Science Education

The Interrogation of Mr. DNA, Part 1 of 3: Extraction

Your first perception as you enter the living room is the sound coming from the television. The character exchanges are intimate, from a movie you can’t quite place. The television set’s ever-changing glow stabs the room with occasional bluish bursts of light. Through the half-shut blinds, the pastoral glow of a full moon gently illuminates frames, tables, a book whose cover curls up.

That’s when you see the body of the woman. It lies against the back wall in an awkward sitting position. The trail of blood above its head belies its recent collapse into a marionette’s resting posture, head crooked, face staring at the floor. Only the next burst of light from the television set can clearly show you the dark blood marring its abdomen and the pool it has formed on the floor next to it.

You look for a pulse but cannot find any.

There’s only one thing left to do.

The team arrives in an obnoxiously large black SUV. Doors open in sync, as part of a well-choreographed ballet. Wearing leather jackets and Gucci shades, the team walks toward the house, backlit by a concentrated battery of car lights, the entire sight seemingly happening in slow motion. The female lead shakes her head, her long blond hair flowing freely in the wind. Each member of the team is packing heat. One can almost hear the cool beats of modern rock accompanying their impressive footsteps.

The male lead pulls up the yellow crime-scene tape and the entire team crosses the threshold. Cops respectfully back up. The experts have arrived.

Wait a minute.

No, wait, sorry.

Reality check.

The composition of crime scene units varies from country to country, even from state to state in the U.S., but it is never made up of gloriously photogenic, heat-packing forensic scientists in civilian clothing with loose-flowing hair. Crime scene techs can have a combination of a high-school degree and a crime scene certificate, or a degree in law enforcement or criminal justice, or simply a high-school degree with the right work experience. In New York City, however, they are detectives. What crime scene technicians generally are not are scientists, with advanced degrees in biology or chemistry, as certain shows would have us believe.

Wearing disposable coveralls and gloves, the technicians enter our crime scene and document it. Samples of the victim’s blood are taken to be tested by the lab. And one observant technician notices blood around the victim’s lips and teeth. Looking into her mouth, the technician sees no blood and concludes that this blood on the victim’s mouth could have been the result of an offensive bite. The assailant stabbed the victim, she lunged at him and bit him. The blood on her mouth could be his.

All of these samples are bagged and sealed and a strict chain of custody is established. The blood samples are transported to a crime lab. There, a forensic scientist is asked two questions: is the blood on the mouth of the victim hers and, if not, whose is it?

In the sped-up, make-believe world of television, we cut to a scene from the B plot. When we return, the forensic scientist grabs a sheet from the printer, seemingly reads the results for the first time, and gives his verdict to his boss. What I want to do is show you what he actually does while we’re busy watching suspect #1 being interviewed after a robbery gone awry.

***

The very first step in DNA profiling consists in extracting the actual DNA from this body fluid known as blood. The reason for this is that components in the blood can inhibit the reactions needed downstream to amplify the DNA. This problem is not solely associated with blood; amplification contaminants are found everywhere. Bile salts and complex sugars can interfere with DNA profiling in feces; melanin can do the same in hair and skin; and the indigo dye in jeans behaves in the same way. For this reason, one must extract a relatively clean DNA sample from whichever medium is brought to the lab.

Let’s call our forensic scientist Greg.

There are many techniques available to Greg for the extraction of DNA from blood. However, given that Greg is employed by a crime laboratory, whose employees may have to testify in court and whose results have the power to change someone’s life and even, in some cases, end it, Greg has to follow very strict protocols. These validated recipes are known in scientific parlance as “standard operating procedures” or SOPs. They have not only been shown to work in the scientific literature, but they have usually also been validated internally, so that the work derived from these procedures can be defended in court.

Greg has thus been trained to perform a DNA extraction using a special resin called Chelex®. Since very little blood was recovered from the victim’s mouth, a few spots were transferred to a sterile piece of blotting paper. Greg takes a clean punch to the bloodied paper and a round cut-out falls into a disposable tube. Greg adds to it a solution of laboratory-grade water and Chelex® and heats the solution up to its boiling point.

Blood is made up of four main components: red blood cells, white blood cells, platelets, and plasma. The latter is the liquid in which blood cells are suspended. It mostly consists of water. Of the three types of blood cells, only one has a nucleus, and thus contains nuclear DNA of the type Greg is interested in: white blood cells. Platelets do not have a nucleus, and neither do red blood cells. Interestingly enough, though, immature red blood cells do possess a nucleus, but this structure and its entire genome are jettisoned to make way for the hemoglobin protein which will carry oxygen. The fact that red blood cells lack a nucleus is unique to mammals, with few exceptions.

What Greg needs to get at is the DNA that is enclosed in the nucleus of the white blood cells in that blood sample. Boiling the sample does most of the job: it disrupts the membranes that essentially form the skin of the cells, thus releasing the contents of these cells in the water-and-Chelex® solution. The membrane of the nucleus is likewise shredded and the numerous proteins contained in the cell are destroyed by the boiling water and the basic pH. It is a calculated carnage at the nanoscopic level, a mass destruction that leaves the DNA unharmed. Why does the DNA escape this blood bath (pun intended) unscathed?

Chelex® is a chelating resin, meaning it has a high affinity for certain electrically charged metals known as “metal ions”. Indeed, Chelex® will bind calcium, manganese, and magnesium, essentially scooping them out of solution like a selective vacuum cleaner. These ions can damage the DNA at boiling temperatures: the Chelex® removes them from solution. Moreover, some of these ions are used as battery packs for proteins the job of which is to cut the DNA into pieces. Take away the batteries and those proteins can’t slice and dice. The result: Bruce Willis’ character after the train crash in Unbreakable. In the middle of all this destruction, the genome lays intact.

Greg then puts the solution in a centrifuge, which spins it at a very high speed, forcing the heavy cellular debris and resin to drop to the bottom of the tube. The DNA remains in solution above this pellet. Greg aspirates it out and he has got himself a sample of unknown DNA ready for testing.

To be continued in Part 2

(Feature picture by Brandon Anderson)

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4 thoughts on “The Interrogation of Mr. DNA, Part 1 of 3: Extraction

  1. Pingback: The Interrogation of Mr. DNA, Part 2 of 3: Amplification | Cracked Science

  2. Pingback: Phosphate, Sugar, and a Ring or Two: A Recipe for Disaster (or DNA) | Cracked Science

  3. Pingback: DNA in the Trenches: How Missing Soldiers Get ID’d Decades After Their Deaths | Cracked Science

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