Molecular Biology: Expression Vectors Quiz
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Questions and Answers

What is the primary disadvantage of plasmid vectors?

  • Inability to express genes in eukaryotic hosts
  • Limited carrying capacity for large DNA fragments (correct)
  • Difficulty in isolating and purifying recombinant plasmids
  • High rates of mutation during replication
  • The presence of multiple selective markers in a plasmid vector is beneficial for gene cloning.

    True (A)

    What is the purpose of using a regulatable promoter in an expression vector?

    To control the expression of the cloned gene, allowing for the production of protein only when desired.

    The use of ______ allows for the production of fusion proteins, enhancing protein stability and detection.

    <p>expression vectors</p> Signup and view all the answers

    Which of the following is NOT a common feature of expression vectors designed for bacterial expression?

    <p>Integration into the host chromosome for stable inheritance (B)</p> Signup and view all the answers

    Uncontrolled expression of a cloned gene can significantly hinder the growth of the host cell.

    <p>True (A)</p> Signup and view all the answers

    Match the following terms with their associated descriptions:

    <p>IPTG = Inducer molecule for T7 RNA polymerase pET vectors = Expression vectors based on the T7 expression system T7 RNA polymerase = A highly efficient RNA polymerase Fusion proteins = Proteins that combine two protein fragments for various purposes PolyHis tag = A peptide sequence used for protein purification using affinity chromatography lac promoter = Inducible promoter in bacteria that is activated by lactose or IPTG</p> Signup and view all the answers

    What is the primary function of T7 RNA polymerase in the pET expression system?

    <p>To efficiently transcribe cloned genes into mRNA for protein synthesis.</p> Signup and view all the answers

    The process of removing salt from a solution by precipitation with isopropanol is called _____.

    <p>post elution</p> Signup and view all the answers

    Which of the following is NOT a desirable property of an ideal cloning vector?

    <p>Resistance to all known antibiotics (C)</p> Signup and view all the answers

    Selectable markers in plasmids allow for easy identification of cells that have not taken up the plasmid.

    <p>False (B)</p> Signup and view all the answers

    What is the purpose of a multiple cloning site (MCS) in a plasmid?

    <p>The MCS contains a series of restriction enzyme recognition sites, allowing for the insertion of foreign DNA at a precise location within the plasmid.</p> Signup and view all the answers

    Match the following properties to their corresponding descriptions:

    <p>Small Size = Facilitates efficient entry into host cells and replication Selectable Markers = Allows for the selection of cells that have taken up the plasmid Unique Restriction Sites = Enable directional cloning and precise insertion of foreign DNA</p> Signup and view all the answers

    The process of inserting foreign DNA into a plasmid in a specific orientation is called _____.

    <p>directional cloning</p> Signup and view all the answers

    PBR322 DNA is a plasmid cloning vector commonly used in E. coli.

    <p>True (A)</p> Signup and view all the answers

    Explain how antibiotic resistance genes serve as selectable markers in plasmid cloning.

    <p>Antibiotic resistance genes allow researchers to identify bacteria that have successfully taken up the plasmid containing the gene. Only bacteria with the plasmid will be able to grow in the presence of the specific antibiotic, thus selecting for transformed cells.</p> Signup and view all the answers

    What is a common method for purifying proteins using specialized vectors?

    <p>All of the above (D)</p> Signup and view all the answers

    Specialized vectors such as pET can increase the level of transcription of the cloned gene and make its transcription subject to specific regulation.

    <p>True (A)</p> Signup and view all the answers

    What is the main purpose of a shuttle vector?

    <p>To transfer cloned DNA between unrelated organisms.</p> Signup and view all the answers

    The ______ tag is a commonly used affinity tag for protein purification, consisting of six consecutive histidine residues.

