Structural Features and Thermodynamics of the J4/5 Loop from the Candida albicans and Candida dubliniensis Group I Introns^,

Abstract

The J4/5 loop of group I introns has tertiary interactions with the P1 helix that position the P1 substrate for the self-splicing reaction. The J4/5 loop of Candida albicans and Candida dubliniensis, 5'GAAGG3'/3'UAAUU5', potentially contains two A.A pairs flanked by one G.U pair on one side and two G.U pairs on the other side. Results from optical melting, nuclear magnetic resonance spectroscopy, and functional group substitution experiments with a mimic of the C. albicans and C. dubliniensis J4/5 loop are consistent with the adenosines forming tandem sheared A.A pairs with a cross-strand stack and only the G.U pair not adjacent to an A.A pair forming a static wobble G.U pair. The two G.U pairs adjacent to the tandem A.A pairs are likely in a dynamic equilibrium between multiple conformations. Although Co(NH(3))(6)(3+) stabilizes the loop by several kilocalories per mole at 37 degrees C, addition of Mg(2+) or Co(NH(3))(6)(3+) has no effect on the structure of the loop. The tandem G.U pairs provide a pocket of negative charge for Co(NH(3))(6)(3+) to bind. The results contribute to understanding the structure and dynamics of purine-rich internal loops and potential G.U pairs adjacent to internal loops.

The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from Its Structure in Crystals of 50S Ribosomal Subunits,

“…The NMR derived distance between A6H2 and A14H1' is 2.6 Å compared to 3.2-4.1 Å in a typical A-form helix so the minor groove is narrowed. Similar constriction or kinking of the backbone has been observed in previous structures involving purine purine sheared pairs (23,55). The U4A15 pair in the NMR structure has a C1'-C1' distance of 10.9 Å whereas the reverse Hoogsteen pair in the crystals has an average C1'-C1' distance of 9.6 Å.…”

Computational approaches for RNA energy parameter estimation

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Trypanosoma brucei ATPase subunit 6 mRNA bound to gA6-14 forms a conserved three-helical structure

“…This suggests that while the scissile base is not involved in Watson-Crick pairing, in agreement with predictions by Seiwert et al (1996), Cruz-Reyes et al (2001), and Lawson et al (2001), it is contained within a highly organized region. This finding was not surprising, because nucleotides in singlestranded areas in a secondary structure are often paired in long-range tertiary interactions, single-strand base stacking, or cross-strand base stacking (Peterson and Feigon 1996;Butcher et al 1997;Zimmermann et al 1997;Znosko et al 2004). Internal loops or bulges are common in RNA structure and create distortions into the geometry of an RNA helix that are often critical for protein recognition (Burkard et al 1999).…”