Protein-DNA Interaction Study Techniques Quiz
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Questions and Answers

What technique is used to study proteins binding to known DNA oligonucleotide probes and the affinity or specificity of the interaction?

  • Electrophoretic Mobility Shift Assay (EMSA) (correct)
  • DNAase footprinting
  • Reporter assays
  • Pull down assays

    • Which technique involves the addition of protein to DNA and then detection antibody to weigh the resulting complex?

  • Electrophoretic Mobility Shift Assay (EMSA) (correct)
  • Pull down assays
  • Reporter assays
  • DNAase footprinting

    • Which technique is specifically used to study the binding of proteins to known DNA oligonucleotide probes?

  • Reporter assays
  • Electrophoretic Mobility Shift Assay (EMSA) (correct)
  • CHIP
  • DNAase footprinting

    • Which technique involves the analysis of protein-DNA interactions by exploring the biological importance of these interactions?

    <p>DNAase footprinting</p> Signup and view all the answers

    Which technique is used to explore protein-DNA interactions by analyzing the biological importance of these interactions and understanding the basis of gene silencing using RNAi?

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

    What is the main difference between siRNA and shRNA?

    <p>siRNA is transient and short-lived, while shRNA allows for long-lasting gene knockdown</p> Signup and view all the answers

    What is the role of DICER in the RNA interference (RNAi) process?

    <p>DICER cleaves double-stranded RNA into small interfering RNAs (siRNAs)</p> Signup and view all the answers

    What is the primary function of RNA interference (RNAi) in cells?

    <p>Post-transcriptionally regulate gene expression at the mRNA level</p> Signup and view all the answers

    What did Andew Fire and Craig Mello win the 2006 Nobel prize of Medicine for?

    <p>The discovery of RNA interference (RNAi)</p> Signup and view all the answers

    What is the main difference between gene knockdown and gene knockout?

    <p>Gene knockdown reduces gene expression, while gene knockout completely eliminates gene function</p> Signup and view all the answers

    What is the role of short hairpin RNA (shRNA) in gene knockdown?

    <p>ShRNA allows for high potency and long-lasting gene knockdown</p> Signup and view all the answers

    What is the main function of the RNA-Induced Silencing Complex (RISC) in RNA interference (RNAi)?

    <p>RISC directs the sequence-specific silencing of the target mRNA molecule by siRNA</p> Signup and view all the answers

    What is the natural function of RNA interference (RNAi) in cells?

    <p>Protect themselves from invaders such as RNA viruses</p> Signup and view all the answers

    Which technique is used to detect protein-DNA interactions by observing the mobility shift of protein-DNA complexes in an agarose gel?

    <p>Electrophoretic Mobility Shift Assay (EMSA)</p> Signup and view all the answers

    Which technique can be used to examine the affinity and number of binding sites between a protein and a specific nucleotide sequence?

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

    Which technique is used to selectively extract protein-DNA complexes from a sample using a DNA probe labeled with biotin?

    <p>Biotinylated DNA pulldown assay</p> Signup and view all the answers

    Which technique is used to investigate genetic regulatory elements' impact on gene expression by monitoring the amount of the reporter protein expressed?

    <p>Reporter assays</p> Signup and view all the answers

    Which technique is an antibody-based technology used to selectively enrich specific DNA-binding proteins along with their DNA targets?

    <p>Chromatin immuno-precipitation (ChIP)</p> Signup and view all the answers

    Which technique can be used to examine the affinity and the number of binding sites between a protein (e.g., MBNL1) and a particular RNA sequence?

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

    Which technique involves the use of antibodies to selectively extract protein-DNA complexes from a sample using a DNA probe labeled with biotin?

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

    What is the primary function of RNA interference (RNAi) in cells?

    <p>Degrading specific mRNA molecules</p> Signup and view all the answers

    What did Andrew Fire and Craig Mello win the 2006 Nobel prize of Medicine for?

    <p>Identification of RNA interference (RNAi)</p> Signup and view all the answers

    What is the main difference between siRNA and shRNA?

    <p>siRNA is double-stranded, while shRNA is single-stranded</p> Signup and view all the answers

    What is the natural function of RNA interference (RNAi) in cells?

    <p>Regulating gene expression</p> Signup and view all the answers

    What is the main purpose of Fluorescence Assisted Cell Sorting (FACS) Flow cytometry?

    <p>To allow simultaneous multiparametric analysis of the physical and molecular characteristics of up to thousands of particles per second.</p> Signup and view all the answers

    What is the purpose of immunoprecipitation technique?

    <p>To purify an antigen present in a complex mixture.</p> Signup and view all the answers

    What is the role of secondary antibody in the immunoblotting technique?

    <p>To conjugate at the surface of bead for downstream analysis.</p> Signup and view all the answers

    What is the purpose of electrophoresis in the immunoblotting technique?

    <p>To migrate proteins on gel according to their size or chemical properties.</p> Signup and view all the answers

    What is the main function of the antibody in the immuno-precipitation technique?

    <p>To immunocapture specific protein from a mixture.</p> Signup and view all the answers

    In immunoassays, which form of ELISA is known for being more specific as the antigen has to bind to two antibodies to be detected?

    <p>Sandwich ELISA</p> Signup and view all the answers

    What is the main purpose of competitive ELISA?

    <p>To compete with the target protein for antibody binding</p> Signup and view all the answers

    What is essential for visualizing proteins in the cytoplasm, nucleus, or organelles using immuno-microscopy?