    <p>His</p> Signup and view all the answers

    Match the specialized vector type with its description:

    <p>Shuttle vector = Can replicate in two different organisms. Expression vector = Designed for efficient protein expression. pMAL vector = Uses MBP fusion protein for purification.</p> Signup and view all the answers

    Which of the following is NOT a characteristic of vectors designed for protein recovery?

    <p>They always result in cytoplasmic expression of the protein (B)</p> Signup and view all the answers

    Vectors designed for protein recovery always require the use of a protease for cleavage of the fusion protein.

    <p>False (B)</p> Signup and view all the answers

    What is the function of a Shine-Dalgarno sequence in expression vectors?

    <p>It guides the ribosome to the start codon for efficient translation.</p> Signup and view all the answers

    What antibiotic resistance gene is present in the pBC KS+ shuttle vector?

    <p>Chloramphenicol (B)</p> Signup and view all the answers

    The pBC KS+ vector replicates in both prokaryotic and eukaryotic cells.

    <p>True (A)</p> Signup and view all the answers

    What is the function of the f1 origin in the pBC KS+ vector?

    <p>The f1 origin allows for single-stranded DNA production.</p> Signup and view all the answers

    The ______ provides a convenient site for inserting foreign DNA into the pBC KS+ vector.

    <p>multiple cloning site (MCS)</p> Signup and view all the answers

    Match the following features of the pBC KS+ vector to their respective functions:

    <p>pUC origin = High copy number replication CAM resistance gene = Selection of transformed bacteria T7/T3 promoters = Production of strand-specific probes lacZ' gene = Blue/white screening for inserts</p> Signup and view all the answers

    Which of the following restriction enzymes are located within the multiple cloning site (MCS) of the pBC KS+ vector?

    <p>All of the above (D)</p> Signup and view all the answers

    The pBC KS+ vector can be used for the production of recombinant proteins.

    <p>True (A)</p> Signup and view all the answers

    What is the purpose of the blue/white screening technique?

    <p>The blue/white screening technique helps identify bacterial colonies that contain the vector with an insert.</p> Signup and view all the answers

    The pBC KS+ vector has a high copy number, meaning that it replicates ______ times in a bacterial cell.

    <p>multiple</p> Signup and view all the answers

    Which of these is NOT a feature of the pBC KS+ vector?

    <p>Ampicillin resistance gene (A)</p> Signup and view all the answers

    What is a common purpose of blue-white screening?

    <p>To identify bacteria containing recombinant plasmids (C)</p> Signup and view all the answers

    The IPTG-inducible vectors can be used to control the expression of target genes.

    <p>True (A)</p> Signup and view all the answers

    What two genes does a typical plasmid carry?

    <p>ampR and lacZ</p> Signup and view all the answers

    During gene cloning, bacterial cells take up recombinant plasmids by _______.

    <p>transformation</p> Signup and view all the answers

    Match the following vectors with their associated companies:

    <p>pGEM series = Promega pGEX series = Pharmacia pKK223-3 = Pharmacia pMAL = New England Biolabs</p> Signup and view all the answers

    Which step involves the use of DNA ligase?

    <p>Insertion of DNA into the vector (C)</p> Signup and view all the answers

    LacZ gene allows bacteria to hydrolyze lactose.

    <p>False (B)</p> Signup and view all the answers

    What method can be used to identify cell clones containing the desired gene?

    <p>Nucleic acid hybridization</p> Signup and view all the answers

    What is the primary role of ethidium bromide (EtBr) in density gradient centrifugation?

    <p>To bind to DNA (C)</p> Signup and view all the answers

    Covalent circles have a lower density than linear DNA when both are saturated with EtBr.

    <p>False (B)</p> Signup and view all the answers

    What pH range is used in the alkaline lysis method to denature DNA?

    <p>12.0-12.5</p> Signup and view all the answers

    The alkaline lysis method involves four basic steps, the first being to resuspend harvested bacterial cells in __________ buffer containing RNase A.

