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July 30, 2013

Essay on DNA Analysis

Introduction and History of DNA findings

Abbreviated as the DNA, the full form of the abbreviation stands for Deoxyribo Nucleic Acid and is the most integral component of the human body that is naturally programmed to contain the phenotypic and genotypic information constituting the organism. With the discovery of this molecule, scientists and molecular biologists were provided the access to unlock the vital codes that contained the secret of life and its existence. Moreover with the discovery of this remarkable molecule, the field and scope of science and genetics experienced tremendous progressive impetus and acquired unprecedented heights of innovation and advancement. Before moving into greater detail about the characteristics, structure and function of the molecule, it is always important to have a look at the fascinating sequel of events and incidents that ultimately led to the discovery of this key molecule.
It might be surprising for many that a pivotal and significant molecule like DNA revolutionized scientific mainstream and flabbergasted scientists and biologists all over the world with its double helix structure in the year 1953 by two prominent biologists of Cambridge University, James Watson and Francis Crick. Even though both these scientists were awarded the Nobel Prize for Medicine the same year, the announcement was itself very contentious in the way as other scientists such as Rosalind Franklin and Maurice Wilkins who had been busy in exploring the different dimensions of the molecule for a much longer period of time than Watson and Crick, were completely marginalized from the limelight and publicity that attracted the winning pair. Moreover it was on the basis of the experimental X-ray diffraction work of Rosalind and Wilkins that provided Watson and Crick the opportunity to disclose the rudimentary facts related to the structural makeover of the DNA.
The controversy that surrounded the award and discovery was later acknowledged by Watson himself in his autobiography named as The Double Helix. Even though the molecule of DNA was discovered quite late, information and scientific evidences outlining the presence of inherent characteristics and their subsequent transfer from generation to generation in the form of parents and their progeny was making rounds in the arena of science since the advent of Monohybrid Inheritance devised by Gregor Mendel. The results of Mendel’s experiments clearly demonstrated and outlined the idea of characteristic inheritance but with the element of DNA molecule missing at that time, his theory was oscillating between skeptism and rejection. The discovery of the DNA molecule in actuality provided concrete, substantiated and scientific proving their authenticity and striking down the options of disapproval or doubt present anywhere.
In addition to this some other scientists who had made valuable contributions in determining the nature and the structural framework of the DNA molecule include Erwin Chargaff who was the first one to find out the combinations and quantity of nitrogenous bases that are an imperative component for the functionality of the molecule.
Oswald Avery in 1944 was the first one to rectify the stereotype that it was in fact DNA and not proteins that was the prime hereditary substance responsible for the transfer of acquired characteristics from one generation to the next. Over five decades have passed since the structure of DNA molecule was first viewed by scientists since then, medical science has gone through various leaps and bounds over such extensive period of time, but the structure of DNA its enthrallment and intrigue that it possess has always been a source of immense inquisitiveness for scientists, geneticists and molecular biologists. Let’s have a look at the structure of this incredible molecule that unlocks the mystery of life and its existence. (Watson and Berry, 2004)
Structure and Types of DNA
           
