Supporting Information

Supporting Information Stable Copper(I)-Mediated Base Pairing in DNA Biswarup Jash and Jens Müller* anie_201802201_sm_miscellaneous_information.pdf

Author Contributions B.J. Investigation: Lead; Writing original draft: Lead J.M. Funding acquisition: Lead; Resources: Lead; Writing review & editing: Lead.

Table of contents Section S1 Experimental section 2 Figure S1 Titration of duplex (R,R) I with Cu I 3 Figure S2 UV melting profiles of duplexes II and III 3 Figure S3 Titration of duplexes (R,R) I and (S,S) I with Ag I 4 Figure S4 CD spectra of duplexes II and III 4 Figure S5 Temperature dependent CD spectra of duplex (S,S) I in the absence of Cu I 5 Figure S6 CD spectra of duplexes (R,R) I and (S,S) I with Ag I 5 Figure S7 UV melting profiles and CD spectra of duplex (S,S) I in the presence of Cu II 6 Figure S8 UV melting profiles and CD spectra of duplex (S,S) I after in situ reduction of Cu II 6 Figure S9 Temperature dependent CD spectra of duplex (S,S) I after in situ reduction of Cu II 7 Figure S10 UV melting profiles and CD spectra of duplex (S,S) I after in situ oxidation of Cu I 7 Figure S11 Comparison of the CD spectra during redox experiments 8 Figure S12 HPLC traces of purified oligonucleotide 8 Figure S13 1 H NMR spectrum of the phosphoramidite 9 Figure S14 31 P NMR of the phosphoramidite 9 Figure S15 ESI MS of the phosphoramidite 10 Section S2 References 10 1

S1. Experimental Section: The phosphoramidite and the oligonucleotides were synthesized as reported previously. [1] The desalted oligonucleotides were characterized by MALDI ToF mass spectrometry using a 3 hydroxypicolinic acid/ ammonium citrate matrix. For quantification of the oligonucleotides, a molar extinction coefficient ԑ 260 = 10.0 cm 2 mmol 1 was used for P. Duplex (S,S) I Duplex (R,R) I Duplex II Duplex III Sequences used for the formation of a [M+H] + / Da Cu I Entry mediated homo base pair Calcd. Found 5 -d(gag GGT (S)-PTG AAA G)-3' Chemical formula: C 136H 160N 58O 72P 12 ODN 1 4129 4129 5 -d(ctt TCA (S)-PAC CCT C)-3' Chemical formula: C 130H 162N 40O 76P 12 ODN 2 3872 3873 5 -d(gag GGT (R)-PTG AAA G)-3' Chemical formula: C 136H 160N 58O 72P 12 ODN 3 4129 4132 5 -d(ctt TCA (R)-PAC CCT C)-3' Chemical formula: C 130H 162N 40O 76P 12 ODN 4 3872 3874 5 -d(gag GGT ATG AAA G)-3' Chemical formula: C 130 H 160 N 59 O 73 P 12 ODN 5 4088 4088 5 -d(ctt TCA TAC CCT C)-3' Chemical formula: C 124 H 163 N 38 O 79 P 12 ODN 6 3821 3821 5 -d(gag GGT GTG AAA G)-3' Chemical formula: C 130 H 160 N 59 O 74 P 12 ODN 7 4104 4105 5 -d(ctt TCA CAC CCT C)-3' Chemical formula: C 123 H 162 N 39 O 78 P 12 ODN 8 3806 3806 Prior to each measurement, the samples were incubated with the respective metal salt applying a heating rate of 1 C min 1 followed by a cooling rate of 0.33 C min 1. Temperature dependent UV spectra were recorded on a Cary100 Bio instrument from 10 C to 70 C at 1 C min 1. In the UV melting profiles the absorbance at 260 nm was normalized according to A norm = (A A min )/(A max A min ). Melting temperature (T m,uv ) values were determined from the maxima of the first derivatives of the respective melting profiles. CD spectra were recorded at 10 C on JASCO J 815 instrument, smoothed and baseline corrected. Temperature dependent CD spectra was recorded from 10 C to 70 C with a heating rate of 0.5 C min 1. CD melting profile were obtained by fitting the molar ellipticity at 284 nm or 303 nm using a sigmoidal equation. The melting temperature T m,cd was determined from the first derivative of the fitted curve. All reagents were degassed three times prior to the measurement to get rid of dissolved oxygen from the solution. [2] Experimental conditions were 1 M duplex, 20 mm NaClO 4, 5 mm MOPS (ph 6.8), 50 mm acetonitrile. [Cu(ACN) 4 ]PF 6 and Cu(ClO 4 ) 2 were used as Cu I and Cu II salt, respectively, throughout all experiments. For the redox experiments, Na 2 SO 3 (500 M) was used as reducing agent and KNO 3 (1 mm) as oxidizing agent. 2