    <p>Tris·Cl–EDTA</p> Signup and view all the answers

    Match the following steps of the alkaline lysis method with their descriptions:

    <ol> <li>Lyse cells = A. Neutralizes the lysate and causes precipitation of contaminants</li> <li>Neutralize lysate = B. Releases the cell contents and denatures DNA</li> <li>Clear the lysate = C. Removes insoluble debris through centrifugation or filtration</li> <li>Resuspend cells = D. Prepares samples for lysis in appropriate buffer</li> </ol> Signup and view all the answers

    Which of the following statements about the binding of DNA to a solid support matrix is true?

    <p>Silica supports binding in the presence of chaotropic salts (A)</p> Signup and view all the answers

    In the alkaline lysis method, potassium dodecyl sulfate (KDS) is used to precipitate plasmid DNA.

    <p>False (B)</p> Signup and view all the answers

    What is the purpose of adding acidic potassium acetate in the alkaline lysis method?

    <p>To neutralize the lysate</p> Signup and view all the answers

    Flashcards

    CCC DNA

    Covalently closed circular DNA, like plasmid DNA, has no free ends.

    Linear DNA

    DNA with free ends, such as fragmented chromosomal DNA, allows more binding of EtBr.

    Ethidium bromide (EtBr)

    A dye that binds to DNA; more binding occurs in linear DNA than CCC DNA.

    Alkaline Lysis Method

    Popular technique for isolating plasmid DNA, using NaOH at pH 12.0-12.5.

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    Step 1 of Alkaline Lysis

    Resuspend bacterial cells in Tris·Cl-EDTA buffer containing RNase A.

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    Step 2 of Alkaline Lysis

    Lyse cells using NaOH/SDS to release cell contents and denature DNA.

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    Binding Plasmid to Solid Support

    Conditions allowing DNA to bind include low salt or chaotropic salts.

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    Elution Process

    Separating plasmids from solid support using high salt buffer or water.

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    α-complementation

    A method for identifying recombinant bacteria using color change in the presence of X-gal.

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    Gene cloning steps

    A process involving five main steps to clone a gene into a plasmid.

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    Vector isolation

    The first step in cloning where the vector and gene-source DNA are collected.

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    Restriction enzyme

    An enzyme that cuts DNA at specific recognition sequences.

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    Transformation

    The process by which bacteria take up recombinant plasmids.

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    Blue-white screening

    A technique to differentiate between recombinant and non-recombinant bacteria based on colony color.

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    Nucleic acid hybridization

    A method to identify desired genes using complementary probes.

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    Recombinant DNA

    DNA formed by combining genes from different sources.

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    Denaturation of DNA

    The process of separating the DNA strands in a plasmid.

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    Plasmid Vector Limitations

    Plasmid vectors can carry up to 10 kb of inserted DNA only.

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    Lambda Phage Vectors

    Genetically modified lambda phage used for larger DNA fragments.

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    Criteria of Expression Vectors

    Essential features for plasmid vectors to express genes effectively.

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    Multicopy Plasmids

    Plasmids that can exist in many copies to enhance gene dosage.

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    Active Expression Control

    Expression is regulated with specific promoter constructs to optimize growth.

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    Fusion Proteins

    Proteins created from joining two or more genes to increase stability and ease of detection.

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    Expression Phase in Culture

    The phase where expression of the gene is induced after cell growth.

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    Post Elution

    Process of removing salt from plasmid using isopropanol.

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    Ideal Cloning Vector

    A cloning vector should be small, selectable, and have unique sites.

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    Selectable Markers

    Genes that allow identification of transformed cells, usually antibiotic resistance.

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    Common Selectable Markers

    Common markers include genes for resistance to ampicillin, tetracycline, chloramphenicol, and kanamycin.

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    pBR322

    A widely used plasmid cloning vector in E. coli with a medium copy number.

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    Multiple Cloning Site (MCS)

    A region with consensus sequences for various restriction enzymes for DNA insertion.

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    Directional Cloning

    Inserting DNA in a specific orientation using two different restriction enzymes.

