Nucleic Acids are macromolecular structures which store and express all the information necessary for building and maintaining life.
DNA (DeoxyriboNucleic Acid) is considered as the repository of the genetic information.
RNAs (RiboNucleic Acids) may be regarded as vectors and translators of the information.

From a chemical point of view, Nucleic Acids are giant linear condensation polymers of Nucleotide sub-units.

A Nucleotide consists of :

• a nitrogenous base: purine (Adenine (A) or Guanine (G)) or pyrimidine (Cytosine (C) or Thymine (T) (or Uracil (U)in RNA)).
• a sugar : Deoxyribose (DNA) or Ribose (RNA).
  
• a phosphate group

A sugar and a base form a Nucleoside.
A Nucleotide is a phosphorylated nucleoside.
Inter-nucleotide linkages are formed by a phosphodiester bond between a 5'-phosphate group and the 3'-hydroxyl group of the next nucleotide sugar.

The nucleotide sequence encodes the informations required for constructing proteins.

• In 1860, F. Meischer a Swiss physician isolated a precipitate substance obtained by treatment of white blood cells nuclei, with alkaline solution. The chemical analysis has showed that this precipitate contained Carbon, Nitrogen, Hydrogen, Oxygen and Phosphorus. Misescher called this substance Nuclein.

• In 1930 A. Kossel and P. Levene proved that Nuclein was a deoxyribonucleic acid.

• In the late 1940's, E. Chargaff discovered the "equimolarity" of bases ([A]=[T], [G]=[C]) and established the coefficient of specificity ((G+C)/(A+T)), which characterise each DNA molecule.

• In 1952, Hershey & Chase demonstrated that DNA molecules are the universal support of heridity.

• In 1953 J. Watson & S. Crick determined the double helix structure of DNA, owing to the important Xray diffraction works made by R. Franklin.

• In 1962 Watson, Crick & M. Wilkins were awarded the Nobel Prize for their discovery.

DeoxyriboNucleic Acid

The Genome is the complete set of instructions to create and maintain an organism alive. DNA molecules are support for the Genome of all living organisms.

The DNA Molecule consist of two unbranched polynucleotides chains (strands) held together in an antiparallel manner by hydrogen bonds formed between specific pairs of bases [Adenine-Thymine] [Guanosine-Cytosine]. Thus the bases sequence (code) in one strands determines the code of the other strands (complementarity).

The joined anti-parallel strands are twisted about each other in the shape of a right-handed double helix. Indeed DNA is often depicted as a twisted ladder in which rungs are bases pairing and sides are deoxyribose-phosphate chains.

The double helix structure is mainly stabilized by hydrogen bonds between bases pairs. Since the hydrophobic bases are stacked inside and the hydrophilic ribose-phosphate chains are on the outside, Van der Waals forces and hydrophobic interactions are also deeply involved in the stabilization of the double helix.

The N-glycosic bonds (sugar-base) are not directly opposite one strand another, therefore two grooves of different width appear between ribose-phosphate chains on the surface of the molecule. In this major or minor grooves, the bases are exposed to solvent and to other molecules. By this way, some chemical and biochemical substances may have interactions with specific bases without disrupting the double helix structure.

There are three natural forms of DNA (A, B and Z). The origin of these different forms are related to the conformation of the sugar (C2'-endo/ C3'-endo) and the orientation of the base relative to the sugar (syn/anti).

Thus depending on base composition and physical conditions (Hydration/Salt-Content), DNA can assume several different conformations (A, B, Z).

Each conformation possesses specific parameters: diameter of the helix, number of bases per tour and distance between plan of bases.

• The B-form is the common natural form, prevailing under physiological conditions of low ionic strength and high degree of hydration. B-DNA arranges 10 nucleotides per helix tour, all of conformation C2'-endo/anti . The plane of the bases is nearly perpendicular to the helix axis and the helix surface exhibits two prominent grooves (major and minor).

