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The Nussinov algorithm is a nucleic acid structure prediction algorithm used in computational biology to predict the folding of an RNA molecule that makes use of dynamic programming principles. [1] The algorithm was developed by Ruth Nussinov in the late 1970s.
Wobble base pairs for inosine and guanine. A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules. [1] The four main wobble base pairs are guanine-uracil (G-U), hypoxanthine-uracil (I-U), hypoxanthine-adenine (I-A), and hypoxanthine-cytosine (I-C).
Nucleic acid secondary structure is generally divided into helices (contiguous base pairs), and various kinds of loops (unpaired nucleotides surrounded by helices). Frequently these elements, or combinations of them, are further classified into additional categories including, for example, tetraloops , pseudoknots , and stem-loops .
Each of the base pairs in a typical double-helix DNA comprises a purine and a pyrimidine: either an A paired with a T or a C paired with a G. These purine-pyrimidine pairs, which are called base complements, connect the two strands of the helix and are often compared to the rungs of a ladder. Only pairing purine with pyrimidine ensures a ...
The chemical structure of DNA base-pairs . A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA.
It is, however, not so simple for single stranded folded functional RNA molecules. Several algorithms have been implemented in software tools for the automated detection of base pairs in RNA structures solved by X-ray crystallography, NMR or other methods. Essentially the programs detect hydrogen bonds between two bases, and ensure their (near ...
The genomic RNA of retroviruses is linked non-covalently to the dimer linkage structure (DLS), a non-coding region in the 5' UTR. For the kissing loop interaction to occur, there is a triple interaction that involves a 5'-flanking purine and 2 centralized bases in the complementary strand.
In RNA, adenine-uracil pairings featuring two hydrogen bonds are equal to the adenine-thymine bond of DNA. Base stacking interactions, which align the pi bonds of the bases' aromatic rings in a favorable orientation, also promote helix formation. The stability of the loop also influences the formation of the stem-loop structure.