Jeffrey R. Vieregg

How RNA Unfolds and Refolds

Understanding how RNA folds and what causes it to unfold has become more important as knowledge of the diverse functions of RNA has increased. Here we review the contributions of single-molecule experiments to providing answers to questions such as: How much energy is required to unfold a secondary or tertiary structure? How fast is the process? How do helicases unwind double helices? Are the unwinding activities of RNA-dependent RNA polymerases and of ribosomes different from other helicases? We discuss the use of optical tweezers to monitor the unfolding activities of helicases, polymerases, and ribosomes, and to apply force to unfold RNAs directly. We also review the applications of fluorescence and fluorescence resonance energy transfer to measure RNA dynamics.

Dynamic nuclear polarization at 9T using a novel 250GHz gyrotron microwave source.

In the 1990s we initiated development of high frequency gyrotron microwave sources with the goal of performing dynamic nuclear polarization at magnetic fields (∼5-23 T) used in contemporary NMR experiments. This article describes the motivation for these efforts and the developments that led to the operation of a gyrotron source for DNP operating at 250 GHz. We also mention results obtained with this instrument that would have been otherwise impossible absent the increased sensitivity. Finally, we describe recent efforts that have extended DNP to 460 GHz and 700 MHz (1)H frequencies.

Selective nucleic acid capture with shielded covalent probes.

Nucleic acid probes are used for diverse applications in vitro, in situ, and in vivo. In any setting, their power is limited by imperfect selectivity (binding of undesired targets) and incomplete affinity (binding is reversible, and not all desired targets bound). These difficulties are fundamental, stemming from reliance on base pairing to provide both selectivity and affinity. Shielded covalent (SC) probes eliminate the longstanding trade-off between selectivity and durable target capture, achieving selectivity via programmable base pairing and molecular conformation change, and durable target capture via activatable covalent cross-linking. In pure and mixed samples, SC probes covalently capture complementary DNA or RNA oligo targets and reject two-nucleotide mismatched targets with near-quantitative yields at room temperature, achieving discrimination ratios of 2–3 orders of magnitude. Semiquantitative studies with full-length mRNA targets demonstrate selective covalent capture comparable to that for RNA oligo targets. Single-nucleotide DNA or RNA mismatches, including nearly isoenergetic RNA wobble pairs, can be efficiently rejected with discrimination ratios of 1–2 orders of magnitude. Covalent capture yields appear consistent with the thermodynamics of probe/target hybridization, facilitating rational probe design. If desired, cross-links can be reversed to release the target after capture. In contrast to existing probe chemistries, SC probes achieve the high sequence selectivity of a structured probe, yet durably retain their targets even under denaturing conditions. This previously incompatible combination of properties suggests diverse applications based on selective and stable binding of nucleic acid targets under conditions where base-pairing is disrupted (e.g., by stringent washes in vitro or in situ, or by enzymes in vivo).

A new 14 GHz electron-cyclotron-resonance ion source for the heavy ion accelerator facility ATLAS

A 14 GHz electron-cyclotron-resonance (ECR) ion source has been designed and built at Argonne National Laboratory. The source is a modification of the AECR [D. J. Clark, C. M. Lyneis, and Z. Q. Xie, 14th Particle Accelerator Conference (PAC), IEEE Conference 91 CH3038-7, 1991 (unpublished), p. 2796 and C. M. Lyneis, Z. Q. Zie, D. J. Clark, R. S. Lam, and S. A. Lundgren, 10th International Workshop on ECR Ion Sources, Oak Ridge, ORNL CONF-9011136, 1990 (unpublished), p. 47.] at Berkeley and incorporates the latest results from electron-cyclotron-resonance (ECR) developments to produce intense beams of highly charged ions, including an improved magnetic confinement of the plasma electrons with an axial mirror ratio of 3.5. The aluminum plasma chamber and extraction electrode as well as a biased disk on axis at the microwave injection side donate additional electrons to the plasma, making use of the large secondary electron yield from aluminum oxide. The source is capable of ECR plasma heating using two diff...

Modelling RNA folding under mechanical tension.

We investigate the thermodynamics and kinetics of RNA unfolding and refolding under mechanical tension. The hierarchical nature of RNA structure and the existence of thermodynamic parameters for base pair formation based on nearest-neighbour interactions allows modelling of sequence-dependent folding dynamics for any secondary structure. We calculate experimental observables such as the transition force for unfolding, the end-to-end distribution function and its variance, as well as kinetic information, for a representative RNA sequence and for a sequence containing two homopolymer segments: A·U and G·C.