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    Screening of Recombinants

    The process of identifying bacteria with the recombinant plasmid containing the DNA of interest.

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    Binding Assays

    Experimental methods used to study binding interactions, such as protein-ligand or protein-protein binding.

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    Antibody Screening

    A process used to identify and select specific antibodies from a pool, which can bind to particular antigens.

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    Export Signals

    Sequences in proteins that direct their transport to specific cellular locations, such as the periplasm or outside the cell.

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    Maltose Binding Protein (MBP)

    A protein used in affinity purification linked to maltose, allowing recovery of fusion proteins.

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    His6 Tag

    A sequence of six histidine residues added to proteins, allowing them to bind metal for purification.

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    Expression Vectors

    Plasmids designed to increase expression of cloned genes in host organisms, aiding protein production.

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    Shuttle Vectors

    Vectors that can replicate in two different organisms, allowing gene transfer between species.

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    Trc Promoter

    A strong hybrid promoter used in certain vectors to drive high levels of gene expression.

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    pUC ori

    Origin of replication that allows high copy number.

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    Chloramphenicol Resistance

    Gene that provides resistance to the antibiotic chloramphenicol.

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    Polylinker

    A short segment of DNA containing multiple restriction sites.

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    Blue/White Screen

    A method to identify recombinant bacteria based on color.

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    ssDNA Production

    Single-stranded DNA production through f1 origin.

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    T7/T3 Promoters

    Sequences that initiate transcription for making probes.

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    Lac Z’

    A gene segment used for blue/white screening in cloning.

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    Study Notes

    Cloning in E. coli - SSCG 2713 - Genetic Engineering (+Lab)

    • Course: Genetic Engineering (+Lab)
    • Course code: SSCG 2713
    • Academic year: 2023/2024-1
    • Instructor: Nurriza Ab Latif (PhD)
    • Institution: Universiti Teknologi Malaysia

    Brain Teaser

    • (No information provided regarding the topic)

    Illustrate the General Steps in Gene Cloning

    • (No information provided regarding the topic)

    Molecular Cloning

    •  Foreign DNA and plasmid are cut with the same restriction enzyme.
    • Restriction enzyme leaves sticky ends on foreign DNA fragment and plasmid.
    • Foreign DNA inserted into plasmid when sticky ends anneal.
    • DNA ligase reattaches DNA backbones, resulting in recombinant plasmids.
    • Plasmids combined with living bacteria.
    • Bacteria may or may not take up plasmids.
    • Bacteria with recombinant plasmids cannot make enzyme (enzyme lacZ the fragment was inserted into).
    • Bacteria also carry a gene for resistance to ampicillin.
    • Bacteria grown on plate with ampicillin and substance altering color with the enzyme lacZ.
    • Ampicillin kills bacteria without plasmid.
    • Color change indicates bacteria with recombinant plasmid.

    What do you know about plasmid?

    • Plasmids are DNA molecules found in bacteria, separate from the bacterial chromosome.
    • They are also referred to as vectors or constructs.
    • (Note: Plasmids also exist naturally in archaea and eukaryotes like yeast and plants.)

    Characteristics of Plasmids

    • Small, typically a few thousand base pairs (bp), and widely distributed in prokaryotes.
    • Consist of a circular double-stranded DNA molecule.
    • Have a single origin of replication.
    • Do not change in size (constant monomeric unit size).
    • Stably inherited in extra-chromosomal state.
    • Self-replicating, able to replicate independently of the chromosome.
    • Often encode genes for proteins (enzymes) protecting the bacterium from one or more antibiotics.

