RNA is versatile in both its structure and function. Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each. If you are interested in RNA as a building block for nano-scale design or if you are analyzing the properties of specific RNA motifs you should find utility in this site.

The junctions in this database were extracted using a junction scanning algorithm from a number of structures from the Protein Data Bank. Coming from parent structures, both NMR and crystal, these junctions may be under contextual constraints. It is possible that these constraints play a critical role in the junction's conformation and stability.

To search for junctions use the form below. If you have questions that are not answered in the Help pages, Contact us.

For more detailed information, please also consult our recent paper:
Bindewald E., Hayes R., Yingling Y., Kasprzak W. and Shapiro B.A.:
RNAJunction: A Database of RNA Junctions and Kissing Loops For Three-Dimensional Structural Analysis and Nanodesign.
Nucleic Acids Res. 2008 January; 36(Database issue): D392-D397

Browse Database test:

kissing loops bulges/internal loops 3-way junctions
4-way junctions 5-way junctions 6-way junctions
7-way junctions 8-way junctions 9-way junctions

Example Structure:

Junction no. 6532 secondary structure of junction 6532
6-way Classification:HS2HS2HS2HS10HS10HS3
Unpaired bases: 29 Angle(s):3:31:33:36:37:64:108:139:141:144:149:150:154:172:174°


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