DNA

Contents

• Basics
• Mutations
• Sequencing and sequence comparison
• Unknown sample analysis

Basics

DeoxyriboNucleic Acid (DNA) is a macromolecule that contains the genetic instructions used in the development and functioning of all known living organisms. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints, since it contains the instructions needed to construct other components of cells, such as proteins and RNA (ribonucleic acid) molecules. The DNA segments that carry this genetic information are called ("coding") genes, but other DNA sequences ("non-coding") have structural purposes, or are involved in regulating the use of this genetic information.

Within cells, DNA is organized into structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms such as animals, plants, and fungi store their DNA inside the cell nucleus, while in prokaryotes such as bacteria it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA, which helps control its interactions with other proteins and thereby control which genes are transcribed.

Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds. Attached to each sugar is one of four types of molecules called bases (Adenine, cytosine, guanine and thymine: abbreviated as A,C,G and T). It is the sequence of these four bases along the backbone that encodes information and is referred to as the DNA sequence. The DNA polymer is considered to be "double stranded" as it is composed of 2 complementary strands of DNA. Individual bases have a corresponding base in the complementary strand, such that an A is always paired with a T, and a C is always paired with a G in the complementary strand. For this reason, the words "base" and "basepair" are often used interchangeably, but both refer to a single site within the DNA. The information contained in the DNA sequence is "read" on the cellular level using the genetic code, which specifies the sequence of the amino acids within proteins based on the base sequences. The code is read by copying stretches of DNA into RNA, in a process called transcription. Most of these RNA molecules are used as a template to synthesize proteins in a process known as translation. Other RNA molecules are used as structures or in regulatory roles.

Mutations

From time to time mistakes in replication, processing, or external influences (like chemicals and radiation), may cause DNA to "mutate." An 'A' might be replaced by a 'G,' or a 'C' by a 'T,' etc. If this occurs in coding DNA it usually results in changes in the corresponding protein. These changes may alter the protein's function, resulting in different individual characteristics, such as blue eyes or brown eyes. However, these changes to proteins may also be detrimental to the health of a cell, or alter the role of that cell. Many times the cell or organism will simply die because it can't function properly. This can be seen in some cancers, birth defects and diseases of the immune system for example. If the mutation occurs in non-coding DNA, it usually will affect the expression of a protein, or it can be entirely harmless in which case these changes in non-coding DNA can be perpetuated. Since mutations in non-coding DNA do not usually affect the subsequent protein, the organism continues to survive and reproduce, passing along that mutated non-coding gene to it's offspring.

Sequencing and sequence comparison

DNA can be analyzed and studied in many ways, but one of the most common and useful ways now widely used in biotechnology is DNA sequencing. In this laboratory procedure stretches of DNA are copied, using a process known as polymerase chain reaction (PCR), then sequenced to determine the exact order of sequential DNA bases (A's, T's, C's, and G's) in that stretch of DNA. Variations on this technique and it's related applications are commonly referred to as DNA fingerprinting, DNA typing, DNA profiling, or simply DNA testing. Genome projects, like the human genome project, employ this technique on a massive scale to completeley sequence all the bases within a genome, like the 3 billion for humans, to determine the order of all the bases within that genome.

When we compare the DNA of different species, we generally compare the non-coding DNA sequences. One could use coding DNA, but because coding DNA shows few mutations, due to the possible harmful effects of those mutations, it shows little variation and often coding sequences from one organism are very similar to those of a very unrelated organism. Humans have many coding genes identical to those in bacteria because we use many of the same cellular processes. However, the non-coding DNA in humans usually looks very different from a bacteria’s non-coding DNA. Therefore, as humans are more closely related to dogs than bacteria non-coding human DNA will be more similar to a dog than a bacterium. Likewise, human non-coding DNA will be a closer match to chimpanzee DNA than dog DNA. DNA found in mitochondria, a cellular organelle that provides most of the cell's energy, is usually examined for phylogenetic sequence analysis because it is more abundant in each cell than nuclear DNA, and it typically accumulates mutations more rapidly than nuclear DNA. As such it can be used to identify genetic relationships of individuals and even genetic relationships of different species.

Unknown sample analysis

Like the example above, the DNA of an unknown organism can be compared to the DNA of most other known species. After decades work, DNA sequences of coding and non-coding genes in many species are known and published and stored in various databases including well organized electronic ones (like GenBank) that can be easily searched for comparison. Therefore, a DNA sequence generated from an unknown sample can be compared to the thousands of previously determined DNA sequences. This type of comparison should reveal both if the sequence is indeed unique, and also what known sequences the unknown sample is most closely related to, as it will contain the fewest number of base differences.

Unlike hair, or footprints, or vague photos or film, DNA evidence is unambiguous. One cannot manipulate, fake, or hoax the DNA of an organisim being investigated (short of complex bioengineering laboratory procedures). It is not a result subject to interpretation or opinion. The bases in a sequence are in a specific pattern that anyone can read clearly. If the original sample is of sufficient quanity and quality, a DNA sequence result is also easily repeatable and verifiable. Therefore, two independent researchers should be able to sequence the same gene from different individuals of the same organism and obtain the exact same sequence or a nearly identical one, accounting for rare individual variations depending on the region of DNA sequenced.