Base pairs with unusual geometries and the interactions between mismatched bases are not explicitly depicted in EteRNA.
Base pairs can be considered the "glue" that holds together a folded RNA. Breaking a base pair that has already formed requires the addition of energy to the RNA.
Base pairing results from a combination of hydrogen bonding and hydrophobic stacking interactions. These interactions are only favorable with certain combinations of bases in specific orientations.
Base pairs vary in strength. The GC pair is stronger than AU or GU pairs due to the presence of an additional hydrogen bond and stronger stacking interactions. Additionally, the energy of a base pair can be altered by exchanging the positions of two paired bases. A GC pair with guanine in the 5' direction of cytosine will not make the same energy contribution as a CG pair with guanine in the 3' direction of cytosine.
Watson-Crick Base Pairs
The AU pair and GC pair are known as Watson-Crick base pairs. These are the most commonly encountered type of base pairs in double-stranded regions of RNA. The geometry of these two pairs in double-stranded RNA is nearly identical.
Watson-Crick Pairs in EteRNA
The GC pair is stronger than the AU pair by up to 2 kcal/mol, and it is more stabilizing when it appears as a closing base pair.
- Main Article: Translation
Wobble pairs are non-Watson-Crick pairs involving bases at the final "wobble" position of the codon-anticodon pair. The ability to form these Jelli Belli :)
In Watson-Crick base pairs, hydrogen bonding between bases involves a specific region of each nucleotide. Nucleotides contain many hydrogen bond donors and acceptors outside of this region that can also participate in base-pairing. Hydrogen bonding between two bases can involve any combination of three general regions, or edges.
Glycosidic Bond Orientation
A glycosidic bond joins the sugar, ribose, and the base in a nucleotide. The glycosidic bonds of the two bases in a base pair can be oriented in the same (cis) or opposing (trans) directions.
Tautomerization alters the arrangement of hydrogen bond donors and acceptors in a base and can allow the formation of additional hydrogen bonds.
Certain noncanonical pairs have common names. For example, a "sheared GA pair" involves hydrogen bonding between the Hoogsteen and Sugar edges of guanine and adenine with a trans- orientation of the glycosidic bond.