Sanger Method: Determining the Termination Goal

Home , Dideoxynucleotide, Sanger sequencing

In 2003 the Human Genome Project project was completed. This event signified that the thirteen-year long, publicly funded, international effort to determine the DNA sequence of the human genome finished two years before it was estimated to be. While this was very exciting and began our efforts of understanding the inner workings of our genome, the real work began decades earlier. DNA sequencing is the process of determining the sequence of nucleotide bases (As, Ts, Cs, and Gs) in a piece of DNA. Sanger sequencing was developed by the British biochemist Fred Sanger and his colleagues in 1977. It was the first practical method for determining the order for the nucleotides of a sample of DNA and remained the dominant method for thirty years. But first - memory dump: The Sanger Method follows roughly the same protocol as PCR. In the space below, write down everything you remember about PCR. From how it works, to what the reagents were - anything that comes to mind, place it in the box below.

Student answers will vary Suggestions of student answers Three steps and associated temperatures Use of thermocycler Reagents used

Goal: To model how Sanger Sequencing builds on the biochemical processes involved in DNA replication and how the applications of DNA sequencing have impacted industry.

Step One: Assemble the Unknown Sequence Build the unknown sequence.

Unknown Sequence 3’ A C T G T G G A C T G A G G A C A T A 3’

Primer & Nucleotides 5’ G A C ______5’

Now, while you “know” the unknown sequence for the sake of this activity, in the lab, Sanger Sequencing is used to determine the unknown sequence.

DNA Nucleotides Dideoxynucleotides Explore the differences between the foam pieces of the DNA nucleotides and dideoxynucleotides. Compare/ Contrast their shapes. Why do you think the foam pieces were designed this way? DNA nucleotides have a 3’ hydroxyl end that allows them to bind to a 5’ phosphate group. The shape of the dideoxynucleotides has changed on the 3’ end. This end would not allow it to bind with another nucleotide.

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Fred Sanger was a biochemist. Before working on DNA and RNA, he investigated the structure and function of protein. He understood the chemical reactions required for elongation of a nucleotide sequence. With that in mind, he proposed a way to utilize that knowledge to terminate a sequence.

Examine the three structures of sugar molecules; ribose, deoxyribose, and dideoxyribose. Like all models, the ones you are using today don’t fully visualize all differences in the biochemistry of the molecules. Consider the chemical structure of the molecules and how that will impact the function of the molecule, especially when bound to phosphates and a nitrogen base.

Ribose Deoxyribose Dideoxyribose found in RNA found in DNA synthetically produced for Sanger Method

CH 2 O CH 2 O CH 2 O 5’ 5’ 5’ C C 1’ C C 1’ C C 1’ 4’ H H 4’ H H 4’ H H H H H C C H C C H H 2’ C C 3’ 3’ 2’ 3’ 2’ HO OH HO H H H

What is the structural difference between Ribose and Deoxyribose ? Think back, what implications did that have in the differences between DNA and RNA? What is the structural difference between Ribose and Deoxyribose ? Think back, what implications Ribosedid that had have two in hydroxyl the differences groups - betweenone at the DNA 2’ carbon and RNA? and one at the 3’ carbon. Deoxyribose only had one hydroxyl at the 3’ carbon. Although the next nucleotide is only supposed to bind at the 3’ carbon, this change means that ribose can technically bind at the 2’ carbon. This would produce a RNA transcript that could potentially be broken. While not ideal, the organism can make more RNA molecules. Now, examine the structure of Dideoxyribose. How will that impact binding?

Dideoxyribose has no hydroxyl groups at either the 2’ or the 3’ carbons. This means that a nucleotide with this sugar can not have a dehydration synthesis reaction occur and can not extend further.

Think ahead, you are Fred Sanger. You have just synthetically produced dideoxyribose and produced the four dideoxy nucleotides, (ddATP, ddTTP, ddGTP, and ddCTP). What is your next step? How do you use this to sequence DNA? Student answers will vary. Students are likely to mention something close to electrophoresis as the next process after an ampli- fication-like reaction. Students might draw on past experiences of telling between gene types using electrophoresis with PCR.

