DNA Fingerprinting: Using DNA for Identification

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As we learn more about DNA, we should apply these concepts to practices used in current sciences. One field that works with DNA on a daily basis is forensic science. Even though 99% of human DNA is the same, the 1% difference causes each person's DNA to be unique, except for that of unusual births, such as twins. By testing tissue samples with gel electrophoresis, a person's DNA code could be discovered, and if the results matched to another set of DNA, then the specific person could be identified. This is applies to forensic investigations in that if DNA is found at a crime scene, it can be matched to a suspect. Since the discovery of DNA technology, multiple people convicted of crime have been exonerated based on DNA evidence. Since this is such an interesting application of science, we are going to explore this topic more through an activity using this source.

To begin with, we are going to read about and analyze the events surrounding the murder trail of Dr. Sam Sheppard.

1. In your opinion, what role (if any) did newspaper stories and editorials have in the outcome of the original trial of Dr. Sam Sheppard?
As I read through the chronicle of events, it became clear to e that media and press coverage played a significant role in this case. A majority of the headlines presented a very biased stance on the trial, pressuring officials to take action. It is usual for this to occur in a murder investigation, but not to this extent. This coverage also caused the jury to have a bias toward the case; there were multiple occasions in which a juror questioned the judge on a topic that had only been discussed in the media, which proved to be false.

2. What is the function of the restriction enzymes in DNA fingerprinting?
Restrictive enzymes, when mixed with DNA, cut molecules at different lengths based on their genetic code. For example, one specific enzyme will cut the DNA when the code "GAATTC" is read. Since everyone's DNA is different, the lengths of these cut sections will differ as well.

3. What is the function of  the agarose gel electrophoresis step?Agarose gel electrophoresis acts as a "molecular strainer", sorting the longer strands of DNA from the shorter strands by the use of positive and negative charges. The shorter strands of DNA will move through the gel much more quickly than the longer strands.

4. Why is a nylon membrane used to blot the DNA?
The nylon membrane is much easier to handle and work with than the agarose gel, and makes viewing the DNA more manageable.

5. What does a dark spot on the X-ray film indicate?
The dark spots on the film represent where the probes sat, attached to the DNA. Together, the spots form the DNA fingerprint.


For the second part of this activity, we are going to use this source. We are going to analyze the case of Ronald Cotton's wrongful conviction, as well as the case of O.J. Simpson.

6. What evidence was initially used to convict Cotton?
Originally, an eyewitness account was used to convict Cotton. When the victim had to identify her attacker, he was not in the line up of suspects, so she selected the person who bared the closest resemblance, which was Ronald Cotton.

7. What did the DNA evidence show?
By using DNA evidence, it became clear that Cotton was innocent, as well as the fact that often times, witnesses are unreliable. This has led to prevention of wrongfully convicting the innocent in the present.


8. How could DNA fingerprinting be used to prevent a false conviction if a case like this was being tried today?
DNA fingerprinting eliminates the chances of convicting the wrong person by ensuring correct identification. It ties a specific person to the scene of a crime without a doubt.

9. What percentage of convicts are unjustly convicted of sexual assault cases, according to Neufeld and Scheck?
According to Peter Neufeld and Barry Scheck, approximately 25% of convicts are unjustly convicted of sexual assault.

10. The O.J. Simpson trial was one of the most visible trials that attempted to use DNA evidence.  In the end, the DNA evidence was not satisfying to the jury, who acquitted Simpson.  What do Neufeld and Scheck believe about the impact of the O.J. Simpson trial on the use of DNA evidence?
Both Neufeld and Scheck believed that O.J Simpson's case showed potential for DNA evidence in forensic cases, however, when the technology is mishandled, it is not useful in the case. When presenting DNA evidence, there can be no room for error.


Overall, DNA evidence has proven very useful in multiple cases, both cold and current. It is amazing to see how science can be applied in different fields, as well as how far technology has advanced.

