RNAJunction Database - FAQ

Frequently Asked Questions

What is an RNA junction?

For the purposes of this database we have considered internal loops, bulges, kissing loops, and junctions to the 9th order (9-way.) Fig. 1 shows one of the 2,337 three-way junctions (3WJ) identified by JunctionScanner. A junction or branchpoint in RNA is defined, by the International Union of Biochemistry and Molecular Biology, as per Lilley et al. 1995, as "the point of connection between a number of different helical segments."

Fig. 1

What are kissing loops and bulges/internal loops?

A kissing loop is an interaction (base-pairing) between two single-stranded portions of bases that pair with each other instead of the opposite strands in their respective helices. An internal loop is a small segment of unpaired bases in a longer paired helix. Bulges are regions in which a strand of a helix has extra inserted bases with no free nucleotides in the opposite strand.

How many junctions have been found?

Our group has documented and made available 13127 junction and kissing-loop structures.

How can I link to a particular junction?

n is the junction id which corresponds to the junction you are looking for.

Who created RNAJunction?

The web site and database were implemented by Bob Hayes, a student in Bruce Shapiro's group, RNA Biology Lab, National Cancer Institute, NIH. The junction data was extracted from the available RNA structures in the PDB database by Eckart Bindewald using a program he developed for that purpose. Energy minimizations on all the junctions were performed by Wojciech K. Kasprzak. Both raw and energy minimized junction files (PDB) are available for downloading.

Valid XHTML 1.0 Transitional