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.
You can browse through the database by selecting a base pairing type from the pull-down menu from Select basepairing edge & sugar orientation type, whose default value is W:WC. Users can select any particular base pair in that type by clicking on that, e.g. A:G W:WC. This gives all details of the base pair, such as its occurrence frequency (810 in the database), interaction energy between the bases, how the base pair was identified in the structures, frequency distribution of the intra-base pair parameters (from X-ray crystal structure data only) and other parameters, such as distances between C1' atoms of the two bases, etc. Mean values (along with standard deviations) of each parameter is also shown. Mean values of the intra-base pair parameters obtained from analysis of the NMR derived structures are also given. You may ask for the context of this base pair in every PDB-ID where this base pair was identified by clicking the Frequency (Total number of Available structures:####)
The selected base pair, between ith and jth residues, often appear in anti-parallel double helical regions, where the next base pair between i+1 and j-1 are also paired. These stacked dinucleotide sequences are shown in Tabular fashio along with their frequenc of observation in the database, mean (and standard deviation, in parenthesis) of stacking overlap between the base pairs in that stack and stacking interaction energy between the two base pairs are also shown.
One can select a stacked base paired dinucleotide sequence from this table, e.g., G:A W:WC::C:G W:WC, which gives details of the stacking orientations between the selected A:G W:WC base pair and a C:G W:WC base pair, which has been observed 227 times in the database. Similar to the base pair cases, you may enquire about context of each of the selected base paired dinucleotides by clicking at the frequency. Several parameters can be analyzed in cases of base paired dinucleotide steps and all of them are shown by respective frequency histograms and mean and standard deviation of each.
In each case, strucure of a best representative of the selected base pair or base paired dinucleotide step is shown using JsMol, from where you can download the example (in mmCif format), measure interesting distances, save image of the same in your desired orientation. Pictorial description of all the parameters, namely buckle, open, propeller, tilt, rise, twist, alpha torsion angle, sugar-pucker, stacking overlap, etc are shown along with frequency distributions of the parameters.
Alternatatively one can use Search... option to obtain same information for a selected base pair. Here one can use presently followed convension of base pair nomenclature or the Leontis-Westhof nomenclature also. As for example, one can type A:G H:ST or AG HST or AG tHS to obtain same result. In order to locate a base paired dinucleotide step, one has to type in the complete information without any white space. Hence, one can get all information of G:C W:WC::C:G W:WC base paired dinuclotide step by searching GCWWCCGWWC.
In Advance Search option one needs to click the desired bases, base pairing edges and Cis or Trans orientations. If some item is not selected all the unselected options are selected by default. In case of Base Pair Step one has to select four bases of the two base pairs, their base pairing edges and orientations.