• The Z-form (Zigzag chain) is observed in DNA G-C rich local region. Z-DNA is longer, thinner and possess an unusual left-handed helix (of 12 bases pairs/tour) with a single narrow deep groove. These Zigzag form mainly results from the alternation of purines (C3'-endo/syn) and pyrimidines (C2'-endo/anti).

• The A-form is sometimes found in some parts of natural DNA in presence of high concentration of cations or at a lower degree of hydration (<65%). A-DNA possess 11 nucleotides per tour (all C3'-endo/anti) and two grooves (a narrow deep major and a wide shallow minor).

• The C-form and D-form are unusual subclasses of B-type. C-DNA is sometimes observed under 45% of hydration while D-DNA is only found in artificial DNA.

The changes in the shape of DNA can affect its binding with proteins and may be involved in some regulation process during replication or transcription.

In Prokaryotic cells (cells without nucleus), the two ends of the DNA molecule are joined to form a circular DNA. The circular DNA is coiled into a super helix and often organized in a compact structure containing various proteins and RNAs, named Nucleoid,

In Eukariotic cells, the DNA is packaged in Chromatin within the nucleus. The structure of chromatin is determined and stabilized through the interaction of the DNA with specific bindings proteins.

Nucleosomes are the fundamental structural packing units of chromatin.
A nucleosome is a complex of DNA tightly wrapped around basic proteins called Histones. The nucleosome core consist of two tetrameric molecules, each having four histone-subunits (H2A, H2B, H3 and H4). The DNA helix coils twice around the histone octamer. It is bound to the nucleosome core through electrostatic interactions between the negatively charged phosphate groups in nucleotides and the positively charged basic amino acids in histones.

An external ninth histone (H1 linker histone) is added which holds the nucleosome structure together. A nucleosome plus one H1-histone is sometimes termed a chromatosome.

Nucleosomes are separated one another by a linker segments of 20-200 nucleotides pairs. This gives unfolded chromatin a "beads-on-a-string" appearance.

With the aid of histones H1, nucleosomes may be packed together and wound into a regular coil called solenoid. A solenoid contains six to eight nucleosomes per turn and forms the 30nm nucleoprotein fibers.

Packaging DNA in nucleosomes and then in solenoid reduce its length by a factor of about 50.

Between cell divisions (Interphase), chromatin exist as a tangle of fibers of 10-30 nm (10^-9m) diameter and 0.25-2 mm length. The unfolded (beads-on-a-string) regions are referred to as euchromatin and the more condensed ones as heterochromatin.

Just before a cell division (Mitosis) the chromatin condense into metaphasis chromosomes. During this condensation the DNA packaging factor increase dramatically from 50 to about 7000. Actually, high order chromatin arrangement is not clearly understood. However, it is generally admitted that nucleoprotein chromatin fibers are folded and organized with specific non-histone proteins, into subdomains of coiled loops. These subdomains are supposed to be wrapped around other specialized proteins to form a chromosome.

A Chromosome is made of two identical, symmetrical DNA molecules called chromatids. The chromatids are joined by a centromere which attach them to the mitotic spindle. Thus, each chromosome contains 2 chromatids, 1 centromere, 4 telomeres (ends of DNA molecules) and many replication origins (ARS :Autonomously Replicating Sequences).

Diploid organisms such as mammals contains two sets of chromosomes. Thus the human cells contains 46 chromosomes (23 pairs), one set inherited from each parent. There are 24 different chromosomes, 22 autosomes and two possible sex chromosomes which define the sex of the holder: X for female (XX), Y for male (XY).

Genes are specific sequences of nucleotides, encoding information required for constructing proteins, the main structural and functional components of cells. Genes are fundamental physical and functional subunits of heredity.

Genome is made of three different types of DNA :
Single Copy DNA consist of genes, found in only one or few places in the genome (75% of genome). It also includes multiple copy genes such as those coding for rRNA or Histones which exist as large clusters of multiple copies (50-10000 copies).
Repetitive dispersed DNA fractions are characteristic short sequences (6-10 np) repeated 100000 - 1,000,000 times in disparate places throughout the genome (15% of genome).
Satellite DNA (10% of genome) is made of highly repetitive sequences, basically confined to the chromosomes centromere and telomeres.

