RNA structures can horbour a number of structural motifs unlike double helical DNA strands. This variety of motifs are catered through the possibility of non-canonical pairing among bases. Structural complexity and functional diversity of these heterogeneous motifs of noncoding RNA get stabilized primarily by Hydrogen bonding and stacking interactions. Structural exploration of canonical and non-canonical pairs with respect to IUPAC guided three rotational parameters and three translational parameters for base pair and base pair steps along with torsion angle and pseudo torsion angle and recently quantified overlap parameters provides a complete overview of base pairs and base pair steps.
Base Pair DataBase (BPDB) is collection of all possible base pairs considering both canonical as well as non-canonical ones in available RNA crystal structures. Explorarion of specific functionalities and model building for both canonical and non-canonical pairs with the help of RNAHelix (both stand alone and server) are some the key features worth mentioning.
Representative Short Forms for Bases:
A ≡ Ade ≡ Adenine
G ≡ Gua ≡ Guanine
C ≡ Cyt ≡ Cytosine
U ≡ Ura ≡ Uracil
Representative Short Forms for Pairing Edge:
W ≡ Watson-Crick Edge
w ≡ Watson-Crick Edge having C-H..O, C-H..N type of hydrogen bonds
P ≡ Protonation in Watson-Crick edge
H ≡ Hoogsteen Edge
h ≡ Hoogsteen Edge having C-H..O, C-H..N type of hydrogen bonds
S ≡ Sugar Edge
s ≡ Sugar Edge having C-H..O, C-H..N type of hydrogen bonds
z ≡ Protonation in Sugar edge
Representative Short Forms for Glycosidic Bond Orientation:
C ≡ Cis
T ≡ Trans
Hydrogens were added by uding Hbuild option of charmm
Interaction Energy calculation is being done using ωB97X-D functional and cc-pvDZ basis set. The schematic diagram on the right shows the Interaction Energy (EInt) calculation strategy used over here.