Nucleic acid structure and properties of DNA

              The genetic information in all living cells is carried in molecules of deoxyribonucleic acid (DNA), which is primarily found in chromosomes. However, DNA is also present in cellular organelles such as mitochondria and chloroplasts. Viruses carry genetic information in either DNA or RNA molecules. When RNA viruses infect cells, the genetic information in RNA is converted to DNA prior to the replication and synthesis of new viral particles. In the case of certain RNA viruses (retroviruses) such as human immunodeficiency virus (HIV), the DNA that is copied from the infecting RNA is permanently integrated into the host chromosomes and the viral genome becomes an integral part of the cell’s genetic information. The structure of DNA was explained by James Watson and Francis Crick in the year 1953. The structure they proposed made it apparent for the first time how genetic information in chemically stored in cells and how it is replicated and transmitted from one generation to the next. The proposed DNA structure also provided insight into the chemical nature of mutations and how they might occur during replication. Scarcely fifty years has passed since that monumental discovery and now we are deciphering the complete sequence of a human genome. This will lead to a chemical understanding of thousands of genetic disorders and the ability to diagnose, prevent, and treat many inherited diseases and cancers.

Components of Nucleic Acids:

A nucleic acid is a polynucleotide that is explained by its three components:
1. A nitrogenous heterocyclic base (either a purine or a pyrimidine) attached to the l'-carbon atom of the sugar by an N-glycosidic bond. In DNA, the purines are adenine (A) and guanine (G) and the pyrimidines are cytosine (C) and thymine (T). The nitrogen bases in RNA are the same except that uracil (U), a pyrimidine, occurs in the place of thymine.
2. A cyclic five-carbon sugar which is ribose in RNA and deoxyribose in DNA. The carbon atoms of the sugar are numbered with a prime to separate them from the carbon atoms in the base in the same nucleotide structure.
3. A phosphate group attached to the 5'-carbon atom of the sugar by a phosphodiester linkage. This phosphate group causes the strong negative charge of both nucleotides and nucleic acids.

            A base linked to a sugar is called a nucleoside; a base linked to a sugar linked to a phosphate is called a nucleotide or a nucleoside phosphate. The nucleotides in nucleic acids are linked to one another by a second phosphodiester bond that combines the 5'-phosphate of one nucleotide to the 3'-OH group of the adjacent nucleotide. This esterified phosphate is known a phosphodiester group.

Adenosine

Guanosine

Cytosine

Thymidine

Base Pairing and Base Composition

The molar content of the four bases in DNA always satisfies the equalities [A] = [T] and [G] = [C] where [ ] denotes molar concentration. These equalities occur because of the base pairing rules in DNA which need that A pair with T and G pair with C in the double-stranded DNA molecule. Because of the base pairing rules it follows that [purines] is equal to [pyrimidines] in all DNA molecules. The overall base composition of DNA differs among organisms. Base composition is shown as the fraction of all bases in DNA that are GC pairs divided by the total number of base pairs, such as ([G] + [C])/[all bases]. This fraction is called the GC content or percent GC. For human beings and other primates, the value of the GC content is nearly 0.5. For lower organisms the value can vary widely; the most extreme variation is found in bacteria where the GC content varies from 0.27 to 0.76 from one genus to another; E. coli DNA contain a GC value of 0.5, which might reflect its close association and evolutionary history with human beings. The higher the GC content of DNA, the more stable is the double stranded helical molecule. This is because GC base pairs possess three hydrogen bonds whereas AT base pairs possess only two.

Base pairing

Tautomerization of Bases:

Inspite of the fact that the bases are chemically very stable, certain hydrogen atoms bound to the bases can experience tautomerization in which they change their locations on the bases. The preferred tautomeric forms of adenine and cytosine are the amino configurations; however, with less likelyhood each can assume the imino configuration. The tautomeric forms of guanine and cytosine are assumed to be the keto configuration. Tautomerization of the bases can happen as the free base and as polynucleotides. If tautomerization of a base ought to occur at the moment of replication of that region of DNA, an incorrect base might be inserted. For instance, the tautomeric form of adenine can be paired with cytosine or the tautomeric form of thymine can be paired with guanine. During subsequent rounds of DNA replication these mismatched base pairs can lead to point mutations in half of the DNA molecules in subsequent cycles of DNA replication and cell divisions. During replication, tautomerization of bases in DNA and ensuing mistakes in base pairing are uncommon, but experiments show that point mutations do arise in this manner and contribute to genetic variation. However, most errors in base pairing that occur during DNA replication are corrected by enzymatic editing or repair functions.

