Outline/Study Guide--Biotechnology Course objective: Students will be able to explain major methods and techniques used in molecular genetics to isolate, recombine, amplify, find and study genes of interest. Necessary for future material on: last five genetics labs. Helpful for Directed Studies and Internships in research labs. In genetic engineering and molecular characterization, what are the physical obstacles to overcome? What techniques are used to overcome these obstacles? Restriction Mapping • What is a restriction enzyme and why does it cut DNA at specific sites? (What is the enzyme’s natural function?) What are sticky ends? Why must two different pieces of DNA be cut with the same enzyme in order for them to be cloned together? • What is the function of electrophoresis and how does it separate molecules? • What is a restriction map? Could you determine a restriction map from a DNA fingerprint on an electrophoresis gel? Biotechnology, cont. Blotting and Probing • What is a Southern blot vs. a Northern blot? When would you use one vs. the other? • Why is hybridizing important? How does a probe “hybridize”? • What specific sequence must a single stranded probe have in order to identify the GOI? How can one make many copies of the Gene of Interest? What advantages and disadvantages exist in each? • How does PCR work? What specific sequence must a PCR primer have in order to amplify the right gene? • What is a vector and what properties must it have in order to be useful? Are all the vectors the same? • What is the Lac Z system for? How does it work? • What is a DNA library? Uses of molecular genetic research Basic research—understanding living organisms at the molecular level (e.g. fruit-fly lifecycle) Applied research—for solving specific biomedical problems (e.g. gene therapy for hemophilia or cystic fibrosis; better livestock or agriculture) Both involve use of recombinant DNA technology (genetic engineering) Obstacles in Molecular Genetics Goal: characterize the Gene of Interest (GOI) • “Macro-isolation” of Gene of Interest – Restriction Digest of DNA – Electrophoresis – DNA Library • “Micro-isolation” of Gene of Interest (GOI) – Southern Blot—Studying DNA (is a particular gene or sequence present in this genome?) – Hybridization (using complementarity to find the GOI on a Southern, Northern, or in PCR) – Sequencing • Amplification of GOI—need to make thousands of copies of one GOI in order to characterize it. – Using restriction sites to clone the GOI into a vector – PCR—Polymerase Chain Reaction • Understanding the GOI – Northern Blot—studying RNA (Which tissue expresses a particular RNA?) – Western Blot—studying protein (does this tissue express a specific protein?) – RT PCR – how much expression of the GOI is found in this tissue? ::::::: Restriction enzymes recognize specific sequences (restriction sites) and generate “sticky” or “blunt” ends ::::::: “sticky” ends (un-paired ss DNA) How DNA from different sources is put together (like Fig 19.1, Brooker) Example of restriction sites within a double-stranded DNA sequence nt position 1 1 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGC CTAGTGTCCAGATAGTGGGATAATTGGTGAGTGCCCTCGAGAGGTACGTAAACCATAAAAGCAGACCCCCCATACGTGCG BanII 80 80 81 81 GATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTA CTATCGTAACGCTCTGCGACCTCGGCCTCGTGGGATACAGCGTCATAGACAGAAACTAAGGACGGAGTAGGATAATAAAT Bsp1286I 160 160 161 161 TCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA AGCGTGGATGCAAGTTATAATGTCCGCTTGTATGAATGATTTCACACAATTAATTAATTACGAACATCCTGTATTATTAT SspI 240 240 241 241 ACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTC TGTTAACTTACAGACGTGTCGGTGAAAGGTGTGTCTGTAGTATTGTTTTTTAAAGGTGGTTTGGGGGGGAGGGGGCGAAG 320 320 321 321 TGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT ACCGGTGTCGTGAATTTGTGTAGAGACGGTTTGGGGTTTTTGTTTCTTGGGATTGTGGTCGGATTGGTCTAAAGTTTAAA EaeI 400 400 401 401 TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAAT ATAGAAAACCGCCATACGTGAAAATTGTCAGTGGGGGGTTGATTGTGTAATAAAAGGGGAGGGTGAGGGTATGATGATTA 480 480 Restriction Digested DNA stained with Ethidium Bromide on an Agarose Gel Fragments of DNA 0 1 What DNA fragments are generated when cut by restriction digestion? What would the electrophoresis gel look like if these fragments were separated by size? 2 3 4 5 6 