The most applicable scientific terminology used to describe the structure of DNA is Double Helical or Double Helix because of the double strands that comprise its structure. The shape of the molecule resembles a winded staircase that is spiraled around each other in an anti-parallel fashion.
Like all other biological macromolecules DNA is also composed of various small units or monomers that are known as nucleotides. These nucleotides are further composed of three different components that play a chief role in making the molecule functional. The three components include a carbohydrate, a nitrogenous base and a phosphate head. The carbohydrate present in the nucleotide structure of DNA is deoxyribose, a five-carbon atom sugar from which the initial name of the molecule has originated. The nitrogenous base does vary among the four different bases that are present in the DNA molecule which includes Thymine, Adenine, Cytosine and Guanine. The functionality of the DNA is highly dependent on the flawless structural framework that is adhered by the rules of complementary base-pairing.
According to the rules of base-pairing adenine only pairs with thymine and guanine will only pair up with cytosine. The reason being that adenine and guanine are classified as Purines which are double ringed in structure and therefore larger in size, guanine and thymine on the other hand are Pyrimidines which are single ringed and smaller in size, in order to maintain a uniformity in the size of the DNA molecule it is important that the base pair together by following a purine-pyrimidine combination. Secondly the shapes of the bases are such that only bases complementary to each other in shape can bond together.
It is also important to mention here that there are hydrogen bonds formed between bases. Adenine and thymine are held together by double hydrogen bonds whereas guanine and cytosine are held by triple hydrogen bonds. Another area of the molecule that requires understanding is that of sugar-phosphate backbone which is held together by special phosphodiester bonds formed between nucleotides as a result of the condensation process that takes place between the monomers. Joining of two nucleotides results in the formation of a dinucleotide which is accompanied with the release of a water molecule also, following a similar pattern repetitive condensation reactions result in the formation of a polynucleotide.
Despite of the fact that there are many types of nucleic acids found in the human body; the overall basic skeletal structure of the polymer remains the same along with the presence of some minor changes which can contribute to substantial changes in terms of the ways that the molecule performs its functions. Some of the major types of DNA found in the human body include B-DNA which is a common form of nucleic acid found in the chromosomes of an organism. B-DNA is found in the right handed helix of the DNA molecule and it is this portion that undergoes transcription during protein synthesis. A-DNA is also found in the right handed helix of the molecule but encompasses greater number of nitrogenous bases than the former one. Z-DNA is the most important part of the left-helix that contains the greatest number of bases than A and B, up to 12 and has therefore the most important role to perform during the time when transcription takes place in a human cell. Apart from these three types of DNA, there is another type which is known as clonal or complementary DNA (Cdna); this complementary strand of DNA is used for executing myriad research on diseases and innovations in the pharmaceutical sector using this type of DNA which is transcribed under suitable laboratory conditions for the creation of genes.

Another major nucleic acid that is present in the human body and plays a crucial role in the process of protein synthesis is the RNA or the ribo nucleic acid. Unlike the DNA, ribo nucleic acid is single stranded, the carbohydrate present in the nucleotide monomers of Ribo Nucleic Acid is ribose unlike deoxyribose and moreover RNA instead of Thymine contains another base named uracil which forms a complementary base-pair with adenine. RNA has greater liberty of movement, unlike DNA which is only restricted to the nucleus of a cell. Another interesting thing to note here is that the DNA when undergoing the process of protein synthesis prepares a corresponding template of a special form of RNA type which is known as messenger ribo nucleic acid. This transcribed single-stranded piece of nucleic acid then moves out of the nuclear premises via the nuclear pores into the cytoplasm where it attaches itself with small but highly effective protein factories known as ribosomes. These ribosomes which serve as the site of protein synthesis perform the process of translation in which the genetic code encrypted on the messenger ribo nucleic acid is decoded in the form of an amino acid or polypeptide chain. In order to bring the amino acids present in the cytoplasm at their desired location, the expertise of another nucleic acid known as the TRNA or the Transfer ribo nucleic acid is required. The Trna acts a vehicle for the amino acids to initiate the process of translation which is facilitated by the enzymatic catalysis provided by Rrna or ribosomal ribo nucleic acid present in the ribosome. A diagrammatic representation further explains the types of DNA and the double helical structure found in the DNA. (Sinden, 1994)

