DNA Notes PDF

Chapter 9 DNA: THE INDISPENSIBLE FORENSIC SCIENCE TOOL FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-1  Introducti...

Chapter 9 DNA: THE INDISPENSIBLE FORENSIC SCIENCE TOOL FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-1  Introduction Portions of the DNA nucleotide sequence are as unique to each individual as fingerprints. The gene is the fundamental unit of heredity. Each gene is a polymer actually composed of DNA specifically designed to carry the task of controlling the genetic traits of our cells. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-2  Introduction The molecular structure of DNA was deduced by Francis Crick and James Watson. The technology of DNA typing had its beginnings in 1985 with the work of Alec Jeffreys. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-3  Introduction DNA is constructed as a very large molecule made by linking a series of repeating units called nucleotides. A nucleotide is composed of a sugar, a phosphorous - containing group, and a nitrogen-containing molecule called a base. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-4  Introduction Deoxyribose sugar Nitrogenous Base Phosphate FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-5  The Bases Four types of bases are associated with the DNA structure: adenine (A), guanine (G), cytosine (C), thymine (T). FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-6  The Bases The bases on each strand are properly aligned in a double-helix configuration, which is two strands of DNA coiled together. As a result, adenine pairs with thymine and guanine pairs with cytosine. This concept is known as base pairing. The order of the bases is what distinguishes different DNA strands. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-7  DNA at Work DNA directs the production of proteins, which are made by combining amino acids. The sequence of amino acids in a protein chain determines the shape and function of the protein. Each group of three nucleotides in a DNA sequence codes for a particular amino acid. – Example: G-A-G codes for the amino acid glutamine, while C-G-T codes for alanine. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-8  DNA at Work If a nucleotide is “changed,” for example a T is substituted for A and G-A-G becomes G-T- G, the “wrong” amino acid is placed in the protein (in this case: glutamine is replaced with valine). FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-9  DNA at Work As a result, the protein may not function correctly and this is the basis for many diseases and health issues. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-10  DNA Replication DNA replicates itself prior to cell division. DNA replication begins with the unwinding of the DNA strands of the double helix. Each strand is now exposed to a collection of free nucleotides that will be used to recreate the double helix, letter by letter, using base pairing. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-11  DNA Replication DNA Unwinding Exposed Strands FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-12  DNA Replication Many enzymes and proteins, such as DNA polymerases, are involved in unwinding the DNA, keeping the DNA strands apart, and assembling the new DNA strands in proper base sequence. Polymerase chain reaction (PCR) is a technique for replicating many small quantities of DNA or broken pieces of DNA found at a crime scene, outside a living cell. The ability to multiply small bits of DNA now means that sample size is no longer a limitation in characterizing DNA recovered at a crime scene. ©2011, 2008 Pearson Education, Inc. FORENSIC SCIENCE: An Introduction, 2nd ed. By Richard Saferstein Upper Saddle River, NJ 07458 9-13  Recombinant DNA Recombinant DNA relies on the ability of certain chemicals, known as restriction enzymes, to cut DNA into fragments that can later be incorporated into another DNA strand. – Useful when producing insulin and growth hormone. Restriction enzymes can be thought of as highly specialized scissors that cut a DNA molecule when it recognizes a specific sequence of bases. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-14  Recombinant DNA Once a portion of the DNA strand has been cut out with the aid of a restriction enzyme, the next step in the recombinant DNA process is to insert the isolated DNA segment into a foreign DNA strand, usually that of a bacterium. As the bacteria multiply rapidly, copies of the altered DNA are passed on to all descendants. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-15  Recombinant DNA FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-16  DNA Typing Portions of the DNA molecule contain sequences of bases that are repeated numerous times, known as tandem repeats. The origin of tandem repeats is a mystery FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-17  DNA Typing To a forensic scientist, these tandem repeats offer a means of distinguishing one individual from another through DNA typing. Tandem repeats seem to act as filler or spacers between the coding regions of DNA. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-18  DNA Typing What is important to understand is that all humans have the same type Two of repeats, but Repeats there is Three Repeats tremendous variation in the number of repeats each of us have. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-19  RFLP Length differences associated with relatively long repeating DNA strands are called restriction fragment length polymorphisms (RFLP) and form the basis for one of the first DNA typing procedures. While all humans have the same type of repeats, there is very wide variation in the number of repeats from person to person Typically, a core sequence consists of 15 to 35 bases in length and repeats itself up to a thousand times. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-20  RFLP The key to understanding DNA typing lies in the knowledge that numerous possibilities exist for the number of times a particular sequence of base letters can repeat itself on a DNA strand. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-21  Electrophoresis A technique analogous to TLC is electrophoresis. – Here, materials are forced to move across a gel-coated plate under the influence of an electrical potential. In this manner, substances such as DNA can be separated by fragment size and characterized. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-22  Electrophoresis FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-23  A Positive RFLP Test Once the DNA molecules have been cut up by a restriction enzyme, the resulting fragments are sorted out by electrophoresis. The smaller DNA fragments will move at a faster rate on the gel plate than the larger ones. The fragments are then transferred to a nylon membrane in a process called Southern blotting. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-24  A Positive RFLP Test To visualize the RFLPs, the nylon sheet is treated with radioactive probes containing a base sequence complementary to the RFLPs being identified (a process called hybridization). FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-25  A Positive RFLP Test Next, the nylon sheet is placed against X-ray film and exposed for several days. When the film is processed, bands appear where radioactive probes stuck to fragments on the nylon sheet. A typical DNA fragment pattern will show two bands (one RFLP from each chromosome). FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-26  A Positive RFLP Test When comparing the DNA fragment patterns of two or more specimens, one merely looks for a match between the band sets. A high degree of discrimination can be achieved by using a number of different probes and combining their frequencies. When using a three-probe system of DNA typing, a typical DNA pattern will show six bands. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-27  A Positive RFLP Test What would it indicate if a suspect only had one band in his lane? FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-28  Capillary Electrophoresis The separation of STRs using capillary electrophoresis: – Evolved from the flat-gel electrophoresis approach – Automates sampling and data collection – Decreases analysis time – Is currently the preferred method FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-29  PCR Testing Polymerase chain reaction is the outgrowth of knowledge gained from an understanding of how DNA strands naturally replicate within a cell. For the forensic scientist, PCR offers a distinct advantage in that it can amplify minute quantities of DNA many millions of times. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-30  PCR Testing Using the low copy number DNA protocol, analysts are able to examine samples containing as few as 18 cells. First, the DNA is heated to separate it. A thermal cycler may be used to copy the DNA. Each cycle of the DNA thermal cycle takes approximately two minutes to complete. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-31  PCR Testing Second, primers (short strands of DNA used to target specific regions of DNA for replication) are added, which hybridize with the strands. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-32  PCR Testing Third, DNA polymerase and free nucleotides are added to rebuild each of the separated strands. Now, this process is repeated 25 to 30 times. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-33  PCR and RFLP PCR technology cannot be applied to RFLP DNA typing. The RFLP strands are too long, often numbering in the thousands of bases. PCR is best used with DNA strands that are no longer than a couple of hundred bases. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-34  PCR Advantages One advantage in moving to shorter DNA strands is that they would be expected to be more stable and less subject to degradation brought about by adverse environmental conditions. The long RFLP strands tend to readily break apart under the adverse conditions not uncommon at crime scenes. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-35  PCR Advantages PCR also offers the advantage in that it can amplify minute quantities of DNA, thus overcoming the limited sample size problem often associated with crime scene evidence. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-36  Short Tandem Repeats The latest method of DNA typing, short tandem repeat (STR) analysis, has emerged as the most successful and widely used DNA profiling procedure. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-37  Short Tandem Repeats STRs are locations on the chromosome that contain short sequences that repeat themselves within the DNA molecule. They serve as useful markers for identification because they are found in great abundance (about 30%) throughout the human genome. It is thought that they may act as spacers between the coded regions of DNA FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-38  STR Advantages STRs normally consist of repeating sequences of 3 to 7 bases in length, and the entire strand of an STR is also very short, less than 450 bases in length. This means that STRs are much less susceptible to degradation and may often be recovered from bodies or stains that have been subjected to extreme decomposition. Means to detect the amelogenin gene are included in commercial STR kits used in crime labs because the gene allows determination of gender. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-39  STR Advantages Also, because of their shortness, STRs are ideal candidates for multiplication by PCR, thus overcoming the previously mentioned limited- sample-size problem often associated with crime-scene evidence. A typical STR DNA type emanating from a single individual shows a two band pattern. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-40  The Power of STR What makes STRs so attractive to forensic scientists is that hundreds of different types of STRs are found in human genes. The more STRs one can characterize, the smaller will be the percentage of the population from which a particular combination of STRs can emanate. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-41  The Power of STR This gives rise to the concept of multiplexing. Using the technology of PCR, one can simultaneously extract and amplify a combination of different STRs. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-42  Standardizing STR Testing Currently, U.S. crime laboratories have standardized on 13 STRs for entry into a national database (CODIS). A high degree of discrimination and even individualization can be attained by analyzing a combination of STRs (multiplexing) and determining the product of their frequencies. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-43  Standardizing STR Testing With STR, as little as 125 picograms of DNA is required for analysis. This is 100 times less than that normally required for RFLP analysis. For example: Y-STR markers are useful when multiple males are involved in a sexual assault. If three men are involved in such an attack the investigators would expect Y-STR analysis to show a maximum of three peaks. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-44  Mitochondrial DNA Another type of DNA used for individual characterization is mitochondrial DNA. Mitochondrial DNA (mDNA) is located outside the cell’s nucleus and is inherited from the mother. Mitochondria are structures found in all our cells used to provide energy that our bodies need to function. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-45  Mitochondrial DNA A single mitochondria contains several loops of DNA. Regions of mitochondria include HV1 and HV2 FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-46  Mitochondrial DNA Testing Mitochondrial DNA typing does not approach STR analysis in its discrimination power and thus is best reserved for samples, such as hair, for which STR analysis may not be possible. Forensic analysis of mDNA is more rigorous, time consuming, and costly when compared to nuclear DNA analysis. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-47  Mitochondrial DNA Testing Also, all individuals of the same maternal lineage will be indistinguishable by mDNA analysis. Two regions of mDNA have been found to be highly variable and a procedure known as sequencing is used to determine the order of base pairs. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-48  Disease and Disorder As currently performed, DNA-profiling technology cannot provide information helpful in determining whether an individual carries a genetic defect. In sickle-cell anemia, abnormal hemoglobin differs from normal hemoglobin by only a single amino acid. Recombinant DNA technology is useful in producing insulin and growth hormone. Gene splicing has made it possible to develop bacteria that can synthesize insulin. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-49  Disease and Disorder Information from the Human Genome Project will: – Help reveal the role and implications of evolution – Reveal the location of a gene on a particular chromosome – Be useful for diagnosing and treating genetic diseases – Aid in understating the underlying causes of cancer FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-50  CODIS Perhaps the most significant tool to arise from DNA typing is the ability to compare DNA types recovered from crime scene evidence to those of convicted sex offenders and other convicted criminals. CODIS (Combined DNA Index System) is a computer software program developed by the FBI that maintains local, state, and national databases of DNA profiles from convicted offenders, unsolved crime scene evidence, and profiles of missing persons. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-51  Packaging Biological Evidence Before the collection of biological evidence begins, it is important that it be photographed and recorded on sketches. Wearing disposable latex gloves while handling the evidence is required. Clothing from victim and suspect with blood evidence must be collected. FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-52  Packaging Biological Evidence The packaging of biological evidence in plastic or airtight containers must be avoided because the accumulation of residual moisture could contribute to the growth of DNA-destroying bacteria and fungi. Each stained article should be packaged separately in a paper bag or in a well-ventilated box. Whole blood collected for DNA typing purposes must be placed in a vacuum tube containing the preservative EDTA FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-53  Packaging Biological Evidence Dried blood is best removed from a surface by using a sterile cotton swab lightly moistened with distilled water that is air dried before being placed in a swab box, then a paper or manila envelope. All biological evidence should be refrigerated or stored in a cool location until delivery to the laboratory. Standard/reference DNA specimens must also be collected, such as blood or the buccal swab (swabbing the mouth and cheek). FORENSIC SCIENCE: An Introduction, 2nd ed. ©2011, 2008 Pearson Education, Inc. By Richard Saferstein Upper Saddle River, NJ 07458 9-54