New School DNA Sequencing: Bacterial ID Lab

Using the "Old-School" Sanger method has been very useful, however, there is another, more recently developed method that has proven far more efficient. This new method is used in modern molecular biology labs as well as forensic investigations. To completely explore this method, you can use the online virtual lab here.

As I worked through the lab, I answered the following questions so that I could gain a deeper understanding of the activity.


1. As the medical technician in charge of this investigation, what are you trying to determine about the tissue sample provided to you?
As a lab technician, I am trying to determine what bacteria is contained in the tissue sample.

2. How did you prepare the DNA to be used in this investigation?
During the investigation, the DNA was prepared by adding digestive enzymes and buffers to a bacterial sample. The microcentrifuge tube containing the sample sat for several hours, and was then heated in order to activate the digestive enzymes. Once the sample was denatured, the sample was placed in a centrifuge to remove cellular debris from the sample.

3. Describe how PCR is used to make copies of DNA sequences.
PCR causes a reaction that can be tested by comparing positive reactions to negative reactions. By running the sample through various temperatures, the double helix structure of the DNA was unwound and separated into single strands, where it was then copied by the DNA polymerase.

4. Summarize the technique used to purify the PCR product.
To purify the PCR product, more buffer is added to the sample.The remaining PCR product is placed into a column and then into a centrifuge, so that only the long lengths of PCR remain with the sample of DNA. While in the column, the product is separated from the non-useful components, and then again when the DNA is separated from the rest of the product. 

5. What is produced during the sequencing prep PCR run?

During the sequencing prep PCR run, the DNA was prepared in 12 sequencing brews that contained primers, buffers, polymerase, nucleotides, and florescent-tagged terminators. This produced multiple DNA strands that varied in length.

6. Describe how the automatic sequencer determines the sequences of the PCR products.
The automatic sequencer determines the sequences of the PCR products through Gel Electrophoresis, where the samples are exposed to positive and negative electric charges. Since DNA contains a negative charge, it is carried to the positively charged area, expressing the notion that "opposites attract". The molecules are separated based on their size. Where they cease movement in the gel, scientists are able to read these bands as the basic genetic code: G,C, A, or T.

7. What does BLAST stand for?
BLAST is an acronym for "Basic Local Alignment Search Tool".

8. What conclusions did you make using the results of the BLAST search?  Did these conclusions support a clinical diagnosis for the patient (what disease did they have)?
After analyzing the results from the BLAST search, it can be concluded that the patient had Bartonella henselae.

I hope you enjoyed this lab as much as I did, while gaining insightful information about DNA sequencing.

GATTACA Reflection

"There is no gene for the human spirit."

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In class, we recently watched the movie GATTACA to evaluate the effects of science and technology upon society. The movie expressed a very intriguing plot in "the not-so-distant future" where the "best" genes can be selected to produce exceptional offspring. Everything can be determined from eye color to the probability of alcoholism. It is still possible to produce children without the use of selective genetics, but the results are considered impure. How does this fictional world compare to the one we are advancing towards? To reflect on the teachings of GATTACA, there are a few questions that we can analyze.

1. The following terms (de-gene-erate, In-valid) were used in the movie. How do they relate to the words we use: degenerate and invalid?

      The words are very similar, but relate more closely to genetics. They take terms tat are used commonly today and applied them to a negative tone to describe human beings that carried less desirable traits.

2. Why do you think Vincent left his family, tearing his picture out of the family photo, after winning the swimming race against his brother?

When Vincent overcame his brother physically, he became re-born in the sense that he realized his potential. All his life, leading up to this point, he lived in the shadow of his brother, and when he realized he didn't have to, he felt he had to cut all ties to the life where he lived in restraint. He had to pursue a future where he could live as he wanted.