Restriction Digested DNA stained with Ethidium Bromide on an Agarose Gel (Ethidium bromide stains all DNA; DNA probes only highlight complementary sequences) But which fragment has my gene of interest? How can I find the right fragment? (use a DNA probe) Obstacles in Molecular Genetics Goal: characterize the Gene of Interest (GOI) • “Macro-isolation” of Gene of Interest – Restriction Digest of DNA – Electrophoresis – DNA Library • “Micro-isolation” of Gene of Interest (GOI) – Southern Blot—Studying DNA (is a particular gene or sequence present in this genome?) – Hybridization (using complementarity to find the GOI on a Southern, Northern, or in PCR) – Sequencing • Amplification of GOI—need to make thousands of copies of one GOI in order to characterize it. – Using restriction sites to clone the GOI into a vector – PCR—Polymerase Chain Reaction • Understanding the GOI – Northern Blot—studying RNA (Which tissue expresses a particular RNA?) – Western Blot—studying protein (does this tissue express a specific protein?) – RT PCR – how much expression of the GOI is found in this tissue? I need lots of copies of my gene of interest. How can I do this? Cloning into a vector •Insert your GOI into another organism’s chromosome •Hitch-hike replication •May also get host organism to express protein of GOI. PCR •Cell free •Test tube •Fast •Limited to already known sequences •Can’t directly make a protein from PCR Cloning of GOI into vector, then into host organism How do I know which restriction enzyme to use? (hint: the foreign GOI must “fit” into the vector) Host organism makes lots of copies of the vector + GOI What must a host chromosome have in order to be useful as a vector? What do you think would happen if this vector did not have an ori? Examples of different types of vectors and host organisms Genome of Interest Human genome Host Organism Vector Size of Insert Yeast YAC (Yeast 100 - 2000 kb Artificial Chromosome) Worm (nematode) genome Firefly genome Bacteria Cosmid < 45 kb Virus l phage < 20 kb Drosophila genome Bacteria Plasmid < 15 kb How do you know when the vector actually has an insert? Use the Lac Z-system Chromosomal DNA from human cells ampR gene Plasmid Vector lacZ gene Gene of interest Unique restriction site Origin of replication Cut the DNAs with same restriction enzyme. Mix the DNAs together. Allow time for sticky ends to base-pair. Add DNA ligase to covalently link the DNA backbones. Vector with another fragment of chromosomal DNA or Recircularized vector Vector with GOI or Recombinant vectors Brooker, fig 19.2 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cloning a gene into a vector, cont. Vector with the gene of interest Recircularized vector or E. coli cell (treated with permeabilizing agents) Vector with another fragment of chromosomal DNA or Mix DNA with E.coli. Permeable E. Coli take up DNA [Transformation] Recircularized vector without an insert Plate cells on media containing X-Gal, IPTG, and ampicillin. Recombinant vector with an insert Blue colony Brooker, fig 19.2 White colony Each bacterial colony is derived from a single cell; so all the cells in a colony are genetically identical. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Lac Z System cont. White colonies contain vector with GOI. Talk with your labmate or student next to you--predict the types of colonies that would grow under these conditions Bacteria-no vector Bacteria”empty” vector Bacteria-vector with GOI (no antibiotic) (All with Ampicillin) Plain agar Plain agar X-Gal Plain agar X-Gal Plain agar Plain agar X-Gal Plain agar X-Gal Talk with your labmate or student next to you--predict the types of colonies that would grow under these conditions Bacteria-no vector Bacteria”empty” vector Bacteria-vector with GOI (no antibiotic) Plain Agar Bacteria-no vector (All with Ampicillin) Agar ampicillin Agar X-Gal Bacteria”empty” vector Agar Ampicillin X-Gal Agar X-Gal Bacteria-vector with GOI Agar Ampicillin X-Gal Obstacles in Molecular Genetics Goal: characterize the Gene of Interest (GOI) • “Macro-isolation” of Gene of Interest – Restriction Digest of DNA – Electrophoresis – DNA Library • “Micro-isolation” of Gene of Interest (GOI) – Southern Blot—Studying DNA (is a particular gene or sequence present in this genome?) – Hybridization (using