Uses of DNA analysis in Forensic Criminology

During the conclusive phases of the 20th century and with the advent of the new millennium a new branch of criminological science that emerged was forensic and criminal sciences. With unprecedented innovations and advancements taking place in the field of forensic criminology over the passage of time, the importance of DNA as the vital link connecting the criminal and crime scene has also increased concomitantly.
In this section we will be looking at some of the crucial questions that are answered by this molecule which play a pivotal role in subsequent stages of criminal investigations. With the emergence of this branch of criminal science in the 1980s, a revolution in the sector of forensic science and law enforcement departments in finding the perpetrator involved in the crime also enhanced to extraordinary levels. The presence of this silent biological witness in forensic labs has played an instrumental role in getting hold of many criminals and at the same time release of many innocent suspects.
The concept of DNA profiling or fingerprinting was first introduced by an English geneticist Alex Jeffreys in the year 1985. While conducting careful experiments with the DNA and its properties Alex noticed that there are certain portions of base sequences in the molecule that continuously undergo repetition. It was further noticed that these portions of base sequences varied from individual to individual. We know these repeated base sequences as VNTRs or Variable Number of Tandem Repeats today and there are special techniques that are employed for the separation of these VNTRs such as electrophoresis and X-ray autoradiography for their collection. These processes will be discussed in greater detail when we discuss the methods of extracting and separating DNA evidence from the crime scene.   
From the details of the research that he conducted he deduced that if a technique to distinguish and separate these lengths of repeated base sequences is devised, the mystery of human identity to which these base sequences belong can be solved easily. By making use of the methodology that was put forward by Alex, the case of Enderby Murder case of 1988 was successfully resolved in which Colin Pitchfork was convicted. (History of Forensic DNA analysis)
Over the passage of two decades forensic science and in tandem to it the advancement in molecular biology has made scientists and criminologists realize the profound significance of DNA in not only resolving a case but also evaluating the evidences collected through various dimensions and magnitudes.
The significance of DNA is resolving criminal issue can also be vindicated from the fact that no DNA is same for two people except identical twins and since fingerprints for every individual are also different hence with the help of DNA Fingerprinting important clues and evidences regarding the crime and the criminal activity conducted can be unearthed.
But at the same time it is also very important to bear in mind that DNA collected from the crime scene can either link a possible suspect to the crime that took place and there is equal probability that it can also eliminate him from the list of suspects rounded from the crime scene, hence the point under consideration in both situations is that accurate DNA Fingerprinting is a critical and cautiously dealt issue when used for crime solving procedures and processes.
A major question that arises is how DNA is collected from the crime scene and what the sources from where DNA evidence can be extracted from. A simple and straightforward answer to this question is that it can be collected from virtually any source that is available and present at the crime scene. These include many things such as used cigarettes, toothpicks, eyeglasses, hat or bandanna, used condoms, bite marks, fingernails, bottles and cans or even from stamps and envelopes.
Each of the things mentioned act as a source for the extraction of DNA which can be used as useful evidence in proving the guilt or innocence of a criminal. From most of these sources it is the saliva that is used as a means of extracting the DNA and this function is fulfilled by only few cells.
Nevertheless it is worth remembering that if a proper or visible stain is not obtained, it does not imply that the quantity of cells being used for DNA typing is low. Furthermore the role of DNA is not just limited to the identification of the source from where it has been obtained from, evidences obtained from this molecule can easily place any individual in the list of suspects that claims of not being present at the crime scene. It can refute the statements of the defendant and hold them responsible for the committing of crime. The deeper we move into the rabbit hole investigating the benefits of this nanometer sized molecule, the greater are the benefits that we will be able to explore.
