Different type of possible base pairs between nucleotides are tabulated

Non-canonical RNA Base Pair Database

- This database provides information about different types of possible basepairs occuring between the nucleotides of RNA. The number of geometries possible between any two base edges are hyperlinked. The basepairs are detected by BPFIND with atleast two hydrogen bonds between the constituents bases from a non-redundant set of structures determined by X-ray crystallography.

-The best structures have been geometry optimized by DFT method. Certain basepairs which occur very rarely, some with very low frequency also are modelled using RNAHelix software prior to geometry optimization. The latest developments in this line can be found at RNA Basepair Database and RNABP COGEST.

	Ade W	Ade H	Ade S	GuaW	Gua H	Gua S	Cyt W	Cyt H	Cyt S	Ura W	Ura H	Ura S
Ade W	two	two	three	two	one	three	four		two	two	two	two
Ade H		two	two	two		one	two		two	two	two	two
Ade S			two	two	two	three	two	two	one	two	two	one
Gua W				one	two	two	three		two	two	one	two
Gua H					one	three	two	two	one	two	one
Gua S						two	four		one	two	one	one
Cyt W							three	two	one	four	one	one
Cyt H									two			two
Cyt S										two	one
Ura W										three	two	two
Ura H											one	one
Ura S

The interaction energy associated with the basepairs are also calculated, which gives us information about the stability of the basepairs. The strucural parametrs which defines the dynamics of the basepairs are calculated by NUPARM. NUPARM-server can also be used. The basepair parametrs are calculated and tabulated for each of the basepairs. The three rotational parametrs buckle, open angle, propeller are given in degree, while the three translational parameters are given in angstrom.

Swati Panigrahi, Rahul Pal and Dhananjay Bhattacharyya