A calibration disk for the correction of radial errors from chromatic aberration and rotor stretch in the Optima AUC™ analytical ultracentrifuge

Using absorbance detection for hs-SV-AUC characterization of adeno-associated virus

Data are presented demonstrating that absorbance detection can be used during high-speed sedimentation velocity analytical ultracentrifugation (hs-SV-AUC) experiments to characterize the size distribution of adeno-associated virus (AAV) drug products accurately. Advantages and limitations of being able to use this detector in this specific type of SV-AUC experiment are discussed.

Development of an advanced multiwavelength emission detector for the analytical ultracentrifuge

An advanced design of the analytical ultracentrifuge with multiwavelength emission detection (MWE-AUC) is presented which offers outstanding performance concerning the spectral resolution and range flexibility as well as the quality of the data acquired. The excitation by a 520 nm laser is complemented with a 405 nm laser. An external spectrograph with three switchable tunable gratings permits optimisation of the spectral resolution in an order of magnitude range while keeping the spectral region broad. The new system design leads also to a significant reduction of systematic signal noise and allows the assessment and control of inner filter effects. Details regarding the very large signal dynamic range are presented, an important aspect when studying samples in a broad concentration range of up to five orders of magnitude. Our system is validated by complementary studies on two biological systems, fluorescent BSA and GFP, using the commercial Optima AUC with absorbance detection for comparison. Finally, we demonstrate the capabilities of our second generation MWE-AUC with respect to multiwavelength characterisation of gold nanoclusters, which exhibit specific fluorescence depending on their structure. Overall, this work depicts an important stepping stone for the concept of multiwavelength emission detection in AUC. The MWE-AUC developed, being to our knowledge the first and sole one of its kind, has reached the development level suitable for the future in-depth studies of size-, shape- and composition-dependent emission properties of colloids.

A new UltraScan module for the characterization and quantification of analytical buoyant density equilibrium experiments to determine AAV capsid loading

A method for characterizing and quantifying peaks formed in an analytical buoyant density equilibrium (ABDE) experiment is presented. An algorithm is derived to calculate the concentration of the density forming gradient material at every point in the cell, provided the rotor speed, temperature, meniscus position, bottom of the cell position, and the loading concentration, molar mass, and partial specific volume of the density gradient-forming material are known. In addition, a new peak fitting algorithm has been developed which allows the user to automatically quantify the peaks formed in terms of density, apparent partial specific volume, and relative abundance. The method is suitable for both ionic and non-ionic density forming materials and can be used with data generated from the UV optical system as well as the AVIV fluorescence optical system. These methods have been programmed in a new UltraScan-III module (us_abde). Examples are shown that demonstrate the application of the new module to adeno-associated viral vector preparations and proteins.

Suitability of double-stranded DNA as a molecular standard for the validation of analytical ultracentrifugation instruments

To address the current lack of validated molecular standards for analytical ultracentrifugation (AUC), we investigated the suitability of double-stranded DNA molecules. We compared the hydrodynamic properties of linear and circular DNA as a function of temperature. Negatively supercoiled, nicked, and linearized 333 and 339 bp minicircles were studied. We quantified the hydrodynamic properties of these DNAs at five different temperatures, ranging from 4 to 37 °C. To enhance the precision of our measurements, each sample was globally fitted over triplicates and five rotor speeds. The exceptional stability of DNA allowed each sample to be sedimented repeatedly over the course of several months without aggregation or degradation, and with excellent reproducibility. The sedimentation and diffusion coefficients of linearized and nicked minicircle DNA demonstrated a highly homogeneous sample, and increased with temperature, indicating a decrease in friction. The sedimentation of linearized DNA was the slowest; supercoiled DNA sedimented the fastest. With increasing temperature, the supercoiled samples shifted to slower sedimentation, but sedimented faster than nicked minicircles. These results suggest that negatively supercoiled DNA becomes less compact at higher temperatures. The supercoiled minicircles, as purified from bacteria, displayed heterogeneity. Therefore, supercoiled DNA isolated from bacteria is unsuitable as a molecular standard. Linear and nicked samples are well suited as a molecular standard for AUC and have exceptional colloidal stability in an AUC cell. Even after sixty experiments at different speeds and temperatures, measured over the course of 4 months, all topological states of DNA remained colloidal, and their concentrations remained essentially unchanged.

Multi-wavelength analytical ultracentrifugation of biopolymer mixtures and interactions

Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recent development made possible by new analytical ultracentrifuge optical systems. MW-AUC extends the basic hydrodynamic information content of AUC and provides access to a wide range of new applications for biopolymer characterization, and is poised to become an essential analytical tool to study macromolecular interactions. It adds an orthogonal spectral dimension to the traditional hydrodynamic characterization by exploiting unique chromophores in analyte mixtures that may or may not interact. Here we illustrate the utility of MW-AUC for experimental investigations where the benefit of the added spectral dimension provides critical information that is not accessible, and impossible to resolve with traditional AUC methods. We demonstrate the improvements in resolution and information content obtained by this technique compared to traditional single- or dual-wavelength approaches, and discuss experimental design considerations and limitations of the method. We further address the advantages and disadvantages of the two MW optical systems available today, and the differences in data analysis strategies between the two systems.

