From a structural average to the conformational ensemble of a DNA bulge

Direct experimental measurements of conformational ensembles are critical for understanding macromolecular function, but traditional biophysical methods do not directly report the solution ensemble of a macromolecule. Small-angle X-ray scattering interferometry has the potential to overcome this limitation by providing the instantaneous distance distribution between pairs of gold-nanocrystal probes conjugated to a macromolecule in solution. Our X-ray interferometry experiments reveal an increasing bend angle of DNA duplexes with bulges of one, three, and five adenosine residues, consistent with previous FRET measurements, and further reveal an increasingly broad conformational ensemble with increasing bulge length. The distance distributions for the AAA bulge duplex (3A-DNA) with six different Au-Au pairs provide strong evidence against a simple elastic model in which fluctuations occur about a single conformational state. Instead, the measured distance distributions suggest a 3A-DNA ensemble with multiple conformational states predominantly across a region of conformational space with bend angles between 24 and 85 degrees and characteristic bend directions and helical twists and displacements. Additional X-ray interferometry experiments revealed perturbations to the ensemble from changes in ionic conditions and the bulge sequence, effects that can be understood in terms of electrostatic and stacking contributions to the ensemble and that demonstrate the sensitivity of X-ray interferometry. Combining X-ray interferometry ensemble data with molecular dynamics simulations gave atomic-level models of representative conformational states and of the molecular interactions that may shape the ensemble, and fluorescence measurements with 2-aminopurine-substituted 3A-DNA provided initial tests of these atomistic models. More generally, X-ray interferometry will provide powerful benchmarks for testing and developing computational methods.A grand challenge in biology is to understand the complex free-energy landscape of macromolecules and to decipher the resulting conformational ensembles. To perform their biological functions, macromolecules must adopt a multiplicity of conformations. Balancing and controlling different conformational states is central to biological processes including protein folding, allostery and signaling, and the stepwise assembly and function of macromolecular machines. To understand these complex molecules requires characterization of their free-energy landscapes—i.e., their equilibrium conformational ensembles. Precise measurements of conformational ensembles could allow quantitative modeling of the folding and function of biological macromolecules, would provide valuable experimental data to test current computational models and assumptions, and might facilitate the rational design of specifically acting inhibitors (1, 2).Techniques including NMR and EPR relaxation have been developed to incisively probe motions in the ensemble on different time scales, ranging from picoseconds to milliseconds (3, 4). Nonetheless, such dynamic information represents an average of the dynamics of the molecules across the conformational ensemble. In special cases, where the ensemble contains slow exchanging conformational states, these states can be separately detected [e.g., relaxation dispersion approaches can detect conformational states interconverting at tens of microseconds to hundreds of milliseconds, and single-molecule FRET (smFRET) can characterize conformational transitions at millisecond or slower time scales (5, 6)]. However, again, each of these states is an average of a more complex local conformational ensemble.To date, successes in reconstructing equilibrium ensembles have mostly relied on experimental measurement of NMR residual dipolar couplings (RDCs) (7, 8). Compared with other NMR techniques, RDCs provide long-range angular structure information that helps to generate equilibrium ensemble models (9). In combination with molecular dynamic simulations, RDCs have been used to generate ensemble models for small disordered proteins (7, 10), DNA duplexes (11), and a RNA bulge motif (12–14). In addition to RDCs, relaxation dispersion and paramagnetic relaxation enhancement have been used to detect and characterize conformational states that are in low abundance in an ensemble (5). Although powerful, these NMR-based methods, like all approaches, have limitations. For example, RDCs have difficulty distinguishing between conformations with similar angular orientations but different translational displacements (15, 16). Additional methods are needed to construct ensembles that can test and complement these current methods.To meet this challenge, we continue to develop, test, and apply the capabilities of a solution X-ray interferometry technique (17, 18). X-ray interferometry can be used to determine site-to-site distance distributions instantaneously because it relies on atomic scattering (17, 19–24). Standard small-angle X-ray scattering (SAXS) measures the sum of the scattering and scattering interference from all atoms in a macromolecule (25). As it would not be possible to decompose this sum and distinguish contributions from specific atoms or atom pairs, standard SAXS provides no site-specific information and is limited to determining the overall size and shape of macromolecules (25). X-ray interferometry overcomes this limitation through the introduction of a pair of site-specifically labeled gold nanocrystal probes and isolation of the scattering interference from this strongly scattering probe pair. This scattering interference can be directly converted into a distance distribution through a Fourier transformation, without the complications of a nonlinear mapping (26). Multiple pairs of gold nanocrystal probes, in different site-specific locations, provide matched-set distance information and increase the information content of the technique (e.g., refs. 17 and 18).Unlike standard ensemble-averaged methods such as FRET that give a single average value for the distance between each probe pair, X-ray interferometry naturally yields a distance distribution between each probe pair. Strategies measuring the time dependence of fluorescence energy transfer (27) or spin echo intensity [double electron–electron resonance (DEER)] (28) are powerful but are limited in their ability to determine an ensemble by the complex relationships between the measured values and the desired probe–probe distances. These complications amplify the uncertainty of determining an average value and introduce even greater uncertainty in determining a distance distribution and the underlying conformational ensemble.Prior results using the DNA double helix as a model experimental system (18) indicate that detailed and quantitative information about solution ensembles can be obtained. For the DNA helix, X-ray interferometry distance distributions were found to quantitatively agree with consensus elastic parameters of DNA (18). Nevertheless, the ensemble of a DNA double helix is simpler than that for most macromolecules and could be well described by broadening from a single conformation using an elastic potential. The ensembles of most biological macromolecules are likely to contain substantial anharmonicities and multiple local free-energy minima.To further test X-ray interferometry as a general method for probing macromolecule equilibrium ensembles and to determine fundamental properties of basic nucleic acid structures, we have applied X-ray interferometry to a nucleic acid helix–junction–helix (HJH) motif, the DNA bulge. DNA bulges can provide a model for the RNA bulges that are more commonly encoded in biology and can be used to engineer nanostructures (29, 30). We chose the A-bulge DNA system for this study to allow comparison with a prior smFRET study that provided models for the average structures of these DNAs (31).