DOI: 10.5281/zenodo.18785314
title: Raw data and data accompanying publication: https://doi.org/10.1261/rna.080106.124

description: Raw data and data accompanying publication:

Jarmolowicz A., Dutta N., Andralojc W., Sarzynska J., Framski G., Baranowski D., Boryski J., Lahiri A., Gdaniec Z., Kierzek E., Kierzek R., The oligonucleotides containing N7-regioisomer of guanosine: influence on thermodynamic properties and structure of RNA duplexes. RNA (2025) 31, 86-99. https://doi.org/10.1261/rna.080106.124

Authors: Aleksandra Jarmolowicz (1), Nivedita Dutta (1,2), Witold Andralojc (1), Joanna Sarzynska (1), Grzegorz Framski (1), Daniel Baranowski (1), Jerzy Boryski (1), Ansuman Lahiri (2), Zofia Gdaniec (1), Elzbieta Kierzek* (1), Ryszard Kierzek* (1)

Affiliation:(1) Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland(2) University of Calcutta, Kolkata-700009, West Bengal, India

* Corresponding authors: E-mails: rkierzek@ibch.poznan.pl, elzbieta.kierzek@ibch.poznan.pl

License: CC BY 4.0

This research has been supported by National Science Center (Poland) grants (UMO-2021/41/B/NZ1/03819 to E.K., UMO-2019/33/B/ST4/01422 and UMO-2022/45/B/ST4/03586 to R.K., UMO-2020/37/B/ST4/03182 and UMO-2018/31/D/ST4/01467 to W.A.). N.D. acknowledges support from the Department of Science and Technology-Innovation in Science Pursuit for Inspired Research (DST-INSPIRE) Senior Research Fellowship (DST/ INSPIRE Fellowship/2018/IF180895). Contents:Data1: Methods: Determination of the structure of N7-guanosine using NMR methods; Calculation of free energies of the N7-guanosine and guanosine tautomers; Reoptimization of glycosidic torsion parameters for 7G-N1H; Calculation of hybridization energies of duplexes using MM/3D-RISM. Tables: Table S1. (A) Calculated properties of the duplexes containing 7G-A base pair from MD simulations (B) Calculated properties of the duplexes containing 7G-G base pair from MD simulations; Table S2. (A) Energetics of the duplexes with 7G-A pair (B) Energetics of the duplexes with 7G-G pair; Table S3. (A) Occurrences (in %) of hydrogen bonds between the 7G-A base pair observed in MD simulations (B) Occurrences (in %) of hydrogen bonds between the 7G-G base pair observed in MD simulations; Table S4. 13C NMR chemical shifts for 7G and G; Table S5. 1H NMR chemical shifts for 7G and G; Table S6. Conformational preferences of 7G-N1H nucleoside. Figures: Figure S1. The aromatic/amino region of 1H NMR spectrum of the 7G-A containing duplexes; Figure S2. The amino portion of the 1H-15N SOFAST-HMQC spectrums of the 7G-A containing duplexes. Figure S3. The imino regions of the standard and 15N-selective 1H NMR spectra of one of the duplexes containing the 7G-G mismatch. Figure S4. Structures of the tautomers of (A) m9Gua, (B) m7Gua; Figure S5. Comparison of the Zero-point-energy (ZPE)-corrected relative free energies of m7Gua, m9Gua tautomers with respect to keto-N1H(T1). Figure S6. Observed stacked geometries ; Figure S7. Observed water occupancy maps. Figure S8. 1H spectrum of 7G in DMSO-d6 at 25 °C; Figure S9. 13C spectrum of 7G in DMSO-d6 at 25 °C; Figure S10. 1H-1H COSY spectrum of 7G in DMSO-d6 at 25 °C; Figure S11. 1H-13C gHSQC spectrum of 7G in DMSO-d6 at 25 °C; Figure S12. 1H-13C gHMBC spectrum of 7G in DMSO-d6 at 25 °C; Figure S13. 1H-15N gHSQC spectrum of 7G in DMSO-d6 at 25 °C; Figure S14. 1H-15N gHMBC spectrum of 7G in DMSO-d6 at 25 °C; Figure S15. Quantum mechanical energy profiles around 𝛘 torsional angles (O4’-C1’-N7-C5) for 7G-N1H corresponding to the four conformational schemes. Figure S16. Energy profiles of the 𝛘+180° (O4’-C1’-N7-C8) torsional angles for 7G; Figure S17. Representative diagrams of the 7G tautomers; AMBER preparatory files; References.