![]() CONSTRUCTION AND CONTENT Junction scanning algorithm Its unique search capability allows the user to identify RNA junctions based on (among other criteria) inter-helical angles, which makes it an important resource for the design of novel RNA nanostructures from building blocks. It is to our knowledge the only currently available database that also contains extracted RNA kissing loop elements. Our RNAJunction database is very useful for analyzing and understanding the principles of RNA structure formation. We have developed a database called RNAJunction that provides information about RNA junctions, kissing loops, internal loops and bulges in an extracted, annotated and searchable form. ( 17 ) describe a NC-IUBMB recommended nomenclature for nucleic acids junctions. This study showed a bias towards coaxial stacking and the importance of ion interactions. Lilley ( 16 ) reviewed helical junctions of DNA and RNA. They found that three-way junctions that contain two helices that are coaxially stacked can be classified into three main families depending on the relative lengths of the connecting loop regions. Lescoute and Westhof ( 15 ) analyzed RNA structures with respect to three-way junctions. The Metals in RNA (MeRNA) database catalogs RNA structures that are bound to metal ions ( 14 ). The provided junctions correspond to complete PDB structures and not the extracted fragments. Among other things, it provides categories for RNA junctions and DNA junctions. The Nucleic Acid Database (NDB) is a database containing annotated and categorized RNA and DNA structures ( 13 ). For each base pair type, NCIR provides information about sequence and structure contexts in which this base pair type has been found. NCIR is a database of non-canonical interactions found in RNA structures ( 12 ). Its classification scheme is based on a directed acyclic graph, allowing a node to have multiple parents. SCOR is a structural database that contains a classification of internal and hairpin loops ( 9–11 ). ![]() Because RNA structures are only part of the content of the PDB, several databases provide additional information by annotating and classifying RNA structures derived from the PDB. The basic repository for experimentally determined nucleic acid structures is the Protein Data Bank (PDB) ( 8 ). Several databases containing RNA structures exist. Thus, characterizing and classifying RNA junctions can lead to a better understanding of the structural and functional capabilities of RNA. It has been shown, for example, that a four-way junction promotes the functional folded state of the hairpin ribozyme ( 7 ). Helical junctions are important for the structural and catalytic properties of RNAs. A database of such structural elements would significantly speed up the design process. These designed RNA structures highlight the importance of loop–loop motifs and helical junctions. The corners of the assembled RNA complexes are based on known helical junctions ( 4 ) or loop–loop interactions ( 6 ). While there are more published examples for DNA systems ( 1–4 ), RNA has also been used to self-assemble into various shapes like squares and triangles ( 4, 5 ). Nucleic acid systems have proven to be very amenable to the design of nanostructures.
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