Recombinant DNA

Learning Objectives

  • Outline the process of molecular cloning of a gene or segment of DNA
  • Describe appropriate methods for cloning eukaryotic genes so their protein products can be expressed (transcribed into mRNA, which is then translated to make protein).
  • Compare and contrast the vectors and procedures used for creating genetically modified bacteria and eukaryotes
  • Describe genome editing with CRISPR-Cas9 – what is required for targeting and how target genes can be modified

Many of our drugs, much of our food, and even our clothing are now produced using recombinant DNA technology. Instead of depending on random mutation, and either natural or artificial selection, we now have the ability to directly manipulate the genes of organisms to create new proteins and new capabilities in our domesticated bacteria, fungi, plants and animals.

Molecular cloning

Molecular biologists coined the term “molecular cloning” to describe the process of selectively replicating a chosen segment of DNA. The cloned DNA segment may be replicated within a cell, using “recombinant DNA” technology, or in a test tube, using the polymerase chain reaction (PCR).

Recombinant DNA technology leads to genetically modified organisms (GMOs). Recombinant DNA requires 3 key molecular tools:

  1. Cutting DNA at specific sites – most often performed by enzymes called restriction endonucleases (restriction enzymes). Restriction enzymes often make staggered cuts at specific 4, 6, or 8-bp palindromic sequences in duplex DNA, leaving characteristic “sticky ends” that can anneal to each other via hydrogen bonding between complementary bases on the single-stranded overhangs.
  2. Ligating DNA fragments with an enzyme called DNA ligase. DNA ligase, the same enzyme used during cellular DNA replication to knit together Okazaki fragments, creates covalent phosphodiester bonds between any two DNA fragments that have been cut by the same restriction enzyme, or have the same compatible “sticky ends”.
  3. A “vector”, such as a plasmid, that can be used to insert a new segment of DNA via restriction enzyme cutting and ligation. The plasmid containing the inserted DNA segment will replicate in host cells.
recombinantplasmid

Basic recombinant DNA techniques – molecular cloning of a gene segment into a plasmid vector. Cutting a plasmid and foreign DNA fragments with a restriction enzyme (e.g., EcoRI) generates “sticky ends”. A mixture of cut plasmid DNA and foreign DNA fragments with sticky ends can be ligated together with DNA ligase to create either a recombinant plasmid, containing a fragment of foreign DNA, or the original “empty” plasmid. Original image created by J. Choi

Also see: http://www.dnalc.org/resources/3d/20-mechanism-of-recombination.html

The alternative to using recombinant plasmids is to directly copy and amplify a specific DNA segment using PCR. PCR requires a pair of primers that correspond to the ends of the desired DNA segment.

http://www.dnalc.org/resources/3d/19-polymerase-chain-reaction.html

Even random DNA segments, where the base sequences are unknown, may be amplified by ligating adapter primers, short synthetic DNA segments of known sequence, to the ends of the target DNA molecules.

Cloning eukaryotic genes

Molecular cloning of eukaryotic genes is often either unfeasible or undesirable, or both, because they contain numerous, large introns. Plasmid vectors have a practical size limit of less than 10 kilo-base pairs (kbp), and PCR is also difficult beyond about 10 kb.

The mRNA, lacking introns, is a compact version of a eukaryotic gene that retains all of the protein coding information. The enzyme reverse transcriptase can be used, along with an oligo-dT primer that is complementary to the polyA tail, to synthesize a complementary DNA (cDNA) molecule. The cDNA can then be cloned into a plasmid or amplified by PCR by ligating adapters that contain restriction endonuclease cleavage sites or PCR primer sequences.

A cDNA is synthesized from mRNA using reverse transcriptase and olig-dT primers. The reverse transcriptase will also degrade the mRNA from the cDNA:mRNA hybrid molecule. DNA polymerase uses the mRNA fragments or random primers to synthesize the 2nd strand of the cDNA molecule. Adapters with restriction endonuclease sites or PCR primer sequences can be ligated to the ends of the completed cDNA to facilitate cloning into plasmids or amplification by PCR. Original illustration by J. Choi

Expressing cloned genes: genetically modified organisms

 

A map of pUC18, Figure 1 from Bensasson et al. 2004 Fig. 1 Heredity 92:483

A genetically modified organism (GMO) is any organisms that has been manipulated so it carries new genetic material, from either a different species or synthesized in the laboratory. The point of creating GMOs is usually to alter their traits, most often so they express a new gene.