Tautomerization

Methylation of Bases:

After the four bases have been incorporated into DNA, they could be changed by methylation, the addition of methyl groups at various positions. The nitrogen bases that are most regularly methylated are guanine and cytosine. Methylation of cytosine residues influences gene regulation in higher living beings, and about 70% of GC base pairs in mammalian cells are methylated. The pattern of  methylation of cytosine molecules is inherited and is different for each species. However, methylation of DNA is not universal; for example, the DNA in the fruitfly Drosophilia is completely unmethylated. Methylation of DNA is primarily the result of two enzymes, Dam methylase and Dem methylase. Dam methylase transfers a methyl group to an adenine from S-adenosylmethionine contained in any GATC sequence in DNA. Dem methylase acts in a similar fashion on cytosine residues in the sequence CCAGG. One or two cytosines in opposite strands of DNA are subjected to methylation. Methylated parts of DNA are identified by proteins that interact with DNA in processes such as replication, recombination, and gene expression. Methylation of DNA also acts as a crucial function in bacteria. Methylation of specific sequences in bacterial DNA rescues the bacterial DNA from hydrolysis by endogenously synthesized restriction endonucleases. Many human genes are methylated distinctively in maternal and paternal chromosomes at CpG nucleotides, a mechanism that is alluded to as imprinting. Because of genomic imprinting, the expression of genes on maternal and paternal chromosomes varies; the loss of imprinting through mutation or some other mechanism can lead to overexpression of critical genes and severe disease. Two inherited diseases that are the consequence of faulty imprinting are Prader-Willi/Angelmann's syndrome (PWS) and Beckwith-Wiedemann syndrome (BWS).The symptoms of PWS are neonatal hypotonia, hypogonadism, obesity, and short stature; the symptoms of BWS are abdominal wall defect, thickening of long bones, and renal abnormalities. The altered gene in BWS codes for insulin-like growth factor-2 (IGF2) and is located on the short arm of chromosome 15. Generally, IGF2 is inactive in the maternal chromosome and active in the paternal chromosome. In some cases of BWS, the child receives two copies of chromosome 15 from the father, a condition known as disomy. These people have double the normal level of IGF2 and suffer from "overgrowth." Low levels of IGF2 might also occur from disomy and lead to abnormal “undergrowth”. Other inherited diseases and cancers might result from mutations that influence imprinting and normal transmission of chromosomes.

Physical and Chemical Structure of DNA:

The Watson-Crick DNA Structure:

In DNA, two polydeoxynucleotide strands are coiled about one another in a double-helical structure as originally proposed by the Watson-Crick (W-C) model. The important features of the W-C model are as follows:

1. The sugar-phosphate backbones of the double helix follow helical paths at the outer edge of the molecule. The sugar-phosphate strands are oriented in antiparallel directions such that the 5'-phosphate end of one strand is opposite the 3'-OH end of its partner. As a result of the antiparallel orientation, if one reads a sequence of bases in a 5' to 3' direction on one strand, one is reading the complementary bases on the other strand in a 3' to 5' direction. The overall width of the double helix is 2.0 nm.
2. The two strands in the double helix are complementary because of the base pairing rules that dictate A = T and G = C. Because of the base pairing rules, the information in DNA is redundant; knowing the sequence of bases in one strand dictates the sequence of bases in the opposite strand.
3. Each base pair in the double helix lies in a plane that is perpendicular to the axis of the helix. Adjacent pairs of bases in DNA are separated by 0.34 nm and rotated with respect to one another so that 10 base pairs occupy each turn of the helix, which repeats every 3.4 nm.
4. Space filling models of DNA reveal two grooves that run the length of the molecule. The major groove is wide and deep and the minor groove is narrow and shallow. These grooves in DNA provide space for other strands of nucleic acids and also for binding of regulatory proteins.

DNA double helix structure