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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A twist grain boundary phase in aqueous solutions of the nucleic acid tetramer GTAC

At high concentration, long Watson/Crick (WC) double-helixed DNA forms columnar crystal or liquid crystal phases of linear, parallel duplex chains packed on periodic lattices. This can also be a structural motif of short NA oligomers such as the 5’-GTAC-3’ studied here, which makes four-base WC duplexes having hydrophobic blunt ends. End-to-end aggregation then assembles these duplexes into columns and columnar phases are stabilized, in spite of breaks in the double helix every four bases. But the new degrees of freedom introduced by such breaks also enable opportunities for a more diverse palette of self-assembly modes, producing striking self-assemblies of DNA that would not be achievable with contiguous polymers. These include recently reported three-dimensional (3D) periodic low-density nanoscale networks of GCCG, and the twist grain boundary (TGB) phase presented here. In the TGB, columns of GTAC pairs assemble into monolayer sheets in which the duplex columns are mutually parallel. However, unlike in the columnar crystals, these sheets stack in helical fashion into lamellar arrays in which the column axis of each layer is rotated through a 60° angle with respect to the columns in neighboring layers. This assembly of DNA is unique in that it the fills a 3D volume wherein the major grooves of columns in each layer mutually enter and interlock with the major grooves of columns in neighboring layers. This locking is optimized by small adjustments in structure enabled by the breaks in the duplex backbones.

DNA↗
DOE OSTI2023

Novobiocin blocks nucleic acid binding to Polθ and inhibits stimulation of its ATPase activity

Polymerase theta (Polθ) acts in DNA replication and repair, and its inhibition is synthetic lethal in BRCA1 and BRCA2-deficient tumor cells. Novobiocin (NVB) is a first-in-class inhibitor of the Polθ ATPase activity, and it is currently being tested in clinical trials as an anti-cancer drug. Here, we investigated the molecular mechanism of NVB-mediated Polθ inhibition. Using hydrogen deuterium exchange-mass spectrometry (HX-MS), biophysical, biochemical, computational and cellular assays, we found NVB is a non-competitive inhibitor of ATP hydrolysis. NVB sugar group deletion resulted in decreased potency and reduced HX-MS interactions, supporting a specific NVB binding orientation. Collective results revealed that NVB binds to an allosteric site to block DNA binding, both in vitro and in cells. Comparisons of The Cancer Genome Atlas (TCGA) tumors and matched controls implied that POLQ upregulation in tumors stems from its role in replication stress responses to increased cell proliferation: this can now be tested in fifteen tumor types by NVB blocking ssDNA-stimulation of ATPase activity, required for Polθ function at replication forks and DNA damage sites. Structural and functional insights provided in this study suggest a path for developing NVB derivatives with improved potency for Polθ inhibition by targeting ssDNA binding with entropically constrained small molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

99 GENERAL AND MISCELLANEOUS↗
NASA NTRS1972

Nucleic acid hybridization with RNA immobilized on filter paper.

RNA has been immobilized in a manner suitable for use in molecular hybridization experiments with dissolved RNA or DNA by a nonaqueous solid-phase reaction with carbonyldiimidazole and RNA 'dry coated' on cellulose or, preferably, on previously activated phosphocellulose filters. Immobilization of RNA does not appear to alter its chemical character or cause it to acquire affinity for unspecific RNA or DNA. The versatility and efficiency of this method make it potentially attractive for use in routine analytical or preparative hybridization experiments, among other applications.

Saxinger, W. C.↗