Watson and Crick utilised the X-ray diffraction studies by Rosalind Franklin and Maurice H. F. Wilkins to conclude the previously mentioned (Infodump2) double helix structure of DNA.

The main features of the model:

• The structure constitutes two polynucleotide chains.

• These two polynucleotide chains making the right-handed double helix structure are held in an antiparallel orientation (with one strand oriented in 3' to 5' direction and the other oriented in 5' to 3' direction).

• As depicted, the sugar phosphate backbone is positioned outside the molecule with bases being projected inside roughly perpendicular to the direction of helical axis. Hence, the bases are stacked on top of each other. The hydrophobic interaction, van der Waals forces and the electron cloud interaction between the stacked bases are crucial to the stability of the structure.

• The two strands are held together due to the hydrogen bonding between the complementary bases (i.e b/w a base on one strand and its associated base on the other strand). Since individual hydrogen bonds are weak, the stands can be separated easily when required. Additionally, the additive strength of the hydrogen bonds contributes to maintaining thermodynamic stability as well as this bond is responsible for base pairing specificity.

• Width = 2 nm; Distance b/w 2 stacked bases = 0.34 nm; 1 helical turn = 3.4 nm.

• Base pairing specificity: adenine (A) binds to thymine (T) and guanine (G) binds to cytosine (C). As previously mentioned the answer lies in hydrogen bonding. If we try to pair A with C, N1 of adenine (hydrogen bond acceptor) lies opposite to the N3 of cytosine (hydrogen bond acceptor). For the bonding to occur, the water molecule in the middle will have to be stripped off the donor and acceptor groups without a possibility of restoration , thus, this bond will be highly unstable. Further more, the tautomeric forms (amino and keto) of the bases also ensure this specific pairing. This specific base pairing fits the base composition analysis on DNA of several animals by Erwin Chargaff. The study revealed 50% of bases are purines and other half are pyrimidines, in other words A = T and G = C --> Chargaff’s rule. However, the %GC varies between animals.

• As a consequence of base pairing, the nucleotide sequence of the two strands is fixed relative to one another. Hence the two chains are said to be complementary.

• The double helix geometry results in two unequal grooves in the structure, major groove and minor groove. The presence of these grooves enables protein interaction with DNA without having to unwind and disrupt the helical structure.

Alternative conformations of DNA as illustrated above:

1. The A form is a right-handed double helix, with ~11 base pairs per helical turn. This form is observed at low humidity conditions. The major groove is narrow and the minor groove is broad. Overall the length is short but the structure is wide (2.2 nm) in comparison to B form .

2. The B form is most common form of DNA and is often observed at high humidity. Like A, it is a right-handed double helix. One helical turn consists of ~10 bp. The major groove is wide and the minor groove is narrow. In comparison to A, the helix is thinner (2 nm) and longer.

3. The Z form, unlike the other 2 forms, is a left-handed helix with a zig-zag arrangement of the backbone. One helical turn consists of 12 bp. This form is thin (1.8 nm) and elongated. The major groove is not as distinct. This form is very rare and is assumed in presence of high concentrations of positive ions.

• RNA is usually single stranded, however, the molecule is capable of forming double helices.

• RNA strand can fold back on themselves as they have regions of self complementarity as well as non-complementarity segments. This leads to formation of stem-loop structures including a hairpin (like the one illustrated above), a bulge or a simple loop. These structures are more similar to A form than B form of DNA.

• Base pairings in RNA: Adenine-Uracil; Guanine-Cytosine; Guanine-Uracil (wobble base pairing). The extra base pairing enhances the chances of self complementarity.

• These stem-loop structures can further form pseudoknot. (Example: In the hairpin depicted above, the exposed bases in the loop can interact with other complementary regions within the molecule and thus form a larger and a more intricate structure i.e. pseudoknot).

• RNA can also form tertiary structures. This allows them to serve as biological catalysts like proteins. These RNA enzymes are termed as ribozymes. RNase P (a ribozyme) is responsible for the transformation of precursor tRNA to mature tRNA. This enzyme is composed of RNA as well as protein. The RNA component alone is the catalyst.