acacgactta tcgccactgg
    2881 cagcagccac tggtaacagg attagcagag cgaggtatgt aggcggtgct acagagttct
    2941 tgaagtggtg gcctaactac ggctacacta gaaggacagt atttggtatc tgcgctctgc
    3001 tgaagccagt taccttcgga aaaagagttg gtagctcttg atccggcaaa caaaccaccg
    3061 ctggtagcgg tggttttttt gtttgcaagc agcagattac gcgcagaaaa aaaggatctc
    3121 aagaagatcc tttgatcttt tctacggggt ctgacgctca gtggaacgaa aactcacgtt
    3181 aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac ctagatcctt ttaaattaaa
    3241 aatgaagttt taaatcaatc taaagtatat atgagtaaac ttggtctgac agttaccaat
    3301 gcttaatcag tgaggcacct atctcagcga tctgtctatt tcgttcatcc atagttgcct
    3361 gactccccgt cgtgtagata actacgatac gggagggctt accatctggc cccagtgctg
    3421 caatgatacc gcgagaccca cgctcaccgg ctccagattt atcagcaata aaccagccag
    3481 ccggaagggc cgagcgcaga agtggtcctg caactttatc cgcctccatc cagtctatta
    3541 attgttgccg ggaagctaga gtaagtagtt cgccagttaa tagtttgcgc aacgttgttg
    3601 ccattgctgc aggcatcgtg gtgtcacgct cgtcgtttgg tatggcttca ttcagctccg
    3661 gttcccaacg atcaaggcga gttacatgat cccccatgtt gtgcaaaaaa gcggttagct
    3721 ccttcggtcc tccgatcgtt gtcagaagta agttggccgc agtgttatca ctcatggtta
    3781 tggcagcact gcataattct cttactgtca tgccatccgt aagatgcttt tctgtgactg
    3841 gtgagtactc aaccaagtca ttctgagaat agtgtatgcg gcgaccgagt tgctcttgcc
    3901 cggcgtcaac acgggataat accgcgccac atagcagaac tttaaaagtg ctcatcattg
    3961 gaaaacgttc ttcggggcga aaactctcaa ggatcttacc gctgttgaga tccagttcga
    4021 tgtaacccac tcgtgcaccc aactgatctt cagcatcttt tactttcacc agcgtttctg
    4081 ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg aataagggcg acacggaaat
    4141 gttgaatact catactcttc ctttttcaat attattgaag catttatcag ggttattgtc
    4201 tcatgagcgg atacatattt gaatgtattt agaaaaataa acaaataggg gttccgcgca
    4261 catttccccg aaaagtgcca cctgacgtct aagaaaccat tattatcatg acattaacct
    4321 ataaaaatag gcgtatcacg aggccctttc gtcttcaaga a

Source: "PBR322", Wikipedia, Wikimedia Foundation, (2023, March 7th), https://en.wikipedia.org/wiki/PBR322.

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References
  1. ^ Watson, N. (1988). "A new revision of the sequence of plasmid pBR322". Gene. 70 (2): 399–403. doi:10.1016/0378-1119(88)90212-0. PMID 3063608.
  2. ^ Balbás P, Soberón X, Merino E, Zurita M, Lomeli H, Valle F, Flores N, Bolivar F (1986). "Plasmid vector pBR322 and its special-purpose derivatives--a review". Gene. 50 (1–3): 3–40. doi:10.1016/0378-1119(86)90307-0. PMID 3034735.
  3. ^ a b "pBR322 Nucleotide Sequences, NCBI Sequence Viewer v2.0".
  4. ^ a b R.W. Old & S.B. Primrose. Principles of Gene Manipulation (5th ed.). pp. 53–61.
  5. ^ Manen D, Caro L (February 1991). "The replication of plasmid pSC101". Mol. Microbiol. 5 (2): 233–7. doi:10.1111/j.1365-2958.1991.tb02103.x. PMID 2041467.
  6. ^ Bolivar F, Rodriguez RL, Betlach MC, Boyer HW (1977). "Construction and characterization of new cloning vehicles. I. Ampicillin-resistant derivatives of the plasmid pMB9". Gene. 2 (2): 75–93. doi:10.1016/0378-1119(77)90074-9. PMID 344136.
  7. ^ Bolivar F, Rodriguez RL, Greene PJ, Betlach MC, Heyneker HL, Boyer HW, Crosa JH, Falkow S (1977). "Construction and characterization of new cloning vehicles. II. A multipurpose cloning system". Gene. 2 (2): 95–113. doi:10.1016/0378-1119(77)90000-2. PMID 344137.
  8. ^ S.B. Primrose & R.M Twyman (17 January 2006). Principles of Gene Manipulation and Genomics (PDF) (7th ed.). Wiley-Blackwell. pp. 64–65. ISBN 978-1405135443.
  9. ^ Balbás P, Soberón X, Merino E, Zurita M, Lomeli H, Valle F, Flores N, Bolivar F (1986). "Plasmid vector pBR322 and its special-purpose derivatives--a review". Gene. 50 (1–3): 3–40. doi:10.1016/0378-1119(86)90307-0. PMID 3034735.
  10. ^ Yanisch-Perron C, Vieira J, Messing J (1985). "Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors". Gene. 33 (1): 103–19. doi:10.1016/0378-1119(85)90120-9. PMID 2985470.
  11. ^ Paulina Balbás; Argelia Lorence, eds. (April 2004). Recombinant Gene Expression: Reviews and Protocols (2nd ed.). Humana Press Inc. pp. 77–85. ISBN 978-1592597741.

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