Abstract
In this study, by combining nuclear magnetic resonance (NMR), circular dichroism (CD), liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS), and gel electrophoresis, we report an unusual topological structure of the RNA G-quadruplex motif formed by human telomere RNA r(UAGGGU) containing 8-bromoguanosine. Results showed that the RNA sequence formed an antiparallel tetramolecular G-quadruplex, in which each pair of diagonal strands run in opposite directions. Furthermore, guanosines were observed both in syn- and anti-conformations. In addition, two of these G-quadruplex subunits were found to be stacking on top of each other, forming a dimeric RNA G-quadruplex. Our findings provide a new insight into the behavior of RNA G-quadruplex structures.
Highlights
Contrary to their DNA counterparts, RNA G-quadruplexes are less diverse in terms of stem strand orientations
There has not been any consistent explanation of why RNA sequences cannot form antiparallel G-quadruplexes, some studies attribute it to the anti-glycosidic conformation of guanosine and the C3′-endo conformation of sugars[32, 33]
There is no report that confirmed any RNA sequences can form an antiparallel G-quadruplex conformation, recently, accumulated evidence showed that RNA G-quadruplexes present some antiparallel features, suggesting that the RNA maybe more polymorphic than initially assumed
Summary
Contrary to their DNA counterparts, RNA G-quadruplexes are less diverse in terms of stem strand orientations. Many works have reported the existence of C2′-endo sugars in RNA G-quadruplexes[8, 24, 25, 34] These observations motivated us to investigate whether an antiparallel RNA G-quadruplex could form in a special sequence context. The incorporation of a methyl or bromine group at the C8 position of dG causes a steric hindrance between the 8-substituent and the ribose ring that favours a syn conformation of 8mdG or 8BrdG. This allows the examination of the structure and thermal stability of G-quadruplexes via appropriate substitutions of dG with 8mdG or 8BrdG
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