complementarity to find the GOI on a Southern, Northern, or in PCR) – Sequencing • Amplification of GOI—need to make thousands of copies of one GOI in order to characterize it. – Using restriction sites to clone the GOI into a vector – PCR—Polymerase Chain Reaction • Understanding the GOI – Northern Blot—studying RNA (Which tissue expresses a particular RNA?) – Western Blot—studying protein (does this tissue express a specific protein?) – RT PCR – how much expression of the GOI is found in this tissue? Which fragment has my gene of interest? How can I find the right fragment? Electrophoresis gel Fig 18-5a Southern blotting: blotting DNA fragments onto a membrane so that it can be probed Which fragment has my gene of interest? How can I find the right fragment? Electrophoresis gel Southern blotting: blotting DNA fragments onto a membrane so that it can be probed DNA has now been transferred to membrane. Identifying the gene of interest (“probing” with a labeled tag) Which fragment will the genespecific probe bind to? I want to identify the b-globin gene. And I want to identify the insulin gene. Expose to film to “see” the radioactive probe How must the single stranded probes be different in order for these two investigators to identify their specific GOI? Pretend this is a Southern Blot (membrane with DNA bound to it). To which piece of ssDNA will the probe hybridize (bind)? 5’-CTAATGT-3’ 5’-GATTACA-3’ Radioactively labeled probe 3’-CGTTATA-5’ 5’-CGATTAT-3’ 5’-GATTACA-3’ 3’-CTAATGT-5’ 3’-GATTACA-5’ Membrane with bound single stranded DNA Pretend this is a Southern Blot (membrane with DNA bound to it). To which piece of ssDNA will the probe hybridize (bind)? 5’-CTAATGT-3’ 5’-GATTACA-3’ Radioactively labeled probe 3’-CGTTATA-5’ 5’-CGATTAT-3’ 5’-GATTACA-3’ 5’-GATTACA-3’ 3’-CTAATGT-5’ 3’-GATTACA-5’ Membrane with bound single stranded DNA Photography Film exposed to probed Southern Blot Bands of DNA that bound weakly to the radioactive probe Bands of DNA that bound to the radioactive probe Southern Blots Can Be Used For Paternity Tests Was Ronald Scott Kidnapped from the Larsons? “Northern blots show the expression pattern of the GOI.” Modern day “Southerns” and “Northerns”— microarray analysis Two distinct forms of large B-cell lymphoma are shown by the expression pattern: GC B-like DLBCL (orange) and Activated B-like DLBCL (blue) ASH ALIZADEH et al. 2000 Screening a gene library for the GOI • DNA (or Gene) Library—collection of host organisms containing DNA vectors with GOI inserts from different parts of the Genome of Interest • Library allows smaller pieces of genome-of-interest to be replicated inside organism and eventually selected based on size, sequence, or sometimes functional protein. XP (colorless) + X (black) Pi Alkaline phosphatase Western Blots Secondary antibody Primary antibody Protein of interest (a) Interactions between the protein of interest and antibodies Obstacles in Molecular Genetics Goal: characterize the Gene of Interest (GOI) • “Macro-isolation” of Gene of Interest – Restriction Digest of DNA – Electrophoresis – DNA Library • “Micro-isolation” of Gene of Interest (GOI) – Southern Blot—Studying DNA (is a particular gene or sequence present in this genome?) – Hybridization (using complementarity to find the GOI on a Southern, Northern, or in PCR) – Sequencing • Amplification of GOI—need to make thousands of copies of one GOI in order to characterize it. – Using restriction sites to clone the GOI into a vector – PCR—Polymerase Chain Reaction • Understanding the GOI – Northern Blot—studying RNA (Which tissue expresses a particular RNA?) – Western Blot—studying protein (does this tissue express a specific protein?) – RT PCR – how much expression of the GOI is found in this tissue? Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. C A C C G T A A G G A C T G (b) Output from automated sequencing Figure 19.17b 19 - 77 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Sequence to be analyzed (target DNA) Primer Primerannealing site 5′ Recombinant vector Many copies of the recombinant vector, primer, dNTPs, fluorescently labeled dideoxynucleotides, and DNA polymerase are mixed together. Incubate to allow the synthesis of DNA. CACCGTAAGGACTddG CACCGTAAGGACddT CACCGTAAGGAddC CACCGTAAGGddA CACCGTAAGddG CACCGTAAddG CACCGTAddA CACCGTddA CACCGddT CACCddG CACddC CAddC CddA ddC Nucleotides added to primer Separate newly made strands by gel electrophoresis. Sequence deduced from gel Laser beam G T C A G G A A T G C C A C Fluorescence detector (a) Automated DNA sequencing 19 - 76 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O O– P O O – O P O– O O P O– Adenine O CH2 5′ 4′ H 3′ H O H 1′ H 2′ H H 2′, 3′-Dideoxyadenosine triphosphate (ddA) Figure 19.16 19 - 73 Obstacles in Molecular Genetics Goal: characterize the Gene of Interest (GOI) • “Macro-isolation” of Gene of Interest – Restriction Digest of DNA – Electrophoresis – DNA Library • “Micro-isolation” of Gene of Interest (GOI) – Southern Blot—Studying DNA (is a particular gene or sequence present in this genome?) – Hybridization (using complementarity to find the GOI on a Southern, Northern, or in PCR) – Sequencing • Amplification of GOI—need to make thousands of copies of one GOI in order to characterize it. – Using restriction sites to clone the GOI into a vector – PCR—Polymerase Chain Reaction • Understanding the GOI – Northern Blot—studying RNA (Which tissue expresses a particular RNA?) – Western Blot—studying protein (does this tissue express a specific protein?) – RT PCR – how much expression of the GOI is found in this tissue? (a) The outcome of a PCR experiment Chromosomal DNA Overview of PCR Primer binding near one end of gene A different primer binding near other end of gene Many PCR cycles (b) The 3 steps of a PCR cycle Many copies of GOI, flanked by regions where primers bind. Site where forward primer binds Site where reverse primer binds Template DNA Denature: Separate DNA with high temperature. Primer annealing: Lower temperature, allows primers to bind template DNA. Forward primer 5′ 3′ 3′ 5′ 5′ 3′ 3′ 5′ 5′ 3′ 3′ 5′ 3′ 3′ 5′ Reverse primer 5′ 3′ 5′ T GCA C CA GC A T C C GA T C ACG T GGT C G T AGG C T AG 3′ Primer extension: Incubate at temperature that allows DNA synthesis to occur. 5′ 3′ 3′ 5′ 3′ 5′ 3′ 5′ Brooker Fig 19.4 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 5′ Reverse primer Necessary items for PCR Forward primer Reverse primer Free nucleotides T A G G T C C C A T G A DNA Polymerase Enzyme (“Taq”) Template DNA PCR: Amplifying DNA in a test tube Reverse primer 5’ 3’ 5’ 3’ Template DNA 3’ 5’ 3’ 5’ 3’ 5’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 5’ 3’ 3’ 5’ 3’ 3’ 5’ 3’ 5’ 5’ 3’ 5’ 5’ 3’ 3’ Forward primer 3’ 3’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’ PCR: Amplifying DNA in a test tube Reverse primer 5’ 3’ 5’ 3’ Template DNA 3’ 5’ 3’ 5’ 3’ 5’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 5’ 3’ 3’ 5’ 3’ 3’ 5’ 3’ 5’ 5’ 3’ 5’ 5’ 3’ 3’ Forward primer 3’ 3’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’ PCR: Amplifying DNA in a test tube Reverse primer 5’ 3’ 5’ 3’ Template DNA 3’ 5’ 3’ 5’ 3’ 5’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 5’ 3’ 3’ 5’ 3’ 3’ 5’ 3’ 5’ 5’ 3’ 5’ 5’ 3’ 3’ Forward primer 3’ 3’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’ PCR: Amplifying DNA in a test tube Reverse primer 5’ 3’ 5’ 3’ Template DNA 3’ 5’ 3’ 5’ 3’ 5’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 5’ 3’ 3’ 5’ 3’ 3’ 5’ 3’ 5’ 5’ 3’ 5’ 5’ 3’ 3’ Forward primer 3’ 3’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’ PCR: Amplifying DNA in a test tube Reverse primer 5’ 3’ 5’ 3’ Template DNA 3’ 5’ 3’ 5’ 3’ 5’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 5’ 3’ 3’ 5’ 3’ 3’ 5’ 3’ 5’ 5’ 3’ 5’ 5’ 3’ 3’ Forward primer 3’ 3’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’ PCR: Amplifying DNA in a test tube Reverse primer 5’ 3’ 5’ 3’ Template DNA 3’ 5’ 3’ 5’ 3’ 5’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 5’ 3’ 3’ 5’ 3’ 3’ 5’ 3’ 5’ 5’ 3’ 5’ 5’ 3’ 3’ Forward primer 3’ 3’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’ PCR: Amplifying DNA in a test tube Reverse primer 5’ 3’ 5’ 3’ Template DNA 3’ 5’ 3’ 5’ 3’ 5’ 5’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 5’ 3’ 3’ 5’ 3’ 3’ 3’ 3’ 5’ 5’ 5’ 3’ 5’ 5’ 3’ 3’ Forward primer 3’ 3’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’ I want to amplify the b-globin gene. What specific thing must be different in these two investigators’ PCR reactions? And I want to amplify the insulin gene. How do I design primers in order to detect (or amplify) specific genes? • 1. 