Salt Dependence of A-Form RNA Duplexes: Structures and Implications

Abstract

The biological functions of RNA range from gene regulation through catalysis and depend critically on its structure and flexibility. Conformational variations of flexible, non-base-paired components, including RNA hinges, bulges, or single-stranded tails, are well documented. Recent work has also identified variations in the structure of ubiquitous, base-paired duplexes found in almost all functional RNAs. Duplexes anchor the structures of folded RNAs, and their surface features are recognized by partner molecules. To date, no consistent picture has been obtained that describes the range of conformations assumed by RNA duplexes. Here, we apply wide angle, solution X-ray scattering (WAXS) to quantify these variations, by sampling length scales characteristic of helical geometries under different solution conditions. To identify the radius, helical rise, twist, and length of dsRNA helices, we exploit molecular dynamics generated structures, explicit solvent models, and ensemble optimization methods. Our results quantify the substantial and salt-dependent deviations of double-stranded (ds) RNA duplexes from the assumed canonical A-form conformation. Recent experiments underscore the need to properly describe the structures of RNA duplexes when interpreting the salt dependence of RNA conformations.

Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering

“…The sequence of the 12base-paired RNA duplex from the simulation is identical to the one reported here. As described in the work by Chen & Pollack (2019), we applied a 3D reference interaction site model (3D-RISM) to model the surrounding (excess) solvent molecules and ions (both cations and anions) for calculation of SWAXS profiles. In order to include solvent and ions and ensure accurate computation of the SWAXS profiles with proper buffer subtraction (Chen & Hub, 2014, the edges of the simulation box are more than 10 Å from all RNA atoms.…”

“…where (q j ) and (S/N) j are the experimental error and signalto-noise ratio at q j , respectively. Note that equation 1here is the same as equation 1in the work by Chen & Pollack (2019) with the exception of the scaling factor which provides absolute calibration. The input data of our ML models consist of about 50 000 curves representing the logarithms of the corrected SWAXS profiles computed under all solution conditions.…”

“…Periodic molecular features are well captured by WAXS, including, for DNA and RNA duplexes, their diameters or the distance between the two phosphate-heavy backbone strands. These periodic structures are manifested as peaks and troughs in 1D scattering profiles (Chen & Pollack, 2019). Their presence or absence may lead to interpretable changes in WAXS profiles (Tiede et al, 2002;Zuo et al, 2006).…”

“…For example, flexible and/or singlestranded regions are known to facilitate various conformational states of RNA molecules (Denny et al, 2018). Recently, two independent studies focused on the structural variation of fully base-paired RNA duplexes, which exhibit sequencedependent (Yesselman et al, 2019) and salt-dependent (Chen & Pollack, 2019) conformations. These works suggest that subtle variations in the RNA stems can affect the precise alignment of contacts that stabilizes tertiary structures, imparting more selectivity to interactions and expanding the biological functionality of RNA (Chen et al, 2018).…”

“…An ensemble optimization method was employed to select sets of structures whose summed, computed scattering profiles best recapitulate the measurement. We found that only a small number of conformations was required to fit the data and interesting salt-dependent conformational differences were recorded (Chen & Pollack, 2019).…”