There are innumerable examples of cases in which the verdict released by the court was revised and rectified after the scientific analysis of DNA and the evidences obtained regarding the suspects was presented in front of the jury. In one such example the DNA analysis of a single piece of detached hair found deep in the victim’s throat provided a crucial piece of evidence for the person who was convicted for capital punishment. In another murder case the DNA of the suspect taken from the saliva taken from a dental impression mold matched with the DNA obtained from the swabbed bite mark on the victim.
Another key issue that rises here is how to verify that the DNA being obtained from the crime scene belongs to the suspect and not from someone else. For such confirmations the method and technique of elimination samples and their collection and analysis is used. It is therefore important for the investigating officer to think ahead to the time when the crime took place. For example in case of a house robbery, the suspect might have drunk a glass of water at the crime scene; it is the responsibility of the officer to collect the DNA samples of suitable people of the household so that they can be matched with the DNA found in the saliva on the glass. The greater is the difference of the DNA samples obtained, the faster is the process of elimination sampling occurrence.
Even in cases of a homicide it is important for the people of the forensic department to obtain the DNA of the victim while conducting the autopsy as it will help in subsequent investigation stages to distinguish the victim’s DNA from other samples that are obtained from the crime scene.
Ethical issue regarding DNA collection and analysis arise when investigating rape cases as in such cases it becomes important to assess the DNA of victim’s recent sexual partners, so that in subsequent stages of criminal investigation they can be eliminated from the list of potential perpetrators if their DNA is found to be different from the one that has been obtained from the semen samples collected from the crime scene. In such cases when DNA collection and analysis becomes mandatory, the person presumed as a potential suspect is approached with extreme sensitivity and is provided a complete explanation regarding the case that is under investigation.
Apart from using elimination samples another method that is used by forensic scientists for the identification of potential suspects is the system of CODIS which stands for Combined DNA Index System. This is basically an electronic database in which the DNA Profiles are installed for the authentic identification of suspects. The database which is similar in nature and function to the AFIS or the Automated Fingerprint Identification System, is being implemented by every state of the country in recent times in which the DNA index of certain criminals convicted of murder, rape and child abuse are present.
When a suspect is convicted of a particular crime the DNA profile of the convict is entered into the DNA database, similar to the procedure that is followed with fingerprints by entering them in the database of AFIS. With the help of technical database like CODIS and AFIS law enforcement agencies and officers do have the potential to identify even in cases where no prior suspects existed.
            The DNA samples collected from the crime scene are taken to the laboratory for obtaining bands of the molecule and match them with the sample that has been collected. The technique and method through which these bands are obtained is known as electrophoresis. The process in itself is a separation technique that is normally employed for the separation of biological molecules that vary in their size and mass. A DNA sample when undergoing electrophoresis is first treated with a special group of enzymes known as restriction endo nucleases which cuts the strands of DNA into various fragments of different sizes depending on the different positions of the restriction sites that are present in the molecule where these enzymes act. These different fragments that vary in length, size and mass are then separated by applying an electric field and these different lengths are visualized using a fluorescent dye, the greater the length of the fragment the lower is its electrophoretic mobility and longer is the time taken. Once electrophoresis is complete, these strands are then treated in a number of ways by applying the process of autoradiography using X-ray radiations to obtain visible and distinct bands of the DNA sample that has been collected. (National Institute of Justice)