    Plasmids: Independent Genetic Elements

    • Independent genetic elements found in bacterial cells.
    • (Diagram shows the bacterial chromosome and plasmids as separate circular structures within the bacterial cell)

    Phenotypic Traits of Plasmid-carried Genes

    • Antibiotic resistance
    • Antibiotic production
    • Degradation of aromatic compounds
    • Bacteriocin production
    • Induction of plant tumours
    • Haemolysin production
    • Enterotoxin production
    • Heavy metal resistance
    • Hydrogen sulphide production
    • Sugar fermentation
    • Host-controlled restriction and modification

    The Common Features of Plasmids

    • Vector element: DNA Sequence initiating replication within a plasmid by recruiting transcriptional machinery proteins.
    • Origin of Replication (ORI): Allows selection of plasmid-containing bacteria
    • Antibiotic Resistance Gene: Allows selection of plasmid-containing bacteria
    • Multiple Cloning Site (MCS): Short segment of DNA with several restriction sites enabling easy insertion of DNA into expression plasmids.
    • Promoter Region: Drives transcription of desired gene. Crucial component for expression vectors, determining cell types expressed.
    • Selectable Marker: Indicates antibiotic resistance genes which allow selection within bacteria. Many plasmids have selectable markers for other cell types.
    • Primer Binding Site: Short single-stranded DNA for initiation of PCR amplification or sequencing.

    Plasmid Map

    • (Diagram showing the location of selectable marker, antibiotic resistance gene, promoter, 5' and 3' primer site, restriction site, and origin of replication within a circular plasmid)

    Categories of Plasmids

    • Multiple copies/cell: Characterized by multiple copies (relaxed plasmids) of 50+ copies per cell. A useful cloning vector needs to be present in multiple copies for large recombinant DNA molecule production.
    • Low copies/cell: This type is also referred to as stringent plasmid, with only one or two copies present per cell.
    • Conjugative: Contains tra genes enabling bacterial conjugation (plasmid transfer) & generally high molecular weight, present as 2-3 copies (low copy number) per chromosome.
    • Non-conjugative: Does not contain tra genes, thus incapable of initiating conjugation, and are usually high-copy number plasmids

    Example of Conjugation and Mobilization

    • Conjugative plasmids carry an origin of transfer (oriT) and encode a relaxase (nes) and coupling protein.
    • Mobilizable plasmids may carry an oriT recognized by the relaxase of the conjugative plasmid.
    • They may encode their own relaxase/oriT pair.
    • They might utilize the mating pore of the conjugative plasmid.

    Plasmids as Cloning Vectors

    • Plasmids modified to contain a limited number of restriction sites and selectable marker genes detecting plasmid presence in the host cell.

    pBR322 DNA

    • Commonly used plasmid cloning vector in E. coli.
    • Copy number - Usually medium (10-100)

    Cloning Sites

    • Regions of DNA containing consensus sequence for restriction enzymes (REs).
    • Called Multiple Cloning Sites (MCS) or polylinker.
    • REs cutting within MCS do not cut elsewhere in the vector.
    • Facilitates target DNA insertion to a specific vector part.

    Directional Cloning

    • Insertion of foreign DNA into a specific orientation.
    • Achieved by making two cleavages with separate restriction enzymes (REs).

    Screening of Recombinants

    • Recombinant plasmid is transformed into bacteria.
    • Plasmids replicate and copy within bacteria.
    • Bacterial cells are plated on a media containing appropriate antibiotic, IPTG, and X-gal.

    Recombinant Selection with pBR322

    • Insertional inactivation of an antibiotic resistance gene

    Cloning into pBR322

    • (Diagram showing the procedure for cloning into the BamHI site (insertional inactivation), including steps like DNA digestion, ligation, transformation, and selection)

    Insertional Inactivation in pBR322

    • (Diagram illustrating the steps involved in the selection of recombinant cells involving insertional inactivation with pBR322. Details on how to distinguish recombinant cells from plasmids with inserts.)

    Recombinant Selection with pUC8

    • (Summary of the process for the selection of recombinants using insertional inactivation of the lacZ gene associated with the pUC8 plasmid)

    Most modern plasmid vectors

    • Employ a different system. 
    • Example pUC8 carries ampicillin resistance gene and lacZ gene (codes for part of enzyme b-galactosidase).