Expression of foreign genes in bacteria

Plasmid vectors for cloning and expression in bacteria (see pUC18 map above) must have

  • An origin of DNA replication (ori) that directs their replication in the host cell
  • restriction endonuclease sites (polylinker) that occur just once on the vector, for insertion of cloned DNA segments
  • a selectable marker gene, such as antibiotic resistance (bla encodes beta-lactamase for ampicillin resistance), so cells that do not contain the plasmid can be eliminated
  • a way to distinguish cells that have the original plasmid from cells that have a recombinant plasmid.
  • a promoter to drive transcription (and translation) of the inserted foreign gene

The last feature is important because the ligation of plasmid and foreign DNA segments favors the plasmid ends re-ligating without a foreign DNA insert, resulting in the original, “empty” plasmid with no foreign DNA insert. Plasmid vectors therefore have the cloning site within a second antibiotic resistance gene or within the lacZ gene (encodes beta-galactosidase). Insertion of a foreign DNA segment will disrupt the gene. Colonies of E. coli cells that have empty plasmids (no inserted foreign DNA) have an intact lacZ gene, produce functional beta-galactosidase, and cleave a colorless dye called X-gal to release the insoluble blue dye X, and turn blue. E. coli cells that have plasmids with foreign DNA inserts make no beta-galactosidase, and are unable to cleave X-gal. These colonies stay white. Blue colonies are discarded, and white colonies are picked for further testing.

Cloning into the 5′ end of the lacZ gene also means that the E. coli cell can express a protein encoded by the inserted DNA. The lac promoter provides a means to regulate transcription, and protein coding sequences in the inserted DNA can be expressed as a fusion protein, containing the first few amino acids of the E. coli beta-galactosidase gene, and any amino acids encoded in the same reading frame by the inserted DNA sequence.

Expression of foreign genes in eukaryotes

Vectors for expression of foreign genes in eukaryotic cells must provide appropriate eukaryotic promoters upstream of the cloning site, for transcription by the eukaryotic host cell, as well as downstream polyadenylation and transcription termination signals. For single-celled organisms such as yeast, and cultured cells, bacterial plasmids containing foreign genes can be transformed into the cells. The plasmid DNA gets into the nucleus, and inserts into random locations in the host cell’s chromosomes. For multicellular organisms, the delivery of genes into the cells of the organism poses special challenges and requires special vectors and delivery methods. We describe these challenges for one application, human gene therapy, in the next section.

Gene therapy

Gene therapy poses a special challenge in delivering recombinant DNA into host cells. Recombinant DNA technology can readily clone a functional copy of a defective gene and insert it into a vector with the correct regulatory sequences. But how can we deliver this functional gene into the cells of a person who has already been born? The most promising techniques use viruses. Viruses evolved to be highly efficient at delivering their own genetic information into host cells. Replacing the viral replication genes with a therapeutic human gene eliminates the ability of the virus to replicate, while co-opting the viral infection mechanism to deliver the therapeutic gene into the nuclei of host cells.

Even then, only a small percentage of cells are infected and repaired (remember these therapeutic viruses can’t replicate to infect other cells). Moreover, benefits of viral gene therapy are short-lived, as the “repaired” cells age, die and are replaced by genetically unmodified cells.

A promising solution to these challenges is to find and genetically modify stem cells, those cells that will continue to divide and replenish the body’s cells for the rest of the patient’s life. Genetically modified stem cells can be returned to the patient’s body and have the potential to supply and replenish genetically modified blood cells and tissues for the rest of the patient’s life.

