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Pressure pushes tRNA^Lys3 into excited conformational states.

ABSTRACT: Conformational dynamics play essential roles in RNA function. However, detailed structural characterization of excited states of RNA remains challenging. Here, we apply high hydrostatic pressure (HP) to populate excited conformational states of tRNA^Lys3, and structurally characterize them using a combination of HP 2D-NMR, HP-SAXS (HP-small-angle X-ray scattering), and computational modeling. HP-NMR revealed that pressure disrupts the interactions of the imino protons of the uridine and guanosine U-A and G-C base pairs of tRNA^Lys3. HP-SAXS profiles showed a change in shape, but no change in overall extension of the transfer RNA (tRNA) at HP. Configurations extracted from computational ensemble modeling of HP-SAXS profiles were consistent with the NMR results, exhibiting significant disruptions to the acceptor stem, the anticodon stem, and the D-stem regions at HP. We propose that initiation of reverse transcription of HIV RNA could make use of one or more of these excited states.

SUBMITTER: Wang J

PROVIDER: S-EPMC10293818 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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Pressure pushes tRNA<sup>Lys3</sup> into excited conformational states.

Wang Jinqiu J Koduru Tejaswi T Harish Balasubramanian B McCallum Scott A SA Larsen Kevin P KP Patel Karishma S KS Peters Edgar V EV Gillilan Richard E RE Puglisi Elisabetta V EV Puglisi Joseph D JD Makhatadze George G Royer Catherine A CA

Proceedings of the National Academy of Sciences of the United States of America 20230620 26

Conformational dynamics play essential roles in RNA function. However, detailed structural characterization of excited states of RNA remains challenging. Here, we apply high hydrostatic pressure (HP) to populate excited conformational states of tRNA<sup>Lys3</sup>, and structurally characterize them using a combination of HP 2D-NMR, HP-SAXS (HP-small-angle X-ray scattering), and computational modeling. HP-NMR revealed that pressure disrupts the interactions of the imino protons of the uridine an ...[more]

PMID: 37339210

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Project description:A family of complexes of the type [Ru(tpbn)(IP-R)(4-pic)]Cl2 (tbpn=2,2'-(4-(tert-butyl)pyridine-2,6-diyl)bis(1,8-napthyridine); 4-pic=4-picoline; IP-R=imidazo[4,5-f][1,10]phenanthroline attached to an aromatic group R for 2-8 and H for 1) were prepared as near-infrared (NIR) absorbing coordination complexes to test whether triplet intraligand excited states (3IL) of higher energy than the lowest-lying triplet metal-to-ligand charge transfer excited states (3MLCT) could effectively generate cytotoxic singlet oxygen (1O2) and elicit in vitro photodynamic therapy (PDT) effects. Aromatic groups ranged from benzene to anthracene, with corresponding triplet state energies that were all significantly higher (approximately 3.7-1.8 eV) than the 3MLCT state estimated at 1.5 eV. Complexes 1-8 absorbed NIR light, with their longest-wavelength peak maxima occurring near 725 nm that extended out to 800 nm. The 1O2 quantum yields for the aromatic-containing compounds were extremely small (ΦΔ=0.07), with correspondingly modest in vitro photocytotoxicities. All compounds were nontoxic without a light trigger, with dark EC50 values >60 μM and most values closer to 100 or greater. EC50 values with visible light were 5-6 (PI=15-20), 7-10 (PI=8-11), and 10-15 μM (PI=6-8) in SKMEL28, A375, and B16F10 cancer cell lines, respectively. With NIR light, these values were even less: 11-16 (PI=5-9), 16-50 (PI=2-6), and 15-19 μM (PI=4-6) in SKMEL28, A375, and B16F10 cancer cell lines, respectively. While measurable, the modest activities and absence of any trend between the 3IL energies and values for ΦΔ or PI demonstrate that 3IL states with energies above the lowest-lying 3MLCT states do not contribute to the overall excited state dynamics responsible for potent PDT effects in previous studies. Lowest-lying 3MLCT states in this family of NIR-absorbing photosensitizers do not produce the requisite 1O2 for effective in vitro photocytotoxic effects, underscoring the need to install 3IL states that are lower in energy than the lowest-lying 3MLCT states in order the create potent NIR-activatable Ru(II) complexes for PDT.

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Pressure pushes tRNA^Lys3 into excited conformational states.

Publications

Pressure pushes tRNA<sup>Lys3</sup> into excited conformational states.

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Pressure pushes tRNALys3 into excited conformational states.

Publications

Pressure pushes tRNA<sup>Lys3</sup> into excited conformational states.

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OmicsDI is part of the ELIXIR infrastructure

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Pressure pushes tRNA^Lys3 into excited conformational states.