RNA internal loops

Disney MD, Childs-Disney JL. Using selection to identify and chemical microarray to study the RNA internal loops recognized by 6 -N-acylated kanamycin A. ChemBioChem. 2007 8 649-656. 

Small molecule binding to RNA internal loops has been studied in both biological systems and SELEX evolved RNA aptamers prepared in vitro. Examples include the A-site decoding region of 16S ribosomal RNA which is a binding site for... 

Figure 1. Definition of RNA Internal Loops. The cylindrical regions denote Watson-Crick base paired helices.

Although the role of RNA internal loops in the formation of RNA tertiary structure is only beginning to be understood, the crystal structure of the P4-P6 domain of the group I intron provides us with an instance of an internal loop which causes an approximately 180° bend between the two long helices which make up the three-dimensional structure and another internal loop which clamps down the two extended helices parallel to each other by forming a tertiary interaction with a tetraloop at the end of the other helbc (5)(7). The role of internal loops in stabilization of intermolecular RNA-RNA complexes has also been studied in several systems as discussed below. 

Internal Loops in RNA Oligomer Crystals. The first crystal structure of an RNA internal loop was solved in 1991(8). The dodecamer rGGACUUCGGUCC (internal loop underlined) forms a duplex in the crystal with an internal loop of consecutive U-G, U-C, C-U and G-U mismatches as shown in Figure 2. The chains of the double helix show two-fold symmetry in the crystal, thus the U-G and U-C pairs are identical to the C-U and G-U pairs. As can be seen, the internal loop generally continues the double helices which surround it by formation of non-Watson-Crick base pairs. The major groove of the A-form helix is opened with respect to a canonical RNA helix. 

Chen, G., Turner, D. H. (2006). Consecutive GA pairs stabilize medium-size RNA internal loops. Biochemistry, 45, 4025. 

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