DOI: 10.5281/zenodo.18785949
title: Raw data and data accompanying publication: https://doi.org/10.1093/nar/gkae1222

description: Raw data and data accompanying publication:

Yildirim I., Andralojc W., Taghavi A., Baranowski D., Gdaniec Z., Kierzek R., Kierzek E., Experimental and computational investigations of RNA duplexes containing N7-regioisomers of adenosine and LNA-adenosine. Nucleic Acids Research, (2025) 53 (1), gkae1222, https://doi.org/10.1093/nar/gkae1222

Authors: Ilyas Yildirim* (1), Witold Andralojc (2), Amirhossein Taghavi (1,3), Daniel Baranowski (2), Zofia Gdaniec (2), Ryszard Kierzek* (2) , Elzbieta Kierzek* (2) 

Affiliation:(1) Department of Chemistry and Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA (2) Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland(3) Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA

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

License:  CC BY 4.0

This work was supported by: National Institutes of Health [R15 GM146199 to I.Y.]; Florida Atlantic University [to I.Y.]; David and Lynn Center for Degenerative Disease Research [to I.Y.]; National Science Centre [UMO-2021/41/B/NZ1/03819 to E.K., UMO-2019/33/B/ST4/01422 to R.K., UMO-2020/37/B/ST4/03182 to W.A., UMO-2018/31/D/ST4/01467 to W.A.].

Contents:Data1: Synthesis of protected N7-regioisomer of adenosine and its phosphoramidite; NMR spectra of 7A and 7AL; Script S1. Script used to perform hydrogen bond analyses; Script S2. In-house PERL script to perform cluster analyses; Script S3. Sample script used to perform MM/3D-RISM and NMODE analyses; Table S1. Mass spectrometry (MALDI) analyses of RNA oligonucleotides; Table S2. Experimental and literature 13C NMR data for A, 7A and 7AL; Table S3. Atom names, types, and RESP charges of 7A; Table S4. Atom names, types, and RESP charges of 7AL; Table S5. Details of each RNA system studied computationally; Table S6. Sample input files used in minimization, equilibration, and production runs; Table S7. Experimental and literature 1H NMR data for A, 7A and 7AL; Table S8. Experimental coupling constants (1H-1H and 13C-1H), pseudorotational parameters, and populations of sugar conformations of A, 7A, and 7AL; Table S9. Structurally significant NOEs observed in 1×1 mismatches; Table S10. Chemical shifts of aromatic/anomeric protons in 7A-G and 7AL-G; Table S11. Chemical shifts of aromatic/anomeric protons in 7A-A and 7AL-A; Table S12. Binding free energy calculations of A-U; Table S13. Binding free energy calculations of 7A-U; Table S14. Binding free energy calculations of 7AL-U; Table S15. Binding free energy calculations of A-C; Table S16. Binding free energy calculations of 7A-C; Table S17. Binding free energy calculations of 7AL-C; Table S18. Binding free energy calculations of A-A; Table S19. Binding free energy calculations of 7A-A; Table S20. Binding free energy calculations of 7AL-A; Table S21. Binding free energy calculations of A-G; Table S22. Binding free energy calculations of 7A-G; Table S23. Binding free energy calculations of 7AL-G; Table S24. Comparison of NOEs to predicted distances for each cluster in 7A-A; Table S25. Comparison of NOEs to predicted distances for each cluster in 7AL-A; Table S26. Comparison of NOEs to predicted distances for each cluster in 7A-G; Table S27. Comparison of NOEs to predicted distances for each cluster in 7AL-G; Table S28. Extended UV-melting data; Figure S1; 1H NMR spectrum of 7-β-D-ribofuranosyladenine in DMSO-d6; Figure S2. 13C NMR spectrum of 7-β-D-ribofuranosyladenine in DMSO-d6; Figure S3. 1H-1H COSY spectrum of 7-β-D-ribofuranosyladenine in DMSO-d6; Figure S4. 1H-13C gHSQC spectrum of 7-β-D-ribofuranosyladenine in DMSO-d6; Figure S5. 1H-13C gHMBC spectrum of 7-β-D-ribofuranosyladenine in DMSO-d6; Figure S6. 1H NMR spectrum of 2′-O,4′-C-Methylene-7-β-D-ribofuranosyladenine in DMSO-d6; Figure S7. 13C NMR spectrum of 2′-O,4′-C-Methylene-7-β-D-ribofuranosyladenine in DMSO-d6; Figure S8. 1H-13C gHSQC spectrum of 2′-O,4′-C-Methylene-7-β-D-ribofuranosyladenine in DMSO-d6; Figure S9. 1H-13C gHMBC spectrum of 2′-O,4′-C-Methylene-7-β-D-ribofuranosyladenine in DMSO-d6; Figure S10. 1H NMR spectrum of 9-β-D-ribofuranosyladenine in DMSO-d6; Figure S11. 13C NMR spectrum of 9-β-D-ribofuranosyladenine in DMSO-d6; Figure S12. 1H-13C gHSQC spectrum of 9-β-D-ribofuranosyladenine in DMSO-d6; Figure S13. 1H-13C gHMBC spectrum of 9-β-D-ribofuranosyladenine in DMSO-d6; Figure S14. Fragment of1H-13C gHMBC spectrum showing long range 1H-1`3C correlations crucial for determination of D-ribofuranosyl moiety position in adenine; Figure S15. Imino regions in 1D 1H NMR spectra recorded at four different temperatures for the duplex containing 7AL:G mismatch; Figure S16. Imino-imino and imino-amino/aromatic regions of the 2D 1H-1H NOESY spectra recorded for 7A-G and 7AL-G mismatches; Supplemental References.