DNA

DNA (deoxyribonucleic acid) is one of two nucleic acids that are a principal aspect of biology, and fundamental to the existence of life as we know it. In vivo, DNA is a macromolecule composed of two oppositely oriented, complementary strands of polymerized nucleotides, joined together by hydrogen bonding between each paired nucleotide. Phosphodiester bonds provide the covalent linkages that allow polymerization of nucleotides into a unique sequence. The sequence is determined by occupation of each base pair by two of four distinct residues, paired in a very specific manner. The sequence is read from the 5' ("five prime") phosphate of the residue at one end to the 3' ("three prime") hydroxyl of the residue at the opposite end of the polymer, hence in the 5' to 3' direction. Because DNA is composed of two such stretches of sequence paired by hydrogen bonding, the opposite orientation of the complementary strands makes it so each end of the macromolecule has both an exposed 5' dibasic phosphate and 3' hydroxyl on two separate deoxyribose rings (the distinct ends of the two polymers), brought into proximity with each other by the hydrogen bonding between the purines and pyrimidines attached to the deoxyribose rings:

5'-(PO42-)(OH)-3' 3'-(OH)(PO42-)-5'

Architecture
Because a person's DNA from one cell (with an average diameter of 0.00001 meters), is on the order of 1 meter in length when stretched out and laid end-to-end, it is naturally arranged within the cell's nucleus into extremely tight and well-organized "bundles" of coiled strands wrapped around proteins.

Double-Helix
The DNA double helix is probably the best known aspect of DNA architecture, and has been represented numerous times in various manners since its discovery by Rosalind Franklin in 1953. The double helix results from the base-pairing between two complementary DNA molecules. Because of the shape of the DNA moecules themselves, and because of the orientations of the hydrogen bonds between them, the DNA macromolecule adopts a double-helical structure in order to minimize steric and thermodynamic strain.

The double helix is created by "wrapping" or "coiling" each DNA molecule around the other, much as the two snakes in a caduceus (but think of one snake oriented in the opposite direction of the other, i.e. head-to-tail). This architecture produces a highly stable (up to 94°C) structure that is fortified by the specific pairing between the nucleotide bases engaging in hydrogen bonding. This structure also makes it so each DNA molecule's backbone (a chain of deoxyribose rings covalently attached to each other by phosphodiester bonds) is oriented away from the hydrogen bonding center, toward the periphery, creating a macromolecule that carries an overall negative charge, due to the free valence electron on the exposed (unbound) oxygen of each phosphodiester bond.

Nucleosomes
The nucleosome is the basic unit of the higher order architecture of DNA within a eukaryotic cell, and provides a scaffold onto which DNA is coiled in order to control its transcription and constrain it within the cell's nucleus. The nucleosome is composed of a strand of DNA wrapped in a very specific manner around histones, which are globular proteins that provide anchoring points for the DNA molecule. The anchoring points are the N-termini (also known as "tails") of the histones, which protrude from the core histone octamer, and physically interact with the negatively charged backbone of the DNA molecule. Depending on the covalent modifications on certain residues within the histone tails, the DNA will bind more or less tightly to the histone octamer.

Each nucleosome particle is composed of a histone octamer surrounded by 127 base pairs of DNA wrapped twice around the octamer. This fundamental unit is repeated along the DNA strand from one end to the other. This is the basis of the "beads-on-a-string" idea of DNA architecture, with the "beads" representing the individual nucleosome particles, and the "string" representing the DNA macromolecule.

Chromatin
Chromatin is composed of nucleosomes coiled tightly onto themselves to form a higher-order structure called the 10nm coil, which itself is coiled into an even higher-order structure, the 30nm coil. The 30nm coil is then packaged into what we know as chromosomes, which are visible under a microscope during karyokinesis.

Chromatin is a collective term often used to describe the higher-order packaging of DNA. This term is also used to distinguish between "naked" (in vitro) DNA and DNA that is packaged in vivo within a eukaryotic cell, and under tight transcriptional control. This is particularly relevant given that regulation of DNA transcription is heavily controlled by the modifications on histone proteins (see epigenetics), making it not only an architectural platform, but a functional one as well.

Replication
DNA replication has evolved over millions of years to enact the very same process throughout time, namely the creation of an exact copy of a cell's DNA before it undergoes division. This process is essential to any organism's survival, and is a crucial component of both mitosis and meiosis.

Mechanism
DNA is replicated by an enzyme known as DNA polymerase (DNA Pol). This enzyme is actually composed of distinct subunits that must all be in place for replication to occur. This complex physically binds to the DNA macromolecule and "melts" the hydrogen bonds between purines and pyrimidines, effectively unwinding the DNA so that each individual strand is exposed. From here, the enzyme complex uses one of the strands as a template for creating a new DNA molecule, faithfully preserving the sequence.

Regulation
The replication of DNA only occurs at very specific points within the cell cycle, and its dysregulation can be extremely detrimental to an organism (see oncogenesis). Because a cell must replicate its DNA in order to pass it on to daughter cells during division, highly regulated checkpoints exist within the cell cycle to ensure its proper timing. Furthermore, because chromatin is scattered throughout the nucleus prior to replication, there also exist finely tuned mechanisms for correctly positioning DNA within the nucleus before, during, and after cell division.

Transcription
Transcription of DNA is the process of transferring the information contained in the DNA molecule (the sequence) to an RNA molecule, which is then either used to dictate protein synthesis or becomes a component of complexes that mediate various functions in transcriptional regulation. Because DNA is copied nucleotide-for-nucleotide into RNA, the name transcription is used to indicate creation of an identical copy of the original template, using a slightly altered set of nucleotides.

Mechanism
DNA is transcribed by an enzyme known as RNA polymerase (RNA Pol), which binds to the DNA macromolecule itself, with the assistance of several adapter proteins, forming what is termed a holoenzyme. This holoenzyme, once "primed" by additional covalent modifications, begins to unravel the two DNA molecules (much in the same way as DNA Pol), and uses one strand as a template off of which to create a new RNA molecule containing exactly the same sequence contained in the DNA template.

Regulation
DNA is contained in the cell's nucleus, where it is segregated according to its transcriptional state. Whereas transcriptionally silent DNA (heterochromatin) is typically physically constrained to the periphery of the nucleus, transcriptionally active DNA (euchromatin) is normally situated toward the center of the nucleus. Furthermore, heterochromatic DNA will often be bound very tightly to the nuclesome, an effect mediated by factors such as histone deacetylases (HDACs), which modify chromatin architecture by removing negatively charged acetyl groups from the histone tails, allowing tighter coiling of the negatively charged DNA around the histones. Conversely, euchromatic DNA is normally more loosely bound to the nucleosome, an effect mediated by factors such as histone acetyl transferases, which attach negatively charged acetyl groups to histone tails in order to repel the negatively charged DNA.