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Considering the immense importance of the non-canonical base pairs in RNA structure, folding and functions, researchers from multiple domains – biology, chemistry, physics, mathematics, computer science, etc., have joined in the effort to understand their structure, dynamics, function and their consequences.
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]
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.
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 ...
A stem-loop occurs when two regions of the same nucleic acid strand, usually complementary in nucleotide sequence, base-pair to form a double helix that ends in a loop of unpaired nucleotides. Stem-loops are most commonly found in RNA, and are a key building block of many RNA secondary structures.
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).
Chemical structures for Watson–Crick and Hoogsteen A•T and G•C+ base pairs. The Hoogsteen geometry can be achieved by purine rotation around the glycosidic bond (χ) and base-flipping (θ), affecting simultaneously C8 and C1 ′ (yellow). [1] A Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A
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).