Boundary convection during velocity sedimentation in the Optima analytical ultracentrifuge

Analytical ultracentrifugation (AUC) provides the most widely applicable, precise, and accurate means for characterizing solution hydrodynamic and thermodynamic properties. While generally useful, boundary sedimentation velocity AUC (SV-AUC) analysis has become particularly important in assessing protein aggregation, fragmentation and conformational variants in the same solvents used during drug development and production. In early 2017 the only manufacturer of the analytical ultracentrifuge released its newest analytical ultracentrifuge, the Optima, to replace the aging second-generation XLA/I series ultracentrifuges. However, SV-AUC data from four Optima units used in the characterization of adeno-associated virus (AAV) have shown evidence of sample convection. Further investigation reveals this problem arises from the design of the temperature control system, which makes it prone to producing destabilizing temperature-induced density gradients that can lead to density inversions. The problem is intermittent and variable in severity within a given Optima unit and between Optima units. This convection appears to be associated mainly with low rotor speeds and dilute concentration of solvent components, i.e., AAV analysis conditions. Data features diagnostic for this problem and strategies for its elimination or minimization are provided.

Analytical ultracentrifugation: still the gold standard that offers multiple solutions

Understanding the nature of macromolecules and their interactions in solution underpins many fields, including biology, chemistry and materials science. The 24th International Analytical Ultracentrifugation Workshop and Symposium (AUC2019, held in Christchurch, New Zealand, August 2019), brought together 77 international delegates to highlight recent developments in the field. There was a focus on analytical ultracentrifugation, although we recognise that this is but one of the key methods in the biophysicist's toolkit. Many of the presentations showcased the versatility of analytical ultracentrifugation and how such experiments are integrated with other solution techniques, such as small-angle X-ray scattering, cryo-electron microscopy, isothermal titration calorimetry and more. This special issue emphasises a wide range of themes covered in the meeting, including carbohydrate chemistry, protein chemistry, polymer science, and macromolecular interactions.

Calibrating analytical ultracentrifuges

Analytical ultracentrifugation (AUC) is based on the concept of recording and analyzing macroscopic macromolecular redistribution that results from a centrifugal force acting on the mass of suspended macromolecules in solution. Since AUC rests on first principles, it can provide an absolute measurement of macromolecular mass, sedimentation and diffusion coefficients, and many other quantities, provided that the solvent density and viscosity are known, and provided that the instrument is properly calibrated. Unfortunately, a large benchmark study revealed that many instruments exhibit very significant systematic errors. This includes the magnification of the optical detection system used to determine migration distance, the measurement of sedimentation time, and the measurement of the solution temperature governing viscosity. We have previously developed reference materials, tools, and protocols to detect and correct for systematic measurement errors in the AUC by comparison with independently calibrated standards. This 'external calibration' resulted in greatly improved precision and consistency of parameters across laboratories. Here we detail the steps required for calibration of the different data dimensions in the AUC. We demonstrate the calibration of three different instruments with absorbance and interference optical detection, and use measurements of the sedimentation coefficient of NISTmAb monomer as a test of consistency. Whereas the measured uncorrected sedimentation coefficients span a wide range from 6.22 to 6.61 S, proper calibration resulted in a tenfold reduced standard deviation of sedimentation coefficients. The calibrated relative standard deviation and mean error of 0.2% and 0.07%, respectively, is comparable with statistical errors and side-by-side repeatability in a single instrument.

Measuring compressibility in the optima AUC™ analytical ultracentrifuge

A method is described to accurately measure the compressibility of liquids using an analytical ultracentrifuge. The method makes use of very large pressure gradients, which can be generated in the analytical ultracentrifuge at high speeds to induce a maximum compression signal. Taking advantage of the new Optima AUC, which offers 10 micron radial resolution, a novel calibration centerpiece for measuring rotor stretch, and a speed-ramping procedure, even the weak compressibility of liquids like water, typically considered to be incompressible, could be detected. A model using the standard expression for the secant-average bulk modulus describing the relative compression of a liquid in the analytical ultracentrifuge is derived. The model is a function of the loading volume and the hydrostatic pressure generated in the analytical ultracentrifuge, as well as the secant-average bulk modulus. The compressibility of water and toluene were measured and the linear secant-average bulk modulus and meniscus positions were fitted. In addition to the measurement of the compressibility of liquids, applications for this method include an improved prediction of boundary conditions for multi-speed analytical ultracentrifugation experiments to better describe highly heterogeneous systems with analytical speed-ramping procedures, and the prediction of radius-dependent density variations.

Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment

Recent advances in instrumentation have moved analytical ultracentrifugation (AUC) closer to a possible validation in a Good Manufacturing Practices (GMP) environment. In order for AUC to be validated for a GMP environment, stringent requirements need to be satisfied; analysis procedures must be evaluated for consistency and reproducibility, and GMP capable data acquisition software needs to be developed and validated. These requirements extend to multiple regulatory aspects, covering documentation of instrument hardware functionality, data handling and software for data acquisition and data analysis, process control, audit trails and automation. Here we review the requirements for GMP validation of data acquisition software and illustrate software solutions based on UltraScan that address these requirements as far as they relate to the operation and data handling in conjunction with the latest analytical ultracentrifuge, the Optima AUC by Beckman Coulter. The software targets the needs of regulatory agencies, where AUC plays a critical role in the solution-based characterization of biopolymers and macromolecular assemblies. Biopharmaceutical and regulatory agencies rely heavily on this technique for characterizations of pharmaceutical formulations, biosimilars, injectables, nanoparticles, and other soluble therapeutics. Because of its resolving power, AUC is a favorite application, despite the current lack of GMP validation. We believe that recent advances in standards, hardware, and software presented in this work manage to bridge this gap and allow AUC to be routinely used in a GMP environment. AUC has great potential to provide more detailed information, at higher resolution, and with greater confidence than other analytical techniques, and our software satisfies an urgent need for AUC operation in the GMP environment. The software, including documentation, are publicly available for free download from Github. The multi-platform software is licensed by the LGPL v.3 open source license and supports Windows, Mac and Linux platforms. Installation instructions and a mailing list are available from ultrascan.aucsolutions.com.