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Figure 3: Cis and Trans Orientations of the glycosidic bond in RNA base pairs. Besides the three edges of interaction, base pairs can also vary in their cis/trans forms. The cis and trans structures depend on the orientation of the ribose sugar as opposed to the hydrogen bond interaction. These various orientations are shown in Figure 3.
The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
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 ...
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.
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 .
Similarly, the simple-ring structure of cytosine, uracil, and thymine is derived of pyrimidine, so those three bases are called the pyrimidine bases. [ 6 ] 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.
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]
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).
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