    Cloning with pUC8

    • Insertional inactivation of lacZ gene.
    • Identification of recombinants via their inability to synthesize b-galactosidase, or blue-white screening. 

    When induced by IPTG

    • The b-galactosidase (lacZ) gene is transcribed.
    • The enzyme uses X-gal as a substrate.
    • Cleaved X-gal yields a blue pigment.

    pUC18 – a Lac selection plasmid

    • Developed by Joe Messing (Waksman Institute, Rutgers University, USA).
    • Small plasmid (2686 bp).
    • Allows relatively large DNA inserts.
    • Replicates 500+ copies per cell.

    Identification of recombinants

    • A single step process.
    • Plating onto agar media containing ampicillin plus X-gal.

    Cloning using pUC18/19

    • (Illustration of the steps cloning procedure using pUC18/19, including steps like digestion, isolation, and annealing of DNA. )

    Plasmid DNA Purification

    • Preparation of plasmid DNA from bacteria follows the steps used to purify total cell DNA.
    • Plasmid DNA and bacterial differ in size and conformation.
    • One key step is host cell lysis.
    • Efficiency of lysis depends on the quality of cell lysate.
    • Cells must be broken sufficiently for plasmid extraction.
    • Chromosomal contamination must be avoided.
    • Gentle lysis is needed.

    One traditional plasmid purification technique

    • Using caesium chloride (CsCl)/ethidium bromide (EtBr) centrifugation.
    • Purified lysates isopycnic centrifuged in CsCI solution containing EtBr.
    • EtBr binds between DNA base pairs, causing DNA unwinding.

    Isopycnic centrifugation

    • Technique used to separate molecules on basis of density.
    • Particle density must be greater than particles to be separated.
    • Particles will not sediment to the tube bottom.

    Ethidium bromide-caesium chloride density gradient centrifugation

    • CCC DNA molecules (e.g. plasmid) have no free ends.
    • They can only unwind to a limited extent. This limits EtBr binding.
    • Linear DNA molecules (e.g. fragmented chromosomal DNA) have no such topological constraints & can bind more EtBr molecules.
    • More EtBr bound, the higher the density of DNA-EtBr complex decreases.
    • Covalent circles (plasmids) are separable from linear chromosomal DNA since more EtBr bind to linear molecules.

    Alkaline Lysis Method

    • Most popular plasmid DNA purification method.
    • Uses NaOH (12.0-12.5 pH range) to denature linear DNA.
    • Does not affect CCC DNA (plasmids).
    • Production of alkaline lysates involves four basic steps:
    • Resuspend harvested bacterial cells in Tris-Cl-EDTA buffer with RNase A.
    • Lyse cells with NaOH/SDS to solubilize phospholipids & proteins.
    • Denature chromosomal/plasmid DNA. RNase A digests released RNA.
    • Neutralize the lysate by adding acidic potassium acetate.
    • Clear lysate by centrifugation/filtration.

    Purification by Binding Plasmid to a Solid Support Matrix

    • Conditions to allow binding must exist in the lysate.
    • Examples of DNA-binding supports: Ion Exchange Resin (low salt) , Diatomaceous Earth (chaotropic salts), Silica (chaotropic salts).
    • Chaotrope denatures proteins (e.g. Guanidine HCI).
    • Wash away impurities with ethanol-based solutions.
    • Dry the support.

    Elution

    • Ion Exchange: high salt buffer
    • Diatomaceous Earth/Silica: water/low salt buffer
    • Post-elution: salt removal by precipitation with isopropanol/ plasmid concentration.

    Plasmid as Cloning Vector

    • Small (low molecular weight), allowing carrying large DNA.
    • Selection: ability to confer easily selectable phenotypic traits in host cells.
    • Unique site for multiple restriction enzymes with readily scorable phenotype

    Why need antibiotic resistance?