DNA Evidence and Prosecution
            We come to the most essential part of our discussion which will be dealing with the procedures that are applied by prosecutors to demonstrate DNA evidences in the courtroom in order to convince the jury that the evidences being presented by the prosecution are completely authentic, credible, unfabricated and transparent. The method that is applied for the presentation of these evidences must convince the jury that the prosecutions approach towards the case is much more fact based and scientifically designed therefore the verdict must be decided in their favor.
Some of the basic and fundamental steps that need to be kept in mind are the ways through which DNA evidence is prepared in a way so that it becomes suitable to be presented in court.
In this context it is important for the prosecutor to have adequate knowledge regarding some intrinsic scientific principles and the ways through which the DNA typing operates. In order to develop an understanding of this scientific knowledge, there are numerous sources that are available at the disposal of the prosecutor himself. These sources can include textbooks, scientific journals, synopsis and seminars based on diverse topics of molecular biology and DNA typing, however it is worth mentioning that the use of each source is affected by time constraints. In addition to this it is also important for the prosecutor to evaluate the results of the different forensic evidences that he has collected from laboratory sources in order to develop a full-fledged and concrete evidence based account regarding the case he is prosecuting.
A problem that is normally encountered by prosecutors in that the mixtures of DNA that are provided by multiple parties in relation to a similar case, complicates the evaluation and assessment for the prosecutor in deriving the authentic and scientific meaning of the evidences that has been presented to him.
Nevertheless it is therefore advisable that the samples of DNA information that are obtained from the laboratory must be carefully scrutinized and frequently explained in order to avoid further complications from emerging in subsequent stages of the case.
In order to prepare an effective and enforcing speech for trial testimony in case involving DNA typing, the pretrial conference is considered as a highly helpful component. This conference discusses and sheds light on the various aspects such as in the determination of the precise nature of the evidentiary and the samples that have been used in the process, the procedures that have been applied by the laboratory during testing of the DNA samples obtained from the crime scene, the academic qualifications, expertise and experience of the testifying proficient and the questions that can be raised or voiced by the defendant lawyer during cross-examination process in the courtroom.
Once the preparation of evidences collected from DNA samples is completed in the pretrial conference, the next step involves looking over and studying the ways and procedures through which these evidences can effectively be communicated to the jury and for this a prosecutor normally makes use of two key approaches.
The first technique with the usage and introduction of testimonial, scientific and demonstrative evidences endeavors to educate the jury with the basics of DNA testing. This involves demonstrating the judge with the help of material evidences the ways in which the DNA and the genes are transmitted from the parents to the progeny. Demonstration may include the nature of DNA and the salient features through which it is used and made suitable for typing and fingerprinting purposes.
Apart from this another approach that is considered more suitable is providing the jury only with the information that is relevant to the concerned case sidelining the fundamentals of the processes applied. In this procedure it is however important to establish jury confidence through the qualification and experience of the DNA expert and by the testimony that has been provided by the witness.
Normally, prosecutors using this approach make use of visual display of the autoradiographic (X-ray) results that have been shown by putting Restricted Fragment Length Polymorphism (RFLP) or of the dot blot analysis.
Additionally, autoradiographic data used for the typing techniques used for the Polymerase Chain Reaction (PCR) are also exhibited. With the use of such data presentation techniques specifically with the use of band patterns that help in demonstrating the relationship through which the suspects and guilty are distinguished from each other is considered as the most appealing and impactful scientific evidence that is presented in the courtroom.
Moreover, frequency data related to populations and the ways through which the DNA in a population varies can also be outlined in the argument and evidences being presented in order to establish a much better, effective and concrete approach towards the case.
Frequency figures and statistics most importantly play an important role to serve the purpose of cementing the viewpoint from the prosecutor to provide the trier of fact in order to outline the rarity of the DNA match between known and suspected samples.
The point that the prosecution is trying to prove in the courtroom can be assaulted by the defense lawyer in a number of ways. Firstly, that the DNA analysis and the various kinds of processes related to it are too new and thus their credibility can be questioned.
Other arguments that can be raised by the defense may refer to the conflicting expert that poses a question regarding the reliability of DNA analysis and that the scientific debate surrounding the issue of DNA analysis weakens the trustworthiness of the test itself.
Prosecution experts in order to counter the allegations and objections voiced by the defense need to have fundamental and basic knowledge regarding the process of DNA analysis. In order to prove the point the prosecution will have to at length describe and explain with the help of concrete, credible and authentic evidences about the time that has been spend in making the process as functional as it is today, the contribution of this process in terms of testing outside the criminal justice system, the absence of any scientifically proven data from the defense side and the experimental and practical proves that the prosecution has to prove their argument. (Clark, 1996)
Conclusion
There remains little doubt today about the myriad benefits that the DNA and its subsequent has brought in the fold of science which has not only provided science and society a completely new dimension of viewing and analyzing problems that are encountered, but has also bolstered the innovations in forensic science to unprecedented levels in contemporary scientific mainstream.

References
Clarke W. George 1996 ‘Effective Use of DNA Evidence in Jury Trials’ published in the Practical Prosecutor Magazine 1996, retrieved from:
National Institute of Justice N/A ‘What Every Law Enforcement Officer Must know about DNA’ retrieved from:
Advancing Criminal Justice through DNA Technology ‘History of Forensic DNA Analysis’ retrieved from:
Watson D. James Berry Andrew 2004 ‘DNA: the secret of life’ Arrow Publishers
Sinden R. Richard 1994 ‘DNA Structure and Function’ Gulf Professional Publishing

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