3. Describe the relationship between Vincent and Anton.

Vincent and Anton have a very interesting relationship that deals with the conflict of average sibling rivalry in addition to the competition for affection based on the imbalance of their genetic situation. (Vincent was conceived naturally while Anton was conceived through selective genetics.) In the present, they also must understand life from the other's perspective, Vincent coping with having nothing expected of him and Anton having everything expected of him.

4. When Jerome Morrow said to Vincent/Jerome, “They’re not looking for you. When they look at you, they only see me,” what did he mean? Can you find any parallels to this type of situation in real life?

Jerome meant that his name had become an idea, not a specific person. By losing his ability to lose his legs, he lost his identity. When Vincent gained Jerome's name, he acquired a world of possibility. Jerome's name had become nothing but a label for a perfect genetic code. This is very similar to things we see in reality, most often in celebrities. When people talk about celebrities, they almost always seem to forget that there is a real human with real emotions attached to the name.

5. Choose your favorite character from the film. Explain why you choose that person. Would you want to be that person? Why? Why not?

My favorite character from the film was Jerome Morrow. He added a sense of humility to the film, showing that there is a part of life that genetics cannot change or predict. He showed that being perfect is not possible. Personally, I would not like to be Jerome, but I am humbled by his story.

6. At the end of the film, you are told that the Doctor knew about Vincent all along. Why did the Doctor go along with the fraud? What would you have done if you were the Doctor?

The doctor went along with the fraud because he understood the importance of being human. He empathized with the trails of living with imperfect genetics, and decided hat Vincent deserved a chance to pursue his aspirations. If I were in the same position the  doctor was in, I would have acted in the same fashion.

7. The technology to do what was done in the movie is definitely possible within the next ten years. Do you think that Vincent’s world could eventually happen in America? Why?

I believe that unless America begins to realize that human life revolves around more than genetics and a spark of electricity, and that life is not an experiment,  the world of GATTACA will easily become a part of society.

8. What do you think is wrong with the society portrayed in "GATTACA"? What is right?

The society of GATTACA is beneficial in the sense that human life will be lengthened and that hereditary diseases will be eliminated. The issues of this society lie in desensitization and the belief that all life can be controlled.

9. What were the screenwriters trying to tell us through the episode of the 12-fingered pianist? Is anything wrong with engineering children to have 12 fingers if, as a result, they will be able to make extraordinarily beautiful music?

The screenwriters were trying to portray how even perfection has flaws. Engineering children to have traits specific to a profession is wrong because it is trying to decide your child's fate for them. This cannot be justified by the outcome.

10. How does the society portrayed in GATTACA resemble the type of society that some Americans were hoping for during the height of the Eugenics movement?

The Eugenics movement was very similar to GATTACA in that the ambition was to select only the "best" genes, eliminating the imperfect ones. Every person would be a "model citizen".

Old School DNA Sequencing: Sanger Method

Before modern technology was available, DNA sequencing was much more tedious and difficult. In the 1950's Dr. Frederick Sanger determined the sequence of amino acids in protein.  This led to the understanding that DNA sequencing was collinear to the sequencing of amino acids. In the 1970's, Dr. Sanger developed a method to determine the exact sequence of nucleotides in a given gene. This method involved placing the DNA sample in  gel that was charred both negatively and positively. The longer strands of DNA would be pulled through the gel slower than the shorter strands, and the DNA separated into bands. The band positions were then "read" in order to determine DNA sequence. To stimulate this, we were given a lab packet in which DNA from four different subjects were tested. We were asked to read each sequence, compare them, and finally determine which subjects carried a disease. Pictures from the lab are posted below. 

In the step above, we determined the sequencing of each subject's DNA by evaluating the bands. This data was then placed in the chart pictured in the last image. 

After comparing the data, it became clear that "Norm" was the only healthy patient. All other subjects showed some disturbance in their DNA that caused them to be effected by the disease. Carol experienced a front shift mutation, Bob experienced a truncation mutation shift, and Abby experienced point mutation. This disease would be unrecognizable were it not for the Sanger Method.