Genome editing

One technology developed in recent years, and being widely adopted in research labs around the world, is CRISPR-Cas9 technology, and variants. CRISPR stands for Clustered Regularly Interspersed Short Palindromic Repeats. Cas9 is a protein enzyme that binds short RNAs made from CRISPR genes to recognize and cleave DNA sequences that match the CRISPR RNAs. This technology enables researchers to delete, add, or replace particular bits of DNA in a cell. Human genome editing may be less controversial than human genetic modification, because no non-human DNA is added. Also, J-Lo is producing a TV series titled with the name of this technique.

Here is a TED talk video by Jennifer Doudna, one of the developers of CRISPR technology:

In essence, Cas9 is a protein that cuts DNA. Whereas restriction endonucleases cut DNA at fixed sites, Cas9 is programmable. Cas9 targets the DNA site to be cut by using a short guide RNA (sgRNA). Cas9 binds the sgRNA, and cuts DNA wherever the sgRNA binds to a complementary DNA sequence. So in any organism where the genome sequence is known, scientists can make an sgRNA to target a particular DNA sequence in the genome, and cut it. When a matching DNA sequence is available, the cell’s DNA repair system uses the matching DNA sequence to repair the break in the DNA.  By providing Cas9 protein, sgRNA, and a homologous template DNA that includes a desired change, scientists have successfully made precise changes in genomes of many kinds of cells and organisms, including cultured human cells.

crispr_overview

CRISPR target sequences require an adjacent TGG, called a PAM motif. A gene combining this target sequence and a tracrRNA gene sequence is put into an expression plasmid along with the Cas9 protein coding gene. This plasmid can be delivered into cells to express CRISPR-Cas9 that will cut the host genomic DNA at the target sequence. CC-BY-SA image by Nielsrca retrieved from Wikimedia

Cas9 protein and sgRNA bound to target DNA, based on structure by Anders et al 2014 Nature. CC-BY-SA by Cas9 Wiki project.

Cas9 protein and sgRNA bound to target DNA, based on structure by Anders et al 2014 Nature. CC-BY-SA by Cas9 Wiki project.

After cleavage by Cas9, the cell's own DNA break repair system will use a homologous DNA sequence to result in replacement of the targeted gene, or use a non-homologous end joining that causes small deletion mutations. Modified by JChoi from CC-BY-SA image by Carroll, D. Genome engineering with zinc-finger nucleases. Genetics Society of America, 2011, 188(4), pp 773-782.

After cleavage by Cas9, the cell’s own DNA break repair system will use a homologous DNA sequence to result in replacement of the targeted gene, or use a non-homologous end joining that causes small deletion mutations. Modified by JChoi from CC-BY-SA image by Carroll, D. Genome engineering with zinc-finger nucleases. Genetics Society of America, 2011, 188(4), pp 773-782.

Put it all together:

In class we will discuss how these concepts are applied to current gene therapy methods undergoing research and development.

Dr. Choi’s lecture video on recombinant DNA technology (in one 39-min chunk, until I find time to redo this in multiple short segments):

B1510_module5-1_RecombinantDNA_2011

5 Responses to Recombinant DNA

  1. asanchez39 says:

    I believe the molecular cloning 3 steps for recombination DNA tech. are out of order. Isn’t Step 3 and step 2 supposed to be switched?

    • Jung Choi says:

      I see your point. I edited to change the word “steps” to “operations” to lessen any sense that these are an ordered sequence. The order of operations would be: first, cut both the target DNA and the vector DNA with restriction endonucleases; second, ligate the target DNA fragments with vector DNA; third, transform bacterial cells with the products of the ligation reaction (if the vector is a plasmid). Thanks for pointing out a potential source of confusion.

  2. Jung Choi says:

    November 2016 – added section on genome editing with CRISPR-Cas9. Modified 2nd and 3rd LOs to be more specific, replaced plasmid cloning figure with new figure that correctly shows sticky ends (using EcoRI as the exemplar restriction enzyme), and two possible products of ligation with foreign DNA fragments.

  3. Jung Choi says:

    A new paper on inhibitors of Cas9, predicted as an evolutionary response by bacteriophage to inhibit cleavage of their genomes by Cas9: http://www.cell.com/cell/abstract/S0092-8674(16)31589-6

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