The human genome is estimated to comprise about 3 billions nucleotide pairs and at least 100000 genes. However it seems that there is no systematic correlation between complexity of an organism and the number of nucleotide pairs (np) per haploid genome. Some plants and amphibian organisms have total DNA amount of about 100 billions np (30 times more than human).

Actually the genome of higher eukaryotes seems to contain a large excess of DNA. In mammals, only about 10% of the genome is known to be expressed in protein encoding or in regulation processing. This excess of DNA is supposed to serve as hiding package, preventing genes from accidental mutations.

Size of genes vary widely in length, from some hundreds to several thousands nucleotides pairs. However, even in longer genes only a small part of the sequence is used to encode informations. The coding regions are named exons and the non-coding interrupting sequences are called introns.
The presence of introns in prokaryotic genes is extremely rare. Generally the more complex and recently evolved the organism, the more numerous and larger the introns.

Some specific DNA regions are dedicated to the control of genes expression. These regulatory sequences are often located at the beginning of the gene (5'side), at its end (3'side) but also sometimes in introns or in exons.

Each time a cell divides into two daughter cells, all the DNA molecule must be duplicated. Duplication of an old DNA molecule into two new DNA molecules is called Replication.

During replication, the DNA helix is unraveled and its two strands are separated. An area known as the replication bubble forms and progresses along the molecule in both direction. Then each DNA strand serves as a template for the synthesis of a new complementary strand.

Each daughter DNA molecule is an exact copy of its parent molecule, consisting of one old and one new DNA strand. Thus the replication is semi-conservative

In humans, the replication occurs at a rate of about 50 nucleotides per second, in prokaryotes this rate may reach 500 nucleotides/second. However eukaryotes have multiple replication bubbles on the same parent DNA, while prokaryotes open a single bubble per DNA molecule.

Since the DNA strands are antiparallel, and replication proceed only in the 5' to 3' direction, one strand named the leading strand forms a continuous copy, while the other named lagging strand forms discontinuous short DNA strings called Okazaki fragments.

Due to the high level of efficiency and fidelity required to ensure the integrity of the genetic flow, the replication is a very complex process wich involves multiple enzymatic activities.

The major activity is taken on by a group of enzymes termed DNA polymerases. The DNA polymerases recruit free nucleotides and match them by base pairing with the complementary nucleotides of the parent strand.
In prokaryotes there are two main DNA polymerases : pol I and pol III.
Though, the polymerase activity of eukariotic cells is a little more complex than those of prokaryotes, there is an equivalent of prokaryote pol III named pol-a and one of pol I named pol-b.

The DNA pol III (or pola) exhibits outstanding proofreading capabilities, wich prevent it to initiate a polynucleotide strand synthesis. Therefore it requires a primer, a short piece of RNA (RNA primer) that it can recognise and elongate.

In order for DNA polymerases to access free unraveled DNA parent strands and start replication, some accessory proteins are involved in the many steps associated with the synthesis and the unwinding -rewinding of the DNA helix. The main accessory proteins are the topoisomerase, the helicase, the SSB protein and the primase.

• The topoisomerases introduce negative supercoils and relieve strains in the double helix at either end of the bubble.

• The helicase unwinds and unzips the DNA helix by breaking the Hydrogen bonds between the base pairs, thus allowing the two strands to separate.

• The SSB proteins (Single Strands Binding) stabilize the single strands thus preventing them to zip back together and to form hairpin loops.

• The primase (RNA polymerase) added to other proteins (forming a Primeosome) makes short pieces of RNA (RNA primers) that are recognised by DNA polymerase III to initiate replication.

• Following the DNA pol III, the DNA pol I removes the RNA primers, and fills in with DNA. Finally, the DNA ligases repair the gaps between DNA Okazaki fragments.

The combination of DNA polymerases with some of the accessory proteins yields an activity identified as DNA polymerase holoenzyme.
The entire activity located in the replication fork is called a Replisome.