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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.
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.
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 ...
Alternate hydrogen bonding patterns, such as the wobble base pair and Hoogsteen base pair, also occur—particularly in RNA—giving rise to complex and functional tertiary structures. Importantly, pairing is the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation. Some ...
An unnatural base pair (UBP) is a designed subunit (or nucleobase) of DNA which is created in a laboratory and does not occur in nature. DNA sequences have been described which use newly created nucleobases to form a third base pair, in addition to the two base pairs found in nature, A-T (adenine – thymine) and G-C (guanine – cytosine).
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. [9] Pseudoknot is an RNA secondary structure first identified in turnip yellow mosaic virus. [10] It is minimally ...
1-cyclohexyl-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate, also known as CMCT or CMC, is the most commonly used carbodiimide for RNA structure probing. [29] [30] Similar to DMS, it can be detected by reverse transcription followed by gel electrophoresis or high-throughput sequencing.