2. 3. 4. 5. 6. www.ncbi.nlm.nih.gov/omim/ search under “hemoglobin” Click on HBB (hemoglobin-beta). 1419000? Click to the map locus (chromosome 11p~~) Click on [141900] on the chromosome itself “RefSeq Gene” in right side bar Use sequence information to design a complementary primer for the 5’ end of the gene, and 3’ end of gene. Difference between “Genomic” and “cDNA” Genomic—DNA exactly as found in the genome, including introns and other non-coding portions of DNA INTRONS-junk DNA 3’ untranslated region 5’ untranslated region EXONS-protein coding cDNA—complementary DNA--made from mature mRNA and thus containing only coding parts of gene Obstacles in Molecular Genetics Goal: characterize the Gene of Interest (GOI) • “Macro-isolation” of Gene of Interest – Restriction Digest of DNA – Electrophoresis – DNA Library • “Micro-isolation” of Gene of Interest (GOI) – Southern Blot—Studying DNA (is a particular gene or sequence present in this genome?) – Hybridization (using complementarity to find the GOI on a Southern, Northern, or in PCR) – Sequencing • Amplification of GOI—need to make thousands of copies of one GOI in order to characterize it. – Using restriction sites to clone the GOI into a vector – PCR—Polymerase Chain Reaction • Understanding the GOI – Northern Blot—studying RNA (Which tissue expresses a particular RNA?) – Western Blot—studying protein (does this tissue express a specific protein?) – RT PCR – how much expression of the GOI is found in this tissue? What does each technique “look like”? 1.) Electrophoresis 2.) Restriction Digest 3.) PCR 4.) Southern Blot 5.) Screening a genomic library 6.) Hybridization with radioactive probe 7.) Cloning of insert DNA into vector, transformation into host organism 8.) Northern Blot Which technique(s) do you use for each purpose (there may be more than one way to solve a problem)? 1. Identifying specific sequences, regulatory regions or genes (including introns). 2.) Determining tissue-specific or stage-specific gene expression. 3.) Cutting of DNA at specific sequences 4.) Separation of DNA fragments by size 5.) Amplification of specific DNA sequences 6.) Expressing an exogenous (foreign) protein in a host or transformed organism. Discuss with student next to you From the techniques discussed so far, how would you determine if Drosophila used hemoglobin? If they do, how would you determine when [what stage] would they use it? Where in their body would they use it? Suppose that you just graduated from college and have started working in a biotechnology firm. Your first job assignment is to clone the pig gene for the hormone prolactin. Briefly explain a strategy you might use to find and clone the pig gene for prolactin. Vectors require a selectable marker such as antibiotic resistance so that: a. the host cell will replicate the vector and GOI [Gene-ofinterest] along with its own chromosome. b. host cells taking up vector can be identified against host cells that have not. c. the host cell is able to have a GOI DNA fragment inserted into it d. host cells with the vector are able to express the GOI. e. none of the above Vectors require a selectable marker such as antibiotic resistance so that: a. the host cell will replicate the vector and GOI [Gene-ofinterest] along with its own chromosome. b. host cells taking up vector can be identified against host cells that have not. c. the host cell is able to have a GOI DNA fragment inserted into it d. host cells with the vector are able to express the GOI. e. none of the above Recombinant DNA Technology: practice questions The following comprehension questions (at end of each chapter section) in Brooker, Concepts of Genetics are recommended: • Comprehension Questions (at end of each section): 19.1,19.2, 19.3. Answers to Comprehension Questions are at the very end of every chapter. • Solved Problems at end of chapter (answers included): S1, S2, S4 • Conceptual questions and Experimental/Application Questions at end of chapter (answers found by logging into publisher’s website, or find them in the book): • Concepts—C1, C2, C4 • Application/Experimental Questions—E1, E2, E3, E4, E5, E6, E12, E13, E14, E15, E16, E17, E24, E25, • A little more challenging—E18, E19 (but first you have to understand alternative splicing [in Ch 17], E21, E22