The DNA Molecule

What is DNA? What does it consists of? How does it function? These are some of the questions that one might ask when he or she hears the word DNA. To me, DNA is a fascinating molecule, that is universally found in all living organisms starting from the simplest viruses to humans. In fact DNA is the molecule of life, the molecule that makes everyone of us an individual with unique characteristics. But what makes this molecule so special?


What is DNA?

First of all what does DNA stands for? DNA is an abbreviation for the chemical name Deoxyribose Nucleic Acid. DNA is a macromolecule, a polymer made up of individual deoxyribonucleic units. Each nucleotide is made up of a nitrogenous base, a sugar and one or more phosphate groups. The sugar in DNA is deoxyribose which lacks an oxygen atom present in ribose. The nitrogeneous base can be either a purine or a pyrimidine, where the purines in DNA are adenine (A) and guanine (G) and the pyrimidines are thymine (T) and cytosine (C). Purine rings are synthesised from a variety of precursors as glutamine, glycine, aspartate, methylenetetrahydrofolate, N10-formyltetrahydrofolate and carbon dioxide. The synthesis of the pyrimidine ring starts with the formation of carbamoylaspartate from carbamoyl phosphate and aspartate, a reaction catalysed by aspartate transcarbamoylase. 

In 1953, Watson and Crick described the double helical structure of DNA obtained by x-ray diffraction analysis, by which information was obtained about the arrangement and dimensions of the molecule. From these observations it was concluded that the molecule is helical and that the bases of the nucleotides are stacked with their planes separated by 0.34 nanometers (nm). It was also observed that the concentration of adenine was equal to that of thymine while that of cytosine was equal to that of guanine, an observation that suggests base complementarity. Watson and Crick also concluded that the DNA molecule is in fact a double helical molecule with a sugar-phosphate backbone on the outer region and the bases at the central core. The bases of one strand are hydrogen bonded to the bases of the other strand forming purine to pyrimidine base pairing A - T and C - G. 

Figure 1. Complementary Base Pairing showing Hydrogen Bonding

The helix creates two external helical grooves, known as the major and minor grooves both of which are large enough to allow other molecules to get into contact with the inner bases. Naturally occurring DNA molecules usually are right-handed helices. There are a number of possible varieties of DNA structures of which the predominant form is the double stranded B helix. Another alternative DNA structure is the A DNA which has 11 bases per turn instead of 10 and its formation is favored under dehydration conditions. The Z helix is a left handed helix, with 12 bases per turn and having a zig-zag structure. In a very large DNA molecule as found in cells, different conformations can coexist in the same molecule.

Figure 2. Alternative DNA structures: A-DNA, B-DNA and Z-DNA


Other DNA forms exist in viruses where it can be found as single stranded molecules. Single stranded DNA is more dense than double stranded form as a result of its compacted structure. Triplex DNA is a triple stranded DNA helix that is found in regions having repeated stretches of purines alternating with stretches of complementary pyrimidines. Under these circumstances one strand of repeats folds back into the major groove of the preceding repeating unit. These structures are usually found at the ends of chromosomes.

One of the most important features of the DNA molecule is complementary base pairing where an A always pairs up with a T and G with C. This base pairing occurs by the formation of hydrogen bonds. This gives the DNA molecule the capability to store genetic information which can be transmitted from one generation to the next. This feature allows the DNA molecule to be copied exactly during DNA replication. Complementary base pairing is possible because of the way hydrogen bonding is formed between A and T and between G and C. Also the structure of DNA is further stabilised by the arrangement of the nitrogenous bases, that are hydrophobic, in the inner part of the molecule with the hydrophilic sugar-phosphate backbone on the outside.

The two polynucleotide strands of DNA double helix are anti parallel having a free 3'-OH and 5'-P terminus at each end of the helix giving a different orientation to the two strands. The G-C content is the percentage G-C of the total number of bases and is observed to be very high (near 50%) in most higher organisms. In lower organisms such as bacteria this G-C content varies widely.


