Quantitative analysis of RNA solvent accessibility by N-silylation of guanosine.

Stefanie A Mortimer, Jeffrey S Johnson, Kevin M Weeks

Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.

Biochemistry 2009 Mar 17

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An important unmet experimental objective is to analyze local RNA structure in a way that is strictly governed by solvent accessibility. Essentially all chemical probes currently used to evaluate RNA (and DNA) structure via formation of stable covalent adducts employ carbon-based electrophiles, which undergo nucleophilic attack from limited spatial orientations and via highly polar transition states. Reaction by these classical electrophiles is therefore gated by both solvent accessibility and additional electrostatic factors. In contrast, silicon electrophiles react via their d-orbitals and consequently can undergo nucleophilic attack from many spatial orientations. In this work, we explore the use of silanes to react indiscriminately with RNA such that the primary factor governing reactivity is solvent accessibility. We show that N,N-(dimethylamino)dimethylchlorosilane (DMAS-Cl) reacts at the guanosine N2 position to yield a near-perfect measure (r >or= 0.82) of solvent accessibility in an RNA with a complex tertiary structure. This silane-based chemistry represents a direct and quantitative approach for probing solvent accessibility at the base pairing face of guanosine in RNA.

Citation

Stefanie A Mortimer, Jeffrey S Johnson, Kevin M Weeks. Quantitative analysis of RNA solvent accessibility by N-silylation of guanosine. Biochemistry. 2009 Mar 17;48(10):2109-14