Predicting Molecular Crowding Effects in Ion-RNA Interactions.

We develop a new statistical mechanical model to predict the molecular crowding effects in ion-RNA interactions. By considering discrete distributions of the crowders, the model can treat the main crowder-induced effects, such as the competition with ions for RNA binding, changes of electrostatic interaction due to crowder-induced changes in the dielectric environment, and changes in the nonpolar hydration state of the crowder-RNA system. To enhance the computational efficiency, we sample the crowder distribution using a hybrid approach: For crowders in the close vicinity of RNA surface, we sample their discrete distributions; for crowders in the bulk solvent away from the RNA surface, we use a continuous mean-field distribution for the crowders. Moreover, using the tightly bound ion (TBI) model, we account for ion fluctuation and correlation effects in the calculation for ion-RNA interactions. Applications of the model to a variety of simple RNA structures such as RNA helices show a crowder-induced increase in free energy and decrease in ion binding. Such crowding effects tend to contribute to the destabilization of RNA structure. Further analysis indicates that these effects are associated with the crowder-ion competition in RNA binding and the effective decrease in the dielectric constant. This simple ion effect model may serve as a useful framework for modeling more realistic crowders with larger, more complex RNA structures.

TBI server: a web server for predicting ion effects in RNA folding.

BACKGROUND: Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²âº, are essential for RNA tertiary structure formation. These ions can possibly become strongly correlated in the close vicinity of RNA surface. Most of the currently available software packages, which have widespread success in predicting ion effects in biomolecular systems, however, do not explicitly account for the ion correlation effect. Therefore, it is important to develop a software package/web server for the prediction of ion electrostatics in RNA folding by including ion correlation effects. RESULTS: The TBI web server http://rna.physics.missouri.edu/tbi_index.html provides predictions for the total electrostatic free energy, the different free energy components, and the mean number and the most probable distributions of the bound ions. A novel feature of the TBI server is its ability to account for ion correlation and ion distribution fluctuation effects. CONCLUSIONS: By accounting for the ion correlation and fluctuation effects, the TBI server is a unique online tool for computing ion-mediated electrostatic properties for given RNA structures. The results can provide important data for in-depth analysis for ion effects in RNA folding including the ion-dependence of folding stability, ion uptake in the folding process, and the interplay between the different energetic components.

Exploring the electrostatic energy landscape for tetraloop-receptor docking.

It has long been appreciated that Mg(2+) is essential for the stabilization of RNA tertiary structure. However, the problem of quantitative prediction for the ion effect in tertiary structure folding remains. By using the virtual bond RNA folding model (Vfold) to generate RNA conformations and the newly improved tightly bound ion model (TBI) to treat ion-RNA interactions, we investigate Mg(2+)-facilitated tetraloop-receptor docking. For the specific construct of the tetraloop-receptor system, the theoretical analysis shows that the Mg(2+)-induced stabilizing force for the docked state is predominantly entropic and the major contribution comes from the entropy of the diffusive ions. Furthermore, our results show that Mg(2+) ions promote tetraloop-receptor docking mainly through the entropy of the diffusive ions. The theoretical prediction agrees with experimental analysis. The method developed in this paper, which combines the theory for the (Mg(2+)) ion effects in RNA folding and RNA conformational sampling, may provide a useful framework for studying the ion effect in the folding of more complex RNA structures.

Quantifying Coulombic and solvent polarization-mediated forces between DNA helices.

One of the fundamental problems in nucleic acids biophysics is to predict the different forces that stabilize nucleic acid tertiary folds. Here we provide a quantitative estimation and analysis for the forces between DNA helices in an ionic solution. Using the generalized Born model and the improved atomistic tightly binding ions model, we evaluate ion correlation and solvent polarization effects in interhelix interactions. The results suggest that hydration, Coulomb correlation and ion entropy act together to cause the repulsion and attraction between nucleic acid helices in Mg(2+) and Mn(2+) solutions, respectively. The theoretical predictions are consistent with experimental findings. Detailed analysis further suggests that solvent polarization and ion correlation both are crucial for the interhelix interactions. The theory presented here may provide a useful framework for systematic and quantitative predictions of the forces in nucleic acids folding.

Designing a polycationic probe for simultaneous enrichment and detection of microRNAs in a nanopore.

The nanopore sensor can detect cancer-derived nucleic acid biomarkers such as microRNAs (miRNAs), providing a noninvasive tool potentially useful in medical diagnostics. However, the nanopore-based detection of these biomarkers remains confounded by the presence of numerous other nucleic acid species found in biofluid extracts. Their nonspecific interactions with the nanopore inevitably contaminate the target signals, reducing the detection accuracy. Here we report a novel method that utilizes a polycationic peptide-PNA probe as the carrier for selective miRNA detection in the nucleic acid mixture. The cationic probe hybridized with microRNA forms a dipole complex, which can be captured by the pore using a voltage polarity that is opposite the polarity used to capture negatively charged nucleic acids. As a result, nontarget species are driven away from the pore opening, and the target miRNA can be detected accurately without interference. In addition, we demonstrate that the PNA probe enables accurate discrimination of miRNAs with single-nucleotide difference. This highly sensitive and selective nanodielectrophoresis approach can be applied to the detection of clinically relevant nucleic acid fragments in complex samples.

Predicting ion-nucleic acid interactions by energy landscape-guided sampling.

The recently developed Tightly Bound Ion (TBI) model offers improved predictions for ion effect in nucleic acid systems by accounting for ion correlation and fluctuation effects. However, further application of the model to larger systems is limited by the low computational efficiency of the model. Here, we develop a new computational efficient TBI model using free energy landscape-guided sampling method. The method leads to drastic reduction in the computer time by a factor of 50 for RNAs of 50-100 nucleotides long. The improvement in the computational efficiency would be more significant for larger structures. To test the new method, we apply the model to predict the free energies and the number of bound ions for a series of RNA folding systems. The validity of this new model is supported by the nearly exact agreement with the results from the original TBI model and the agreement with the experimental data. The method may pave the way for further applications of the TBI model to treat a broad range of biologically significant systems such as tetraloop-receptor and riboswitches.

Acoustic transmission enhancement through a periodically structured stiff plate without any opening.

We report both experimentally and theoretically that enhanced acoustic transmission can occur in the subwavelength region through a thin but stiff structured plate without any opening. This exotic acoustic phenomenon is essentially distinct from the previous related studies originated from, either collectively or individually, the interaction of the incident wave with openings in previous structures. It is attributed to the structure-induced resonant excitation of the nonleaky Lamb modes that exist intrinsically in the uniform elastic plate. Our finding should have an impact on ultrasonic applications.

Surface resonant-states-enhanced acoustic wave tunneling in two-dimensional phononic crystals.

We show that by placing a metal plate next to a two-dimensional phononic crystal, acoustic waves can tunnel through the combined structure at a specific frequency that lies inside the band gap of the phononic crystal. The enhanced transmission is attributed to the coupling of the input waves with the acoustically resonant states created between the metal plate and the phononic crystal. Experiments are in excellent agreement with the theoretical predictions.

Acoustic Bloch oscillations in a two-dimensional phononic crystal.

We report the observation of acoustic Bloch oscillations at megahertz frequency in a two-dimensional phononic crystal. By creating periodically arrayed cavities with a decreasing gradient in width along one direction in the phononic crystal, acoustic Wannier-Stark ladders are created in the frequency domain. The oscillatory motion of an incident Gaussian pulse inside the sample is demonstrated by both simulation and experiment.