Denaturation and re-naturation of nucleic acids

Denaturation of DNA occurs when the hydrogen bonding between the two anti-parallel strands are broken and the two strands open up, yielding two single strands of DNA. This is also known as melting of DNA and is usually accomplished either by heat or chemically. Upon melting the viscosity of the DNA decreases and UV absorption at 260 nm increases. DNA strands with higher GC content are more stable because of the three hydrogen bonds between them and thus will require a higher temperature to melt such strands. The melting temperature (Tm) is the temperature at which 50% of the strands are denatured and so there are 50% of the strands that occur as single strands. This process can be reversed and is known as re-naturation (or re-association) where hydrogen bonds between the strands form again. Re-association kinetics showed that in eukaryotes the genome consists of highly repetitive sequences that have lower C0t where C0 is the initial concentration of single stranded DNA in moles per litre of nucleotides and t is the time measured in minutes for re-association. This means that repetitive sequences re-associate before other unique sequences in a mixture of single stranded DNA. So re-association kinetics revealed the complexity of eukaryotic genomes when compared to those of prokaryotes. The time at which half of the single stranded molecules re-associate is known as C0t1/2 and is proportional to the size of the genome, a method that was useful to assess the genome size of viruses and bacteria.


DNA topology

DNA topology refers to supercoiling of DNA in a way that such a large macromolecule is packaged inside cells. To make a simple analogy, DNA supercoiling is similar to when twisting a piece of circular rubber band while holding it with the other hand. This will cause the rubber band to start coiling on itself and so decrease in size and becomes more compact. When DNA is supercoiled and so more compact, the sedimentation velocity increases when compared to a less compact molecule of the same molecular weight. The linking number is equal to the number of complete turns where in a normal Watson-Crick right handed helix it is equal to 20 complete turns (L=20). If the ends of the molecule are sealed then the molecule is said to be in a "relaxed" form (energetically). If the circle is cut open and unturned by 2 turns the linking number will be 18 and this will create a temporary energetically strained molecule which will in turn form two negative supercoils (left handed) in the opposite direction to enhance physical stability. Writhing (W) is equal to the number of super helix turns. In nature, in both prokaryotes and eukaryotes, nicking and unwinding as well as re-sealing of DNA molecules is accomplished by a group of enzymes known as topoisomerases that can be either of type I or II. Topoisomerase type I reduces negative supercoils while topoisomearse type II (gyrase) introduces negative supercoils. In higher organisms topoisomerases might be useful during transcription to unwind DNA from nucleosomes making it more accessible to molecules involved in the process. Negatively super twisted molecules are found as plasmids in bacteria, mitochondrial DNA and in nuclear DNA through association with histones.


Figure 3. DNA supercoiling


Ribonucleic acid (RNA)

The structure of RNA is similar to that of DNA with the following small differences. In RNA the sugar in the backbone of the molecule is ribose instead of deoxyribose and the nucleoside thymine is replaced by uracil. Also most RNA molecules are single stranded and not double stranded, but it can form secondary structures by folding on itself where there is self complementarity. Another important feature of RNA is that most RNA molecules function on their own unlike DNA where genes have to be transcribed and translated into protein, and it is actually the protein product of the gene that functions. This characteristic of RNA molecules supports the hypothesis that DNA was preceded by RNA before the first living cells existed. There are different classes of RNA molecules that have different functions on their own. These include ribosomal RNA (rRNA), messenger RNA (mRNA) and transfer RNA (tRNA) mainly involved in protein synthesis. In the process of protein synthesis gene sequences are first transcribed to mRNA (catalysed by RNA polymerases) since the nucleotides are complementary to DNA with uracil base pairing with adenine (since it replaces thymine). Messenger RNA is then translated into protein with the aid of other RNA molecules such as rRNA and tRNA. Also different classes of RNA molecules are involved in gene regulation such as microRNA (miRNA), small interfering RNA (siRNA) and antisense RNA. RNA genomes that can occur as single stranded or double stranded are often found in different viruses such as the Human Immunodeficiency Virus (HIV).

Figure 4. Predicted RNA secondary structure




Concepts of Genetics, 5th Edition, (1997) Prentice Hall Inc, New Jersey, USA

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