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DOE OSTI2020

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling

The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Enhancing reactivity of SiO + ions by controlled excitation to extreme rotational states

Optical pumping of molecules provides unique opportunities for control of chemical reactions at a wide range of rotational energies. This work reports a chemical reaction with extreme rotational excitation of a reactant and its kinetic characterization. We investigate the chemical reactivity for the hydrogen abstraction reaction SiO + + H 2 → SiOH + + H in an ion trap. The SiO + cations are prepared in a narrow rotational state distribution, including super-rotor states with rotational quantum number ( j ) as high as 170, using a broad-band optical pumping method. We show that the super-rotor states of SiO + substantially enhance the reaction rate, a trend reproduced by complementary theoretical studies. We reveal the mechanism for the rotational enhancement of the reactivity to be a strong coupling of the SiO + rotational mode with the reaction coordinate at the transition state on the dominant dynamical pathway.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Extreme confinement of hydrogen gas within fullerenelike nanoporous carbon

Nanoporous carbons and carbon nanostructures can store hydrogen at cryogenic temperatures but lack the volumetric and gravimetric capacity to be industrially significant. Recent inelastic neutron scattering experiments suggest a highly dense phase of hydrogen at temperatures well above the melting point of solid hydrogen. However, it remains unclear how pore geometry and intermolecular interactions enable these dense phases to exist, with dispersion (van der Waals) or electrostatic/induction suggested to be the key effects in slit and curved pores but their relative contributions have yet to be quantified. In this paper, we perform benchmark electronic structure calculations allowing the interactions between planar and curved aromatic molecules with hydrogen to be accurately determined. Dispersion was found to dominate over electrostatic and inductive effects with some many-body charge transfer (Dobson type-A) effects needed to capture the most highly curved structures. Density functional methods that include type-A many-body effects were found to accurately describe the intermolecular interactions at a fraction of the cost of coupled-cluster simulations and these approaches were used to calculate the energies inside large carbon bowl and slit pores. The interaction energies inside the bowl pores were found to depend on the orientation of the hydrogen molecule. This rotational barrier, modeled as a quantum hindered rotor, could reproduce the peak splitting observed in inelastic neutron scattering experiments, with weak splitting arising from bowl-like fullerene pores and strong splitting from highly confining nanotubelike pores. Increasing the fraction of such curved pores in nanoporous carbons may therefore offer a pathway to enhance their hydrogen-storage capacity. Moreover, the preferential adsorption of ortho hydrogen on nanotubelike pores could enable the storage of high-density hydrogen without the need to remove heat produced during the ortho-para hydrogen conversion.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Active Thermochemical Tables: the thermophysical and thermochemical properties of methyl, CH 3 , and methylene, CH 2 , corrected for nonrigid rotor and anharmonic oscillator effects

The thermophysical properties (isobaric heat capacity, entropy, enthalpy increment) of two prominent radicals, methyl, CH 3 , and methylene, CH 2 , were computed using the Nonrigid Rotor Anharmonic Oscillator (NRRAO) approach and compared to their RRHO counterparts, demonstrating significant differences between the results from the two approaches. Methylene presents a typical case in which the NRRAO thermophysical properties have significantly higher values than their RRHO counterparts at higher temperatures. In the case of methyl, the positive anharmonicity of the umbrella motion causes an opposite effect, and the NRRAO corrected thermophysical properties have lower values than their RRHO counterparts. The NRRAO corrected thermophysical properties, in turn, affect the resulting thermochemical properties. Here, two reactions important in combustion modelling were tested: the recombination of methyl radical with hydrogen atoms to form methane, and the recombination of two methyl radicals to form ethane. The related NRRAO equilibrium constants differ significantly from their RRHO analogs, and the consequences for chemical modelling are discussed. Also reported are the most current ATcT enthalpies of formation for CH n (n = 4-0) species and for C 2 H 6 , together with the tightly related sequential bond dissociation enthalpies along with the CHn series.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2026

Improved Accuracy in Semi-Experimental Structure Determination by Resolving Problems Associated with Rotation of Principal Inertial Axes of Isotopologues: Structures of 1,3-Oxazole ( c -C 3 H 3 NO)

The rotational spectrum of the normal isotopologue of 1,3-oxazole (c-C 3 H 3 NO) was observed from 43 to 750 GHz. Over 3900 transitions for the ground vibrational state are measured, assigned, and least-squares fit to sextic centrifugally distorted-rotor Hamiltonians. The measured frequencies and resulting spectroscopic constants from this extended spectral range, combined with previous measurements of the nuclear quadrupole coupling constants, will facilitate astronomical searches for oxazole across the majority of the range of modern radiotelescopes. Spectra for a set of 30 oxazole isotopologues, which include multiple isotopic substitutions of each atom, are used to determine the first semi-experimental equilibrium ($r$$^{SE}_{e}$) structure and semi-experimental substitution structure ($r$$^{SE}_{e}$), each using CCSD(T) computed values for the vibration–rotation interaction and electron-mass corrections. The large number of isotopologues, including 21 isotopologues observed for the first time, and the redundant substitutions of each atom provide sufficient spectroscopic information to determine the $r$$^{SE}_{e}$ structure with the expected high level of accuracy and precision (0.0001 or 0.0002 Å in bond distances and 0.013 to 0.025° in bond angles). In the course of this study, we analyzed a known issue for some $r$$^{SE}_{e}$ structure determinations of near-oblate asymmetric tops in which inclusion of individual isotopologues degrades the structure determination. We demonstrate that this problem primarily arises from the difference in the values of the computed vibration–rotation interaction corrections as evaluated at the computed re geometry vs the $r$$^{SE}_{e}$ geometry of the “real” molecule. Our solution to this problem substantially improves the $r$$^{SE}_{e}$ structure of oxazole and likely can be generalized to many other molecules.

Chemical structure↗