What is a common secondary structure of RNA?

Stem-loop or hairpin loop is the most common element of RNA secondary structure. 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’.

How is RNA structure determined?

Structure is one of our best hints about RNA function, and so high-resolution methods such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are routinely applied to determine RNA three-dimensional (3-D) structures.

What is the purpose of RNA secondary structure prediction?

The secondary structure prediction algorithm predicts the lowest free energy structure, which is the most probable secondary structure. It also predicts low free energy structures, called suboptimal structures, which suggest possible alternative structures (Zuker, 1989).

Does RNA have secondary or tertiary structure?

RNA molecules usually come as single strands but left in their environment they fold themselves in their tertiary structure because of the same hydrogen bonding mechanism. Helices, also known as stems, are formed intra-molecularly .

Which of the following is incorrect about the prediction of RNA secondary structure?

1. Which of the following is incorrect about the prediction of RNA secondary structure? Explanation: The energy of each predicted structure is estimated by the nearest- neighbor rule by summing the negative base-stacking energies for each pair of bases in double-stranded regions.

What causes RNA secondary structure?

In the first step—for example, as the RNA is cooled from a high temperature—base pairs form to produce a secondary structure of stems, mismatches, loops, and bulges. In the second step, the tertiary structure forms with specific loop–loop or loop–bulge interactions or with other long-range RNA–RNA interactions.

Does RNA secondary structure?

The RNA secondary structure is mainly composed of a stem structure formed by complementary pairing of contiguous bases and a cyclic structure formed by non-pairing of bases.

How can you predict the secondary structure of RNA?

The most popular approach for predicting RNA secondary structures is based on thermodynamic models, such as Turner’s nearest-neighbor model3,4, in which a secondary structure is decomposed into several characteristic substructures, called nearest-neighbor loops, such as hairpin loops, internal loops, bulge loops, base- …

Why does RNA form more complex structures than DNA?

Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule.

Which of the following is untrue about 3D PSSM?

9. Which of the following is untrue about 3D-PSSM? Explanation: First, protein structures in a superfamily based on the SCOP classification are superimposed and are used to construct a structural profile by incorporating secondary structures and solvent accessibility information for corresponding residues.

Which of the following is not a form of RNA?

Thymine base is not present in RNA. In RNA, uracil is found in place of thymine.

Which of the following best describes DNA’s secondary structure?

The secondary structure of DNA is best described as A) double antiparallel helical strands. The structure of DNA is a double helix, two parallel strands that are joined in the middle and twist around each other.