<CHAP NUM="13" ID="CH.00.013">chapter 13
<FM><TTL>DNA—The Indispensable Forensic Science Tool</TTL>
<KTSET><TTL>Key Terms</TTL>
<KT>amelogenin gene</KT>
<KT>amino acids</KT>
<KT>buccal cells</KT>
<KT>chromosome</KT>
<KT>complementary base pairing</KT>
<KT>deoxyribonucleic acid (DNA)</KT>
<KT>electrophoresis</KT>
<KT>epithelial cells</KT>
<KT>human genome</KT>
<KT>hybridization</KT>
<KT>low copy number</KT>
<KT>mitochondria</KT>
<KT>multiplexing</KT>
<KT>nucleotide</KT>
<KT>picogram</KT>
<KT>polymer</KT>
<KT>polymerase chain reaction (PCR)</KT>
<KT>primer</KT>
<KT>proteins</KT>
<KT>replication</KT>
<KT>restriction enzymes</KT>
<KT>restriction fragment length polymorphisms (RFLPs)</KT>
<KT>sequencing</KT>
<KT>short tandem repeat (STR)</KT>
<KT>substrate control</KT>
<KT>tandem repeat</KT>
<OBJSET><TTL>Learning Objectives</TTL>
<P>After studying this chapter you should be able to:
<OBJ><P><INST>< </INST>Name the parts of a nucleotide and explain how they are linked together to form DNA</P></OBJ>
<OBJ><P><INST>< </INST>Understand the concept of base pairing as it relates to the double-helix structure of DNA</P></OBJ>
<OBJ><P><INST>< </INST>Contrast DNA strands that code for the production of proteins with strands that contain repeating base sequences</P></OBJ>
<OBJ><P><INST>< </INST>Explain the technology of polymerase chain reaction (PCR) and how it applies to forensic DNA typing</P></OBJ>
<OBJ><P><INST>< </INST>Contrast the newest DNA-typing technique, short tandem repeats (STRs), with previous DNA-typing technologies</P></OBJ>
<OBJ><P><INST>< </INST>Describe the difference between nuclear and mitochondrial DNA</P></OBJ>
<OBJ><P><INST>< </INST>Understand the use of DNA computerized databases in criminal investigation</P></OBJ>
<OBJ><P><INST>< </INST>List the necessary procedures for the proper preservation of bloodstained evidence for laboratory DNA analysis</P></OBJ></P></OBJSET></FM>
<KT>Y-STRs</KT></KTSET> <CASE NUM="1" TY="CS"><TTL>O.J. Simpson—A Mountain of Evidence</TTL>
<P>On June 12, 1994, police arrived at the home of Nicole Simpson only to view a horrific scene. The bodies of O. J. Simpson’s estranged wife and her friend Ron Goldman were found on the path leading to the front door of Nicole’s home. Both bodies were covered in blood and had suffered deep knife wounds. Nicole’s head was nearly severed from her body. This was not a well-planned murder. A trail of blood led away from the murder scene. Blood was found in O. J. Simpson’s Bronco. Blood drops were on O. J.’s driveway and in the foyer of his home. A blood-soaked sock was located in O. J. Simpson’s bedroom, and a bloodstained glove rested outside his residence.</P>
<P>As DNA was extracted and profiled from each bloodstained article, a picture emerged that seemed to irrefutably link Simpson to the murders. A trail of DNA leaving the crime scene was consistent with O. J.’s profile, as was the DNA found entering Simpson’s home. Simpson’s DNA profile was found in the Bronco along with that of both victims. The glove contained the DNA profiles of Nicole and Ron, and the sock had Nicole’s DNA profile. At trial, the defense team valiantly fought back. Miscues in evidence collection were craftily exploited. The defense strategy was to paint a picture of, not only an incompetent investigation, but one that was tinged with dishonest police planting evidence. The strategy worked. O. J. Simpson was acquitted of murder.</P></CASE>