    • Allows selection of cells containing recombinant plasmid.
    • Recombinant plasmid carries gene for antibiotic resistance.
    • Allows selection of cells containing recombinant vector and not others.

    Selectable Markers

    • Necessary for easy identification of transformed cells.
    • Common markers are antibiotic resistance genes (ampicillin [amp], tetracyclin [tet], chloramphenicol [cam], kanamycin [kan]).

    Virtually all plasmids

    • Carry resistance to one or more antibiotics.
    • Plasmid produces protein that destroys the antibiotic.
    • Makes all bacteria that carry the plasmid immune to the antibiotic.

    Cloning Sites: Restriction Enzymes

    • Restriction enzymes recognize specific DNA sequences and cut at these sequences. 
    • Restriction enzymes with sites recognized by the MCS will not cut anywhere else in the vector.
    • These sites allow target DNA to be inserted into specific locations.

    Directional Cloning

    • Inserts DNA into plasmid in a particular orientation using two unique sites and restriction enzymes.

    Screening of Recombinants – Selection with Antibiotic Media

    • Bacteria plated on media containing the appropriate antibiotic.
    • Only transformed bacteria survive due having plasmid and antibiotic resistance.

    Screening by pBR322 Inactivation

    • Insertional inactivation of antibiotic resistance genes.
    • Recombinant plasmids can be easily distinguished from non-recombinant.
    • Selection for antibiotic-resistant cells followed by examination for sensitivity/resistance to antibiotic of interest. 

    Recombinant Selection with pUC8

    • Insertional inactivation of the lacZ gene.
    • Screening via a blue-white screening method.
    • Colonies of recombinant plasmids are white.
    • Transformants without insert are blue.

    Cloning Vectors in pUC18/19

    • lac selection system, usually blue/white screening system that detects the presence of recombinant colonies.
    • (illustration of the process of using the blue/white screening method for detection of recombinants or vectors with insertions)

    IPTG-Inducible Vectors (e.g., PGEM, pGEX, pKK223-3, PMEX, pTrc99A, pMAL)

    • Specialized vectors.
    • Increase transcription level of cloned genes.
    • Transcription regulated by specific promoter systems.
    • Include signals to enhance translation efficiency

    Expression Vectors and Shuttle Vectors

    • Developed for prokaryotic and eukaryotic hosts, facilitating efficient expression of cloned genes in specific host.
    • Include signals to enhance translation efficiency

    Shuttle Vector: pYES2

    • Cloning vector that stably replicates in two unrelated organisms (e.g. bacterium and yeast).

    Shuttle Vector: pSE420

    • Developed by Invitrogen.
    • Strong hybrid promoter upstream of lac operator and lambda promoter.
    • Effective mRNA translation due to Shine-Dalgarno sequence.

    Shuttle Vector: pBC KS+

    • Contains pUC ori, high copy number, resistance to CAM (chloramphenicol), polylinker, blue/white screening for insertions (lacZ), and T7/T3 promoters to create DNA strand-specific probes.

    Transformation of bacterial cells

    • Techniques for transformation: uptake of DNA from the environment into bacterial cells.
    • E. coli not naturally transformable, and physical and/or chemical treatment is required.
    • Chemically treated cells for transformation are chemically competent.
    • Chemical competent cells: salt treatment followed by a heat shock step.

    Transformation Methods: Chemical Competency (CaCl2)

    • Perturbing the cell membrane using chaotropic agents/chemicals.
    • A small proportion of cells becomes competent to take up DNA.

    Principles of CaCl2 Transformation

    • Thawing cells on crushed ice.
    • Adding DNA.
    • Incubating on ice.
    • Raising the temperature to 37°C with shaking.
    • Adding SOC media.
    • Placing on ice for two minutes.
    • Heat shock at 42°C.

