Opto-Electrostatic Determination of Nucleic Acid Double-Helix Dimensions and the Structure of the Molecule–Solvent Interface

Abstract

A DNA molecule is highly electrically charged in solution. The electrical potential at the molecular surface is known to vary strongly with the local geometry of the double helix and plays a pivotal role in DNA–protein interactions. Further out from the molecular surface, the electrical field propagating into the surrounding electrolyte bears fingerprints of the three-dimensional arrangement of the charged atoms in the molecule. However, precise extraction of the structural information encoded in the electrostatic “far field” has remained experimentally challenging. Here, we report an optical microscopy-based approach that detects the field distribution surrounding a charged molecule in solution, revealing geometric features such as the radius and the average rise per basepair of the double helix with up to sub-Angstrom precision, comparable with traditional molecular structure determination techniques like X-ray crystallography and nuclear magnetic resonance. Moreover, measurement of the helical radius furnishes an unprecedented view of both hydration and the arrangement of cations at the molecule–solvent interface. We demonstrate that a probe in the electrostatic far field delivers structural and chemical information on macromolecules, opening up a new dimension in the study of charged molecules and interfaces in solution.

Far-Field Electrostatic Signatures of Macromolecular 3D Conformation

“…In general, our measurements of the renormalization factor, η, are in good agreement both with our calculated values and with prior theoretical estimates for charged rods and disks (Supporting Information section 3.4). , Thus, our study further suggests that beyond detecting coarse-grained morphological features of molecular 3D conformation (e.g., elongated/unfolded or compact/globular), precise measurements of electrostatic energies may further shed light on finer-grained structural attributes such as periodicities and spacings in ordered molecular charge distributions …”

“…The cylinders have a radius r cyl = 1.2 nm, a length corresponding to a rise per base pair value of 0.34 nm, and carry a uniform charge density σ = q str /A, where A is the total surface area of the structure. 31 Distributions of dimensionless electrical potential…”

“…29,30 Thus, our study further suggests that beyond detecting coarse-grained morphological features of molecular 3D conformation (e.g., elongated/unfolded or compact/globular), precise measurements of electrostatic energies may further shed light on finer-grained structural attributes such as periodicities and spacings in ordered molecular charge distributions. 31 Our interaction-based definition of molecular effective electrical charge implies that the free energy of interaction between a molecule and a charged entity in solution may be written as F(r) = q eff ϕ(r), where ϕ(r) is the electrical potential created by the charged entity at the location of the molecule, r. 8 This definition of interaction free energy is the same as the potential of mean force between a charged object generating a , where R = 4 nm and q str = −240 e. q m and q eff values for the nanostructures are very similar to q eff values for spheroidal surface charge distributions of similar R g ("plus" symbols in (a)). We use a sphere of radius R = 4 nm to model the DNA tetrahedron, prolate spheroids I and II to mimic the rod and the bundle respectively, and an oblate spheroid to model the square-tile.…”

“…Individual nanostructures were modeled as an assembly of smooth charged cylinders each representing a segment of double helical DNA. The cylinders have a radius r cyl = 1.2 nm, a length corresponding to a rise per base pair value of 0.34 nm, and carry a uniform charge density σ = q str / A , where A is the total surface area of the structure . Distributions of dimensionless electrical potential on the surfaces of the nanostructures (ψ s ) as well as in the surrounding electrolyte in the vicinity of the nanostructure (ψ) are displayed in Figure .…”

Single-Molecule Trapping and Measurement in a Nanostructured Lipid Bilayer System

“…In this study, we demonstrate electrostatic trapping and effective charge measurements on single molecules in nanostructured slit systems whose surfaces are passivated using SLBs carrying net electrical charge. Electrostatic free energies associated with the molecule–surface interaction are inferred from experimentally measured potential-well depths in the molecular trapping process as described in detail in previous work and recapitulated briefly in the following section. ,− In earlier studies, we worked with silicon dioxide surfaces and used measured free energies inferred for charged molecular species in order to infer their effective charge, q eff (refs , − ). In this study, we use double stranded DNA molecules of known effective charge in order to infer the surface electrical properties of supported lipid bilayers.…”