<BM><P>The discovery of <KT>deoxyribonucleic acid (DNA)</KT><SIDEIND NUM="1" ID="MN2.13.001"/> , the deciphering of its structure, and the decoding of its genetic information were turning points in our understanding of the underlying concepts of inheritance. Now, with incredible speed, as molecular biologists unravel the basic structure of genes, we can create new products through genetic engineering and develop diagnostic tools and treatments for genetic disorders. For a number of years, these developments were of seemingly peripheral interest to forensic scientists. All that changed when, in 1985, what started out as a more or less routine investigation into the structure of a human gene led to the discovery that portions of the DNA structure of certain genes are as unique to each individual as fingerprints. Alec Jeffreys and his colleagues at Leicester University, England, who were responsible for these revelations, named the process for isolating and reading these DNA markers <ITAL>DNA fingerprinting</ITAL>. As researchers uncovered new approaches and variations to the original Jeffreys technique, the terms <ITAL>DNA profiling</ITAL> and <ITAL>DNA typing</ITAL> came to be applied to describe this relatively new technology. This discovery caught the imagination of the forensic science community, for forensic scientists have long desired to link with certainty biological evidence such as blood, semen, hair, or tissue to a single individual. Although conventional testing procedures had gone a long way toward narrowing the source of biological materials, individualization remained an elusive goal. Now DNA typing has allowed forensic scientists to accomplish this goal. The technique is still relatively new, but in the few years since its introduction, DNA typing has become routine in public crime laboratories and has been made available to interested parties through the services of a number of skilled private laboratories. In the United States, courts have overwhelmingly admitted DNA evidence and accepted the reliability of its scientific underpinnings.</P>
<H1>What Is DNA?</H1>
<P>Inside each of 60 trillion cells in the human body are strands of genetic material called <KT>chromosomes</KT><SIDEIND NUM="2" ID="MN2.13.002"/>. Arranged along the chromosomes, like beads on a thread, are nearly 25,000 genes. <BOLD>The gene is the fundamental unit of heredity. It instructs the body cells to make proteins that determine everything from hair color to our susceptibility to diseases.</BOLD> Each gene is actually composed of DNA specifically designed to carry out a single body function. Interestingly, although DNA was first discovered in 1868, scientists were slow to understand and appreciate its fundamental role in inheritance. Painstakingly, researchers developed evidence that DNA was probably the substance by which genetic instructions are passed from one generation to the next. But the major breakthrough in comprehending how DNA works did not occur until the early 1950s, when two researchers, James Watson and Francis Crick, deduced the structure of DNA. It turns out that DNA is an extraordinary molecule skillfully designed to carry out the task of controlling the genetic traits of all living cells, plant and animal.</P>
<P>Before examining the implications of Watson and Crick’s discovery, let’s see how DNA is constructed. DNA is a <KT>polymer</KT><SIDEIND NUM="3" ID="MN2.13.003"/>. As we learned in <OLINK LOCALINFO="CH.00.008">Chapter 8</OLINK>, a polymer is a very large molecule made by linking a series of repeating units. In this case, the units are known as <KT>nucleotides</KT><SIDEIND NUM="4" ID="MN2.13.004"/>. A nucleotide is composed of a sugar molecule, a phosphorus-containing group, and a nitrogen-containing molecule called a <ITAL>base.</ITAL></P>
<P><LINK LINKEND="FG.13.001">Figure <FIGIND NUM="1" ID="FG.13.001"/>13–1</LINK> shows how nucleotides can be strung together to form a DNA strand. In this figure, S designates the sugar component, which is joined with a phosphate group to form the backbone of the DNA strand. Projecting from the backbone are the bases. The key to understanding how DNA works is to appreciate the fact that only four types of bases are associated with DNA: adenine, cytosine, guanine, and thymine. To simplify our discussion of DNA, we will designate each of these bases by the first letter of their names. Hence, <ITAL>A</ITAL> will stand for adenine, <ITAL>C</ITAL> will stand for cytosine, <ITAL>G</ITAL> will stand for guanine, and <ITAL>T</ITAL> will represent thymine. Again, notice in <LINK LINKEND="FG.13.001">Figure 13–1</LINK> how the bases project from the backbone of DNA. Also, although this figure shows a DNA strand of four bases, keep in mind that in theory there is no limit to the length of the DNA strand; in fact, a DNA strand can be composed of a long chain with millions of bases.</P>
