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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 ...
There are diverse structures of RNA base quadruplexes. Four consecutive guanine residues can form a quadruplex in RNA by Hoogsteen hydrogen bonds to form a “Hoogsteen ring” (See Figure). [12] G-C and A-U pairs can also form base quadruplex with a combination of Watson-Crick pairing and noncanonical pairing in the minor groove. [17]
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 ...
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.
The stem-loop structure (also often referred to as an "hairpin"), in which a base-paired helix ends in a short unpaired loop, is extremely common and is a building block for larger structural motifs such as cloverleaf structures, which are four-helix junctions such as those found in transfer RNA. Internal loops (a short series of unpaired bases ...
Watson-Crick base pairs in a siRNA. Hydrogen atoms are not shown. Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general, adenine (A), cytosine (C), guanine (G), or uracil (U). Adenine and guanine are purines, and cytosine and uracil are pyrimidines.
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.
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).