Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment

Abstract

Nucleic acid-based technologies are an emerging research focus area for pharmacological and biological studies because they are biocompatible and can be designed to produce a variety of scaffolds at the nanometer scale. The use of nucleic acids (ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA)) as building materials in programming the assemblies and their further functionalization has recently established a new exciting field of RNA and DNA nanotechnology, which have both already produced a variety of different functional nanostructures and nanodevices. It is evident that the resultant architectures require detailed structural and functional characterization and that a variety of technical approaches must be employed to promote the development of the emerging fields. Small-angle X-ray and neutron scattering (SAS) are structural characterization techniques that are well placed to determine the conformation of nucleic acid nanoparticles (NANPs) under varying solution conditions, thus allowing for the optimization of their design. SAS experiments provide information on the overall shapes and particle dimensions of macromolecules and are ideal for following conformational changes of the molecular ensemble as it behaves in solution. In addition, the inherent differences in the neutron scattering of nucleic acids, lipids, and proteins, as well as the different neutron scattering properties of the isotopes of hydrogen, combined with the ability to uniformly label biological macromolecules with deuterium, allow one to characterize the conformations and relative dispositions of the individual components within an assembly of biomolecules. This article will review the application of SAS methods and provide a summary of their successful utilization in the emerging field of NANP technology to date, as well as share our vision on its use in complementing a broad suite of structural characterization tools with some simulated results that have never been shared before.

Ultra-compacted single self-amplifying RNA molecules as quintessential vaccines

“…A clear dependence of the scattering intensity on the D 2 O/H 2 O ratio was observed, allowing determination of the contrast matching point at about 80% of D 2 O (Fig. 3C), a value similar to the one previously reported for RNA (20). The contrast matching point of PEI is much lower than that of RNA (32% of D 2 O), therefore, only a low mass fraction of PEI can be present in the compacted RNA molecules.…”

Small-Angle Scattering from Fractals: Differentiating between Various Types of Structures

“…With the recent advances of its derivative techniques, i.e., grazing-incidence [3], anomalous [4], scanning [5] or magnetic [6] SAS, the range of applications has been greatly extended. This includes now a much larger class of hierarchical materials, i.e., materials in which the structural elements themselves have a structure, such as biological macromolecules [1,[7][8][9], polymers [10][11][12][13], composites [14][15][16][17] or cellular solids [18][19][20].…”

Editorial for the Special Issue on “Nucleic Acid Architectures for Therapeutics, Diagnostics, Devices and Materials”

“…This special issue assembles 11 original articles (with seven research manuscripts and four reviews) which nicely outline several advances made in the field of RNA and DNA nanotechnology. Unified by the versatile use of the intriguing biopolymers, these manuscripts explore the various facets of nucleic acid nanostructures such as design, production, and characterization of RNA and DNA nanoassemblies [1,2,3,4], rational design of functional molecular machines [5,6,7,8], immunorecognition of nucleic acid nanoparticles [8], in vivo delivery of therapeutic nucleic acids [9,10], and nucleic acid-based biosensors [11]. We anticipate this special issue to be accessible to a wide audience, as it explores not only the biological aspects of nucleic acid nanodesigns, but also different methodologies of their production, their interactions with other classes of biological molecules, physicochemical characteristics, and possible applications.…”

“…The majority of characterization techniques of nucleic acid nanostructures involve the use of electrophoretic mobility shift assays, atomic force microscopy, cryogenic electron microscopy, or dynamic light scattering; each approach has its unique benefits and drawbacks. Oliver et al propose a new approach to characterizing nucleic acid nanoparticles using small angle X-ray or neutron scattering [4]. Their in-depth review examines the structural and chemical requirements for studying various biomolecules in their natural confirmations.…”