<P>The information just discussed was well known to Watson and Crick by the time they set about to detail the structure of DNA. Their efforts led to the discovery that the DNA molecule is actually composed of two DNA strands coiled into a <ITAL>double helix.</ITAL> This can be thought of as resembling two wires twisted around each other. As these researchers manipulated scale models of DNA strands, they realized that the only way the bases on each strand could be properly aligned with each other in a double-helix configuration was to place base <ITAL>A</ITAL> opposite <ITAL>T</ITAL> and <ITAL>G</ITAL> opposite <ITAL>C</ITAL>. Watson and Crick had solved the puzzle of the double helix and presented the world with a simple but elegant picture of DNA (see <LINK LINKEND="FG.13.002">Figure <FIGIND NUM="2" ID="FG.13.002"/>13–2</LINK>).</P>
<P>The only arrangement possible in the double-helix configuration was the pairing of bases <ITAL>A</ITAL> to <ITAL>T</ITAL> and <ITAL>G</ITAL> to <ITAL>C,</ITAL> a concept that has become known as <KT>complementary base pairing</KT><SIDEIND NUM="5" ID="MN2.13.005"/>. Although <ITAL>A–T</ITAL> and <ITAL>G–C</ITAL> pairs are always required, there are no restrictions on how the bases are to be sequenced on a DNA strand. Thus, one can observe the sequences <ITAL>T–A–T–T</ITAL> or <ITAL>G–T–A–A</ITAL> or <ITAL>G–T–C–A.</ITAL> When these sequences are joined with their opposite number in a double-helix configuration, they pair as follows:</P>
<P></P>
<P>Any base can follow another on a DNA strand, which means that the possible number of different sequence combinations is staggering! Consider that the average human chromosome has DNA containing 100 million base pairs. All of the human chromosomes taken together contain about three billion base pairs. From these numbers, we can begin to appreciate the diversity of DNA and hence the diversity of living organisms. DNA is like a book of instructions. The alphabet used to create the book is simple enough: <ITAL>A, T, G,</ITAL> and <ITAL>C.</ITAL> The order in which these letters are arranged defines the role and function of a DNA molecule.<SIDEIND NUM="3" ID="MN1.13.003"/></P>
<H1>DNA at Work</H1>
<P>The inheritable traits that are controlled by DNA arise out of its ability to direct the production of complex molecules called <KT>proteins</KT><SIDEIND NUM="7" ID="MN2.13.007"/>. Proteins are actually made by linking a combination of <KT>amino acids</KT><SIDEIND NUM="8" ID="MN2.13.008"/>. Although thousands of proteins exist, they can all be derived from a combination of up to twenty known amino acids. The sequence of amino acids in a protein chain determines the shape and function of the protein. Let’s look at one example: The protein hemoglobin is found in our red blood cells. It carries oxygen to our body cells and removes carbon dioxide from these cells. One of the four amino acid chains of “normal” hemoglobin is shown in <LINK LINKEND="FG.13.003">Figure <FIGIND NUM="3" ID="FG.13.003"/>13–3(a)</LINK>. Studies of individuals afflicted with sickle-cell anemia show that this inheritable disorder arises from the presence of “abnormal” hemoglobin in their red blood cells. An amino acid chain for “abnormal” hemoglobin is shown in <LINK LINKEND="FG.13.003">Figure 13–3(b)</LINK>. Note that the sole difference between “nor...
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