Secondary structure is the set of interactions between bases, i.e., which parts of strands are bound to each other. In DNA double helix, the two strands of DNA are held together by hydrogen bonds. The nucleotides on one strand base pairs with the nucleotide on the other strand. The secondary structure is responsible for the shape that the nucleic acid assumes. The bases in the DNA are classified as purines and pyrimidines. The purines are adenine and guanine. Purines consist of a double ring structure, a six membered and a five membered ring containing nitrogen. The pyrimidines are cytosine and thymine. It has a single ringed structure, a six membered ring containing nitrogen. A purine base always pairs with a pyrimidine base (guanine (G) pairs with cytosine (C) and adenine (A) pairs with thymine (T) or uracil (U)). DNA's secondary structure is predominantly determined by base-pairing of the two polynucleotide strands wrapped around each other to form a double helix. Although the two strands are aligned by hydrogen bonds in base pairs, the stronger forces holding the two strands together are stacking interactions between the bases. These stacking interactions are stabilized by Van der Waals forces and hydrophobic interactions, and show a large amount of local structural variability.[7] There are also two grooves in the double helix, which are called major groove and minor groove based on their relative size.
The secondary structure of RNA consists of a single polynucleotide. Base pairing in RNA occurs when RNA folds between complementarity regions. Both single- and double-stranded regions are often found in RNA molecules. The antiparallel strands form a helical shape.[3] The four basic elements in the secondary structure of RNA are helices, loops, bulges, and junctions. Stem-loop or hairpin loop is the most common element of RNA secondary structure.[8] Stem-loop is formed when the RNA chains fold back on themselves to form a double helical tract called the stem, the unpaired nucleotides forms single stranded region called the loop.[9] Secondary structure of RNA can be predicted by experimental data on the secondary structure elements, helices, loops and bulges. Bulges and internal loops are formed by separation of the double helical tract on either one strand (bulge) or on both strands (internal loops) by unpaired nucleotides. A tetraloop is a four-base pairs hairpin RNA structure. There are three common families of tetraloop in ribosomal RNA: UNCG, GNRA, and CUUG (N is one of the four nucleotides and R is a purine).UNCG is the most stable tetraloop.[10] Pseudoknot is a RNA secondary structure first identified in turnip yellow mosaic virus.[11] Pseudoknots are formed when nucleotides from the hairpin loop pairs with a single stranded region outside of the hairpin to form a helical segment. H-type fold pseudoknots are best characterized. In H-type fold, nucleotides in the hairpin loop pairs with the bases outside the hairpin stem forming second stem and loop. This causes formation of pseudoknots with two stems and two loops.[12] Pseudoknots are functional elements in RNA structure having diverse function and found in most classes of RNA. DotKnot-PW method is used for comparative pseudoknots prediction. The main points in the DotKnot-PW method is scoring the similarities found in stems, secondary elements and H-type pseudoknots.[13}