Inhibiting sterilization-induced oxidation of large molecule therapeutics packaged in plastic parenteral vials

For many years, glass has been the default material for parenteral packaging, but the development of advanced plastics such as cyclic olefin polymers and the rapidly increasing importance of biologic drugs have provided new choices, as well as more stringent performance requirements. In particular, many biologics must be stored at non-neutral pH, where glass is susceptible to hydrolysis, metal extraction, and delamination. Plastic containers are not susceptible to these problems, but suffer from higher gas permeability and a propensity for sterilization-induced radical generation, heightening the risk of oxidative damage to sensitive drugs. This study evaluates the properties of a hybrid material, SiOPlas™, in which an ultrathin multilayer coating is applied to the interior of cyclic olefin polymer containers via plasma-enhanced chemical vapor deposition. Our results show that the coating decreases oxygen permeation through the vial walls 33-fold compared to uncoated cyclic olefin polymers, which should allow for improved control of oxygen levels in sensitive formulations. We also measured degradation of two biologic drugs that are known to be sensitive to oxidation, teriparatide and erythropoietin, in gamma and electron beam sterilized SiOPlas™, glass, and uncoated cyclic olefin polymer vials. In both cases, solutions stored in SiOPlas™ vials did not show elevated susceptibility to oxidation compared to either glass or unsterilized controls. Taken together, these results suggest that hybrid materials such as SiOPlas™ are attractive choices for storing high-value biologic drugs. LAY ABSTRACT: One of the most important functions of parenteral drug containers is safeguarding their contents from damage, either chemical or physical. Glass has been the container material of choice for many years, but concerns over breakage and vulnerability to chemical attack at non-neutral pH have spurred the rise of advanced plastics as alternatives. Plastics solve many problems associated with glass but introduce several of their own, including increased gas permeation and generation of oxidizing radicals during sterilization. In this article, we evaluate SiOPlas™, a hybrid material consisting of plastic with a thin multilayer coating applied to the interior, for its ability to overcome these two problems. We find that SiOPlas™ is much less permeable to oxygen than uncoated plastic, and that two biologic drugs stored in gamma and electron beam sterilized SiOPlas™ vials do not display elevated levels of oxidation compared to either glass or unsterilized vials. This suggests that hybrid materials such as SiOPlas™ can exhibit the best qualities of both glass and plastic, making them attractive materials for storing high-value parenteral drugs.

Structure–Property Relationships of Oligonucleotide Polyelectrolyte Complex Micelles

Polyelectrolyte complex micelles (PCMs), nanoparticles formed by electrostatic self-assembly of charged polymers with charged-neutral hydrophilic block copolymers, offer a potential solution to the challenging problem of delivering therapeutic nucleic acids into cells and organisms. Promising results have been reported in vitro and in animal models but basic structure-property relationships are largely lacking, and some reports have suggested that double-stranded nucleic acids cannot form PCMs due to their high bending rigidity. This letter reports a study of PCMs formed by DNA oligonucleotides of varied length and hybridization state and poly(l)lysine-poly(ethylene glycol) block copolymers with varying block lengths. We employ a multimodal characterization strategy combining small-angle X-ray scattering (SAXS), multiangle light scattering (MALS), and cryo-electron microscopy (cryo-TEM) to simultaneously probe the morphology and internal structure of the micelles. Over a wide range of parameters, we find that nanoparticle shape is controlled primarily by the hybridization state of the oligonucleotides with single-stranded oligonucleotides forming spheroidal micelles and double-stranded oligonucleotides forming wormlike micelles. The length of the charged block controls the radius of the nanoparticle, while oligonucleotide length appears to have little impact on either size or shape. At smaller length scales, we observe parallel packing of DNA helices inside the double-stranded nanoparticles, consistent with results from condensed genomic DNA. We also describe salt- and thermal-annealing protocols for preparing PCMs with high repeatability and low polydispersity. Together, these results provide a capability to rationally design PCMs with desired sizes and shapes that should greatly assist development of this promising delivery technology.

Selective Oligonucleotide and MRNA Pull-Down with Shielded Covalent Probes

Shielded covalent (SC) probes combine programmable base pairing, molecular conformation change, and activatable covalent crosslinking to achieve selective and durable capture of nucleic acid targets, including efficient discrimination of SNPs. Capture yields appear consistent with the thermodynamics of probe/target hybridization, allowing rational probe design. We will demonstrate RNA pull-down using surface-immobilized SC probes, exploiting covalent target capture to remove unwanted material using stringent washes, and then reversing the crosslinks to recover the targets. RNA pull-downs using SC probes will provide a powerful framework for exploring the in vivo binding partners of RNAs.

Sensitive and selective nucleic acid capture with shielded covalent probes

Nucleic acid probes are used for diverse applications in vitro, in situ, and in vivo. In any setting, their power is limited by imperfect selectivity (binding of undesired targets) and incomplete affinity (binding is reversible and not all desired targets are bound). These limitations stem from reliance on base pairing to both reject off-targets and retain desired targets. To address this selectivity/affinity tradeoff, shielded covalent probes achieve selectivity via conformation change and durable capture via covalent crosslinking of a photoactive nucleoside analog. In vitro assays show that mismatches are efficiently rejected and desired targets are durably captured. For probes designed to reject two-nucleotide mismatches, desired targets are captured nearly quant. Single-nucleotide mismatches are discriminated near the thermodn. limit. The probes operate isothermally and crosslinking activation is rapid with low-cost light sources. If desired, crosslinks can be reversed to release the target after capture. We envision a wide array of applications.