The Structure Of DNA

In the late 19th century, there was a growing curiosity about the field of molecular biology and how things in our body worked at the molecular level. This led to extensive research in the early 20th century by upcoming scientists to know how genes present in our cells helped in the regulation and functioning of the chemical processes that take place in our body.

In 1953, the discovery of the twisted, double helix, ladder-like structure of DNA by James Watson and Francis Crick marked a great milestone in the history of molecular biology. Their discovery let us have an insight into the genetic code and protein synthesis. Watson and Crick knew it from the start that the functioning of the DNA was heavily dependent on the structure it had and so they began discovering the structure of the DNA by carrying out experiments. This meant that they had to take up the arduous task of correlating and immersing themselves completely into various fields of science like genetics, biochemistry, chemistry, physical chemistry and X-ray crystallography. After years of experimentation, studying and gathering knowledge from the discoveries of other scientists as well, Watson and Crick had a structure sufficiently complex and simple enough to be the master molecule.

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They put forth that DNA was a double stranded helical structure which resembled a twisted ladder. On unwinding the two strands ran parallel to each other. Each strand having a polynucleotide sequence with complex nucleotides running along its length. Nucleotides are the building blocks of both RNA and DNA and constitute the genetic material. They also play an important role in cell signalling and to transport energy throughout the cell. The nucleotides consist of three main parts – the sugar group, the phosphate group and any one of the four nitrogen bases i.e. Adenine, Guanine, Cytosine and Thymine. Adenine and Guanine come under the category of Purines while Thymine and Cytosine come under the category of bases called Pyrimidines. Their model was also based on Chargaff’s rule. The rule stated that the concentration of the nitrogenous base Thymine (T) was always equal to the concentration of the nitrogen base Adenine (A) and the concentration of the nitrogen base Guanine (G) was always equal to the concentration of the nitrogen base Cytosine (C). The bases present in the nucleotide of one strand, pair up with the appropriate bases present on the other strand to form a complex called as a “base pair”. The bases in this base pair are linked together by the means of strong hydrogen bonding. The linking always takes place between the bases Adenine and Thymine and the bases Guanine and Cytosine (in case of DNA) and Guanine and Uracil (in the case of RNA).

As mentioned above, there is the presence of sugar in the nucleotide. This sugar is a pentose sugar, which means it is a 5-Carbon sugar. The carbons are numbered sequentially, to help keep track of where the functional groups are attached. The sugar is modified to be a ribose sugar, in the case of RNA, and a deoxyribose sugar, in the case of DNA. The term deoxyribose was coined because the sugar lacks a hydroxyl group and shows only the presence of a hydrogen atom i.e. there is absence of one oxygen atom at the 2’ prime carbon. This difference of one oxygen atom is very essential for enzymes to be able to differentiate between an RNA and a DNA molecule. Although DNA and RNA have similarities, they are built from slightly different sugars and their base substitution is also different. While DNA uses Thymine, RNA uses Uracil. Both Thymine and Uracil bind to Adenine.

Other than the nucleotides and the sugar, there is also the presence of a phosphate group. This phosphate group consists of a central phosphorous atom. One oxygen atom is connected to the phosphorous atom and the 5-Carbon in the sugar. To form chains, like in case of ATP (Adenosine Triphosphate), the phosphate groups link together and form links that look like O-P-O-P-O-P-O, with two additional oxygen atoms attached to the phosphorous atom, one on either side of the atom.

The nitrogen base is attached to the primary or first carbon. The 5th number carbon is attached to the phosphate group. There can be the presence of one, two or even three phosphate groups in a free nucleotide, which are attached in the form of a long or short chain to the 5-Carbon of the sugar. When nucleotides connect to form the genetic material of either DNA or RNA, the phosphate group of one nucleotide attaches to the 3-carbon of the sugar of next nucleotide via a phosphodiester bond. This phosphodiester linkage makes the important sugar-phosphate backbone of the nucleic acid and furthermore adds to the stability of the DNA molecule.

The two strands of DNA consisting of several polynucleotides have their own directionality and run anti-parallel to each other. The phosphodiester bond between the nucleotides between 3’ and 5’ carbons leads to the 5’ and 3’ carbons respectively on both the ends of the strands to be exposed. Hence, the strands are labelled as 3’ strand and 5’ strand. These are also called as the phosphoryl end and the hydroxyl end respectively, by the virtue of the chemical functional group present at the ends of the respective strands. These strands also possess the ability of winding and unwinding according to the need of the cell. One strand has the directionality 5’ to 3’ while the other has the directionality of 3’ to 5’. Hence, they are said to be running anti-parallel to each other with their own different directionalities. This confers them very different biochemical properties and causes them to behave very differently in molecular genetic processes. Thus, it is essential to recognize and distinguish between these two strands for the ease of understanding of all the biochemical and molecular genetic processes they carry out in the body.

The DNA double helix structure also consists of several grooves. The grooves are further classified as major groove and minor groove. These grooves are the consequence of the uneven stacking that causes the phosphodiester backbone to face outward and the nitrogenous bases to face inward. This uneven stacking leads to the creation of the – major and minor grooves. The B-form of DNA (the most common form of DNA) which we know has 10 base pairs per turn, is a very stable structure and the stability of this structure is not only because of the hydrogen bonding between the base pairs but also because of the stacking up of the base pairs in the double helix structure, as there is creation of pi-pi interaction between the aromatic rings of the bases that are stacked next to each other and those who share electron probabilities. In detail, the formation of the major and minor groove is because of the asymmetrical attachment of the backbone sugars through glyosidic bonds. The grooves have similar depth in the B-form DNA but the major groove is considerably wider than the minor groove hence the term “major” groove and “minor” groove. These grooves act as base-pair recognition and binding sites for proteins and hence are of utter importance to the DNA molecule.

All of these structural modifications and specifications are the reason the DNA molecule can carry out and regulate all the biochemical processes that take place in an organism.