    Transformation Methods: Electroporation

    • Exposing bacterial cells to high intensity electric pulses.
    • Disrupting the cell membrane to make it permeable to exogenous molecules.
    • Good alternative for bacteria failing to transform using chaotropic agents.

    Electroporation (in vitro)

    • Combining target cells in a conductive solution with molecules to be introduced into cells.
    • Placing in a cuvette with metal electrodes.
    • Delivering an electrical pulse.

    Considerations before Bacterial Electroporation

    •  Healthy culture: mid-exponential growth cells that actively divide.
    • Cells free of salts: remove them with ice-cold 0.5 M sucrose solution.
    • Keeping things cold: keep everything cold. 
    • Carefully pipette cells.
    • Dry cuvette before use.

    Outcome of Uncontrolled Expression

    • Expression commonly negatively affects the growth of host cells, making the process hazardous.
    • Usually needs tightly regulated promoters.
    • Expression divided into two phases: cell growth & expression phase.

    Common Expression Machinery

    • (Diagram showcasing the components involved in expression machinery, like the promoter region, ribosome binding site (RBS), the coding sequence, fusion protein, multiple cloning site (MCS), and termination region.)

    Fusion Proteins

    • Increased protein stability.
    • Easy detection using spectrophotometry, binding assays, and antibody screening.
    • Containing export signals for protein transportation into periplasm or outside the cell.

    Vectors for Construction of Fusion Proteins - List

    • List of vectors (with their fusion partners and comments on their roles.)

    Allow affinity purification – List

    • Lists of Fusion Partners and corresponding Affinity Ligands

    Engineered protease site allows to remove fusion partner

    • (Diagram illustrating an engineered protease site within a fusion protein, facilitating the removal of the fusion partner for purification.)

    Vectors designed for protein recovery

    • Vectors designed for protein recovery: using Maltose Binding Protein and Amylose Column;
    • Cytoplasmic expression.
    • Protein recovery using amylose affinity column.
    • Fusion protein recovered using Factor Xa protease.

    Vectors designed for protein recovery:

    His Tags

    • Using His6 Tags-add six consecutive His residues to either end of protein-bind metals.
    • Metal chelate chromatography.

    Purification of recombinant fusion proteins (with intein) expressed in E. coli

    • (Detailed diagram illustrating the experimental protocol for purification of recombinant fusion proteins (with intein) expressed in E. coli that are produced from recombinant protein containing plasmids.)

    Specialized Vectors

    • Vectors designed for specific applications - protein expression, gene expression, cellular analysis.
    • Examples: expression vectors, shuttle vectors.

    Expression Vector

    • Expression vectors developed for prokaryotic/eukaryotic hosts.
    • Many cloned genes don't express efficiently in a new host.
    • pET is an example. It contains genes to increase transcription level, subject to specific regulation; includes signals for translation efficiency.

    Shuttle Vector: pYES2

    • A cloning vector that can stably replicate in two different organisms (e.g., a bacterium and yeast).
    • Allows for the transfer of cloned DNA between organisms.

    Shuttle Vector: pSE420

    • Developed by Invitrogen Corp
    • Contains polylinker, multiple cloning site (MCS)
    • trc promoter (trp+lac) - strong hybrid promoter upstream of lac O (operator) & lambda PL promoter
    • S/D Shine-Dalgarno sequence - on resulting mRNA for efficient translation; T1 and T2 – two transcriptional terminators- prevents transcription of the entire vector; lac I – lac repressor which regulates transcription. 

    Shuttle Vector: pBC KS+

    • pUC ori (high copy number), CAM (chloramphenicol) resistance, polylinker, blue/white screen for inserts (lac Z'), can produce ssDNA (f1 ori). T7/T3 promoters to create DNA strand-specific probes.

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    Test your knowledge on expression vectors in molecular biology. This quiz covers topics such as the advantages and disadvantages of plasmid vectors, the role of T7 RNA polymerase, and the features of ideal cloning vectors. Challenge yourself with questions on gene cloning and protein expression.

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