DNA Extraction Lab

As we learn more about DNA, it is great to apply the concepts we learn so that we can gain an even deeper understanding. In this post, I am going to describe a lab we did in class in which we extracted DNA from wheat germ. In order to do this, our instructor had us work in groups so that we could collaborate our knowledge.

To begin the lab, we measured out 1 gram of raw wheat germ. This germ was then placed in a 50 ml test tube where it was mixed with 20 ml of hot tap water for 3 minutes. After being stirred, 1/4 teaspoon of detergent was added to the mixture. This was again stirred. 5 minutes after adding the detergent, we added 14 ml of alcohol. This was done very carefully so that the alcohol would not mix with the germ mixture. This was necessary in the extraction process, as DNA precipitates at the water-alcohol interface. The image below shows this step being done.

After doing this, the test tube had to sit for a few minutes so that the DNA could precipitate. After a short wait, we collected the DNA by using a wooden stick.

Overall, this was a really fun lab that expanded my knowledge of DNA.

From DNA to Protein: The Central Dogma

As we are aware, DNA is found in protein, but how does it get there? After all, DNA is located in the nucleus of all cells, and ribosome build protein. In order to cross the nucleus membrane in order for protein to be made, there has to be a step in-between that will transfer the DNA code to the ribosome, but what is that step? The answer lies in the process of the central dogma, and the material RNA. RNA, as you can predict, is very similar to DNA. Instead of having dioxyribose material, like in DNA, RNA contains ribose. As we will learn, RNA will be the key component to the central dogma, allowing protein to be successfully made. For now, we are going to define a few terms related to this process. To view the vocabulary, please click here.

DNAi Timeline

Like most things, DNA would not be as well understood as it is today without the contributions from multiple researchers. This post is going to detail the work from some of these contributing scientists that helped develop the current understanding of DNA. A great resource for information on other scientists that contributed work to the evolution of the idea of DNA can be found at this address. This is also the resource that was used for this post.

Martha Chase, Alfred Hershey, and the "Blender Experiment"
In the early 50's, a group of researchers at the Cold Spring Harbor Laboratory were researching bacteriophage genetics (also referred to as phage genetics). Phage are viruses that target, attack, and infect bacteria. At this time, it was already known that phage was constructed with an outer casing of protein that surrounded in inner core of DNA. It was also known that phage relied on bacteria to reproduce, and that phage attached themselves to bacteria by their tails. It was hypothesized that after attaching, the phage pumped genetic material into the bacterial host, causing the bacterial enzymes to be replaced by new phage particles. In 1952, Martha Chase and Alfred Hershey dedicated their work to discovering why the bacteria transformed into a phage producing organism, proving whether or not DNA was a transforming principle. Through chemical analysis, it was discovered that DNA contained high amounts of phosphorus and zero amounts of sulfur. This information was in contrast to the known information about protein, which contains sulfur but no phosphorus. This information was used in an experiment to test which component entered the bacteria for infection. This was designed in a way that radioactive phosphorus (32P) and radioactive sulfur (35P) to selectively label the phage DNA and protein. The radio labeled phage was then combined with unlabeled bacteria so that the phage could attach. The attachment was then disrupted as the culture was mixed in a Waring blender. The samples were then spun in a centrifuge in an attempt to separate the phage from the bacteria. This attempt was successful, and due to the fact that the phage is lighter than the bacteria, it remained suspended in the test tube while the bacteria collected at the bottom in the form of a pellet. After evaluating the sample 35P, it was discovered that the newly produced phage from the bacteria did not contain any radioactive sulfur, unlike the protein coat of the parent phage.  In contrast, the sample 32P contained newly produced phage from the bacteria that was contaminated with radioactive 32P. From this, it was determined that phage DNA was used inside the bacteria to produce new phage, confirming that DNA is the genetic material.

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