The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.
The side-by-side interactions of nucleobases contribute to the organization of RNA, forming the planar building blocks of helices and mediating chain folding. Dinucleotide platforms, formed by side-by-side pairing of adjacent bases, frequently anchor helices against loops. Surprisingly, GpU steps account for over half of the dinucleotide platforms observed in RNA-containing structures. Why GpU should stand out from other dinucleotides in this respect is not clear from the single well-characterized H-bond found between the guanine N2 and the uracil O4 groups. Here, we describe how an RNA-specific H-bond between O2'(G) and O2P(U) adds to the stability of the GpU platform. Moreover, we show how this pair of oxygen atoms forms an out-of-plane backbone 'edge' that is specifically recognized by a non-adjacent guanine in over 90% of the cases, leading to the formation of an asymmetric miniduplex consisting of 'complementary' GpUpA and GpA subunits. Together, these five nucleotides constitute the conserved core of the well-known loop-E motif. The backbone-mediated intrinsic stabilities of the GpU dinucleotide platform and the GpUpA/GpA miniduplex plausibly underlie observed evolutionary constraints on base identity. We propose that they may also provide a reason for the extreme conservation of GpU observed at most 5'-splice sites.
Lu
Xiang-Jun
XJ
Department of Biological Sciences, Columbia University, New York, NY 10027, USA. xl2134@columbia.edu
Olson
Wilma K
WK
Bussemaker
Harmen J
HJ
D000227:Adenine Nucleotides / Q000737:chemistry*; D019143:Evolution, Molecular; D006150:Guanine Nucleotides / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry*; D020871:RNA Stability; D014500:Uracil Nucleotides / Q000737:chemistry*
D000227:Adenine Nucleotides; D006150:Guanine Nucleotides; D014500:Uracil Nucleotides; D012313:RNA