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Steps 1. Grab your needed materials ○ Nucleotide bags ○ Primer Sequences; placed to the side in a stack 2. Using the Unknown Sequence as a guide and following nucleotide base pairing rules: ○ First add the primer to the 3’ end of the unknown sequence. ○ Then, use the nucleotide bags to add free nucleotides to the 5’ end of the primer. 3. When you pull a dideoxynucleotide, ddNTP, where N stands for any one of the nucleotide bases, then that strand is complete. Separate that single strand from the Unknown Sequence. 4. Repeat this process, starting first with adding a primer to the 3’ end of the Unknown Sequence and then add nucleotides as you did in step three.

Look at the strands you created. Use this space to make observations and write down any questions that come up along the production of these strands. Where do you think this process will go next? What is the “end goal” of the Sanger Method?

Student answers will vary. Encourage them to stop and process what they have done. Encourage questions and predictions for what will happen in subsequent cycles.

Student reflections should refer back to the presence of the dideoxynucleotides and the use of a sequence of DNA that has been terminated.

Models are only as good as your memory. Try your best to draw at least two of the strands that you produced. Label the: primer, deoxynucleotide (dNTP), and dideoxynucleotide (ddNTP).

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What Just Happened? The Sanger Method follows the same generalized protocol as PCR. Both of these protocols are run in a thermocycler at very specific temperatures.

Think back. How did the PCR reaction work? What temperatures were used? Why were they used? What enzyme (polymerase) was utilized? Why did it have to be this enzyme, not a “regular” human DNA Polymerase III? • Denature: 95oC - dsDNA sequences separated • Anneal: 55oC - Primers are annealed/attached to the ssDNA sequences. • Extend: 72oC - Taq polymerase is used to extend/elongate the DNA strands from the 3’ end of the primer.

PCR Steps Taq was used because it would not denature at the high temperatures, where DNA Polymerase III would have. Is it logical that these two protocols would be similar in nature? Why/Why not? Yes because it is roughly the same purpose.

In truth, Kary Mullis, who is credited with inventing PCR while working at the Cetus Corporation, did not “discover” PCR until 1983, six years after Fred Sanger invented PCR in 1977. How might Mullis have utilized Sanger’s protocol and experimental findings in his creation of PCR? If you were Mullis, what information would you be most curious about looking into? Sanger's protocol illustrated that a gene could be replicated synthetically. Mullis was most interested in somehow detecting a point mutation by using a oligonucleotide primer and ddNTPs. However this would not ensure a specific site within the vast genome. Mullis was most curious about increasing specificity of the target sequence.

Looking at these two images of the models for both Sanger Sequencing and PCR to answer the following question: What are the differences between the Sanger Sequencing PCR products of these two protocols? • dsDNA vs. ssDNA • Number of primers used

How do the differences relate to the scientific or investigative purpose of the protocol/experiment? Purpose of Sanger is to determine the sequence, whereas PCR is to amplify a section of DNA

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What Happens Next? The Sanger Method utilized chain terminated sequences to determine the sequence of DNA in a specific fragment. Look at all of the single stranded, chain terminated sequences that you have produced.

Why is the Sanger method also known as the chain termination method? The sequences are cut short by the addition of a dideoxynucleotide.

Propose a way to organize these strands that makes the most logical sense. Use the lines below to explain how/why you organized your bands. Draw a sketch of how you organized it in the blank area. Student answers will vary.

What would happen if these fragments were run on a gel? How would you organize the gel / utilize the wells in the gel so that the result could be used to give you the sequence of bases in the DNA sample? Student answers are dependent on the sequence lengths that they produce. Gel should basically be organized from the largest to the shortest DNA band length.

Remember, with DNA electrophoresis, the smaller fragments will be able to travel faster through the pores in the agarose gel. This will mean that they will appear farther down the gel than the longer fragments that will travel slower.

Using the space below, create both a table in the space below that organizes your data as well as a predicted gel for your results.

Student answers are dependent on the sequence lengths that they produce. Gel should basically be organized from the largest to the shortest DNA band length.

Now, utilize both the physical model and the picture that you just produced to answer the following questions: Given your model, what is the sequence of the DNA that you analyzed, from 5’ to 3’? Should mirror the sequence on page 1 of the activity.