    <p>Permeabilization of cells</p> Signup and view all the answers

    What is the purpose of epitope mapping in antibody design and vaccine development?

    <p>To experimentally identify the binding sites of antibodies on their target antigen</p> Signup and view all the answers

    Which technique is a high-throughput approach to map epitopes by adding an antibody to an array of synthetic peptides from the antigen?

    <p>Overlapping peptide scan technique</p> Signup and view all the answers

    What is the primary difference between polyclonal and monoclonal antibodies?

    <p>Polyclonal antibodies are a population of antibodies binding different epitopes of the same antigen, while monoclonal antibodies bind a single epitope on the antigen.</p> Signup and view all the answers

    How are hybridomas obtained for producing monoclonal antibodies?

    <p>By fusing single lymphocytes from immunized mice with a single cancer cell.</p> Signup and view all the answers

    What is the primary function of enzyme immunosorbent assays (ELISA)?

    <p>Diagnosing infectious agents such as viruses and quantitatively measuring substances in blood like hormones, cytokines, and chemokines.</p> Signup and view all the answers

    Why are animals like rabbits, goats, and donkeys usually employed to produce polyclonal antibodies?

    <p>Due to their larger size, which allows for easier blood serum isolation and purification.</p> Signup and view all the answers

    What is the advantage of using monoclonal antibodies in therapy?

    <p>They are more specific and reproducible between batches.</p> Signup and view all the answers

    Study Notes

    Protein-DNA Interactions Techniques

    • Electrophoretic Mobility Shift Assay (EMSA) is used to detect protein-DNA interactions by observing the mobility shift of protein-DNA complexes in an agarose gel.
    • EMSA can be used to examine the affinity and number of binding sites between a protein and a specific nucleotide sequence.
    • DNAase footprinting is a technique that detects DNA-protein interactions by identifying DNA regions protected from enzymatic cleavage when bound to a protein.
    • Biotinylated DNA pulldown assay selectively extracts protein-DNA complexes from a sample using a DNA probe labeled with biotin.
    • Reporter assays, such as the luciferin/luciferase system, are used to investigate genetic regulatory elements' impact on gene expression by monitoring the amount of the reporter protein expressed.
    • Chromatin immuno-precipitation (ChIP) is an antibody-based technology used to selectively enrich specific DNA-binding proteins along with their DNA targets.
    • ChIP can be used to study a particular protein-DNA interaction, multiple protein-DNA interactions, or interactions across the entire genome.
    • In ChIP, DNA and associated proteins on chromatin in living cells or tissues are crosslinked to preserve DNA-protein interactions before shearing the DNA-protein complexes into fragments.
    • EMSA can be used to examine the affinity and the number of binding sites between a protein (e.g., MBNL1) and a particular RNA sequence.
    • DNAase footprinting detects DNA-protein interaction by identifying DNA regions protected from enzymatic cleavage when bound to a protein.
    • Biotinylated DNA pulldown assay selectively extracts protein-DNA complexes from a sample using a DNA probe labeled with biotin.
    • Reporter assays, such as the luciferin/luciferase system, are used to investigate genetic regulatory elements' impact on gene expression by monitoring the amount of the reporter protein expressed.

    Harnessing the Immune System for Antibody Production

    • Antibodies are produced in response to antigens and are naturally produced by B-lymphocytes in the body's adaptive immune system.
    • Antibodies are composed of two heavy chains and two light chains, with a variable region containing the specific antigen binding site and a constant region divided into five different classes.
    • The two major classes of antibodies used in immunochemistry are polyclonal and monoclonal antibodies, each with distinct characteristics and applications.
    • Polyclonal antibodies are a population of antibodies binding different epitopes of the same antigen, generated by different B cell clones and primarily used for research and diagnosis.
    • Polyclonal antibodies are produced in animals by injecting them with antigens, isolating and purifying the antibodies from the animal blood serum.
    • Monoclonal antibodies bind a single epitope on the antigen, are generated by a single B-cell clone called hybridoma, and are used in various fields including therapy due to their specificity and reproducibility.
    • Hybridomas are obtained by fusing single lymphocytes from immunized mice with a single cancer cell, and the clone producing the antibody with the best properties is selected and grown in large quantities.
    • Antibodies can be conjugated with various molecules to allow detection by colorimetric and fluorimetric methods, immuno selection, immuno precipitation, and immunoassays.
    • The vast majority of immunoassays, particularly enzyme immunosorbent assays (ELISA), are commonly used for diagnosing infectious agents such as viruses and quantitatively measuring substances in blood like hormones, cytokines, and chemokines in research and hospital settings.
    • Polyclonal antibodies are cheaper to produce but less specific and more variable from batch to batch, while monoclonal antibodies are more expensive to produce but have less batch to batch variation and are more specific.
    • Animals like rabbits, goats, and donkeys are usually employed to produce polyclonal antibodies due to their larger size, while mice and rats are not used as they are too small.
    • Monoclonal antibodies are used in therapy due to their specificity and reproducibility between batches, and they can be tested for reactivity to the antigen and grown in large quantities.

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    Related Documents

    Module 3 - Analysis of Protein-DNA Interactions PDF
    Immunochemical Techniques HSS 3109 PDF

    Description

    Test your knowledge of techniques used to study protein-DNA interactions with this quiz. Explore methods such as EMSA, DNAase footprinting, biotinylated DNA pulldown assay, reporter assays, and chromatin immuno-precipitation (ChIP).

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