Scheme 1. Rotation around the glycosidic bond leads to the syn-conformation, that in turn, stabilizes the 8-oxoG:A basepair mismatch. Biophysical properties,

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Scheme 1. Rotation around the glycosidic bond leads to the syn-conformation, that in turn, stabilizes the 8-oxoG:A basepair mismatch. Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA—a study of duplex, hairpins and the aptamer for preQ1 as models Nucleic Acids Res. 2016;45(4):2099-2111. doi:10.1093/nar/gkw885 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 1. (A) Sequences used with underlined Gs indicating positions where 8-oxoG was incorporated; (B) UV-vis spectra of strands 1–4 (1-blue, 2-red, 3-green, 4-purple) displaying a hyperchromic shift at ca. 310 nm as a function of number of modifications; and (C) spectra representing RNA:RNA and RNA:DNA heteroduplexes (2:5/2:6, 2 μM) and single stranded RNA (2, 7 μM). Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA—a study of duplex, hairpins and the aptamer for preQ1 as models Nucleic Acids Res. 2016;45(4):2099-2111. doi:10.1093/nar/gkw885 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 7. ITC data for the recognition of ONs 21–23 toward preQ<sub>1</sub> is shown. ITC for ON 22 was taken with [RNA] = 5.5 μM in the case shown. Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA—a study of duplex, hairpins and the aptamer for preQ1 as models Nucleic Acids Res. 2016;45(4):2099-2111. doi:10.1093/nar/gkw885 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 3. Sequence and hairpins formed for structure 8–12 (left) and H-bonding network previously reported to stabilize the –UUCG– loop (57), determined via NMR and Raman (right). Blue and red dotted lines represent H-bonding that provides stabilization or destabilization respectively. Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA—a study of duplex, hairpins and the aptamer for preQ1 as models Nucleic Acids Res. 2016;45(4):2099-2111. doi:10.1093/nar/gkw885 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 4. Sequence and hairpins formed for structure 13–16 along with their corresponding T<sub>m</sub> values. Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA—a study of duplex, hairpins and the aptamer for preQ1 as models Nucleic Acids Res. 2016;45(4):2099-2111. doi:10.1093/nar/gkw885 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 5. Sequence and hairpins formed for structure 17–19 along with the corresponding 17-17΄ transformation under high salt concentrations and 8-OMe modified ON 17-OMe. T<sub>m</sub> values were obtained via CD by measuring the ellipticity change at 270 nm. Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA—a study of duplex, hairpins and the aptamer for preQ1 as models Nucleic Acids Res. 2016;45(4):2099-2111. doi:10.1093/nar/gkw885 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 6. Sequence corresponding to the aptamer of a preQ<sub>1</sub>-I riboswitch (A) and the proposed structural transformation in the presence of Mg<sup>2+</sup>, (B) and the small molecule preQ<sub>1</sub> (C), before/after 8-oxoG modification at positions G5 and G11 (labeled in red, ONs 21–23). The structure of preQ<sub>1</sub> is shown with its charge density representation in the background. Provided tables indicate the measured T<sub>m</sub> values for each ON, recorded via CD at 270 nm (T<sub>m</sub> measurements for PK are displayed in the inset, lower left corner). Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA—a study of duplex, hairpins and the aptamer for preQ1 as models Nucleic Acids Res. 2016;45(4):2099-2111. doi:10.1093/nar/gkw885 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 2. Representative CD spectra of (A) RNA:RNA duplex (2:5), (B) RNA:DNA heteroduplex (2:6) and (C) hairpin (8) obtained at 20°and 75°C. Spectra for other oligonucleotides had the same features. Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA—a study of duplex, hairpins and the aptamer for preQ1 as models Nucleic Acids Res. 2016;45(4):2099-2111. doi:10.1093/nar/gkw885 Nucleic Acids Res | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com