What questions would a scientific investigator still be faced with after your gel would run? How could we change the procedure to make sure all of the questions were answered? Depending on the class, there is likely to be gaps in the sequence of DNA due to that particular segment not coming up, due to chance

Investigators will alter the time they allot for the reaction to ensure that all spaces are accounted for.

What if you got multiple copies of a single chain termination sequence? ○ How do you model this with your physical model? ○ How would this appear on the gel? • In the model: Stack on top of each other - as they also modeled with PCR. • In the gel: Darker colored bands.

Next Generation Sequencing The Sanger form of sequencing was widely used for forty years. However, it was not without issues. The Sanger Method works for small sections of DNA (>500bp), but with scientists looking to sequence larger genomes, it became clear that the scale and efficiency of each step within the protocol needed to be evaluated and investigated for possible improvements. The 1990s had many transformations for sequencing protocol, including an automated, color- coded method. Dideoxynucleotides were synthetically treated once again to have a fluorescent tag added to them. Now dubbed dye-terminator sequencing, the overall protocol remained the same, however, instead of the final products being run on a gel, they were now read by a computer. This process, called capillary Clockwise from above: Gel electrophoresis was the electrophoresis, greatly improved the quality of the first way that sequencing data was portrayed to sequencing data as well. Chromatograms were now scientists. Capillary electrophoresis not only eliminated utilized to represent the output of sequencing data. the pouring of gels, but also simplified both the When looking for patterns in data, this new form extraction and interpretation of fluorescent signals given off by dyed ddNTPs. Chromatograms displayed the of output greatly aided scientists in their quest to results in an easy to read graph that both color coded understand genomes of various organisms. the bases as well as displayed the sequence data

Looking at a Sanger gel, why do you think scientists moved away from this practice? Hard to tell the sequence - there is a large room for error and misreading of the gel.

Sanger sequencing is still utilized today for small bp length samples. Why do you think this is the case? Smaller sequences will happen faster and for less total spending via Sanger. For short sequences Sanger gels are easier to read. As the sequence gets longer, the gel gets harder to read.

What are some other conditions/required improvements that you believe scientists wanted to improve on with genome sequencing? What infrastructure or technological improvements would be needed to make these gains? Scientists would have wanted to move towards an automated way of gathering data to remove some potential for human error. To do this, the technology would have to be not only invented, but the protocols improved to match the change. This would also help to afford scientists the ability to do longer segments of DNA/ whole genome sequencing, which is not possible with Sanger sequencing.

Faster is not Better… Enough As with everything in life, we search for ways to continue improving. DNA sequencing was not void of this intrepid mindset. One of the biggest drivers with this progression has been the cost. It is clear the scope and scale of genomics research is driven by the associated costs of understanding the genome itself. In 2001, the Human Genome Project (HGP) cost $2.7 billion over the 13 years it took to sequence. Currently, the price, as seen in the NIH graph to the right, hovers around $1000, a considerable cut in costs from 2001. In addition, a whole genome can now be sequenced in as little as a day.

In the summer of 1986, James Watson called a meeting at Cold Spring Harbor Laboratory located on the North Shore of Long Island, NY. One of the biochemical researchers there was Kary Mullis. What did Mullins work on? Kary Mullins worked on PCR. How could his research help initiate / propel the HGP? PCR technology would have allowed for short segments of the genome to be amplified.Then, Sanger sequencing could be utilized to determine the sequence of those short products. The first genomes sequenced were of small, model organisms. In fact, in 1998 C. elegans was the first animal genome completely sequenced. Why would scientists advocate for model organisms to be sequenced first? How does this parallel pre-clinical trials? These organisms had a shorter sequence. In addition, the lessons learned from sequencing these model organisms could be utilized when sequencing the human genome.

In May 2000, President Bill Clinton grew tired of the apparent arms race between the two groups racing to sequence the human genome and the money/tense nature it was creating. He sent a two word note to a member of the Department of Energy saying simply, “Fix this!”. On June 26, 2000, a press conference was conducted to announce the completion of the HGP. In truth, the project would not finish until February 2001 when competing articles were simultaneously published in both Science and Nature.

Why would the President want this “arms race” cut short? President Clinton did not like the optics of this race, nor did he truly want a private company (Celera) to announce completion prior to the government funded venture (NIH - Human Genome Project)