Figure S1. a) Increase of the melting temperature T m,uv of duplex (R,R) I upon the addition of Cu I ; b) change of the CD spectra of duplex (R,R) I upon the addition of Cu I. Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8). Figure S2. a) UV melting profiles of duplex II (A:T), before and after the addition of one Cu I per duplex; b) UV melting profiles of duplex III (G:C), before and after the addition of one Cu I per duplex. Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8). 3

Figure S3. Increase of the melting temperature T m,uv of a) duplex (S,S) I (22 37 C) and b) duplex (R,R) I (23 42 C) upon the addition of Ag I. Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8). Figure S4. a) CD spectra of duplex II (A:T), before and after the addition of one Cu I per duplex; b) CD spectra of duplex III (G:C), before and after the addition of one Cu I per duplex. Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8). 4

Figure S5. a) Temperature dependent CD spectra of duplex (S,S) I (P:P), before addition of Cu I ; b) sigmoidal fit of the molar ellipticity at 284 nm of duplex (S,S) I at different temperatures. Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8). The spectra were recorded from 10 C to 70 C with a data interval of 5 C and a heating rate of 0.5 C min 1. The spectra were smoothed and baseline corrected. The molar ellipticity at 284 nm was fitted with a sigmoidal equation (R 2 = 0.99), and a CD derived melting temperature of 22 C was obtained from that fit. Figure S6. a) CD spectra of a) duplex (S,S) I and b) duplex (R,R) I upon the addition of increasing amounts of Ag I. Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8). 5

Figure S7. a) UV melting profiles of duplex (S,S) I in the absence and presence of one Cu II per duplex; b) CD spectra of duplex (S,S) I in the absence and presence of one Cu II per duplex. Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8). Figure S8. a) UV melting profiles of duplex (S,S) I in the absence and presence of Cu II and Na 2SO 3 (reducing agent, R.A.); b) CD spectra of duplex (S,S) I in the absence of presence of Cu II and Na 2SO 3 (reducing agent, R.A.). Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8), 500 M Na 2SO 3. 6

Figure S9. a) Temperature dependent CD spectra of duplex (S,S) I after incubation with one Cu II per duplex in the presence of Na 2 SO 3 ; (b) sigmoidal fit of the molar ellipticity at 303 nm of duplex (S,S) I at different temperatures. Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8), 500 M Na 2SO 3. The spectra were recorded from 10 C to 70 C with a data interval of 5 C and a heating rate of 0.5 C min 1. The spectra were smoothed and baseline corrected. The molar ellipticity at 303 nm was fitted with a sigmoidal equation (R 2 = 0.99), and a CD derived melting temperature of 40 C was obtained from that fit. Figure S10. a) UV melting profiles of duplex (S,S) I in the absence and presence of Cu I and KNO 3 (oxidizing agent, O.A); b) CD spectra of duplex (S,S) I in the absence and presence of Cu I and KNO 3 (oxidizing agent, O.A). Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8), 1 mm KNO 3. 7

Figure S11. Overview of CD spectra of duplex (S,S) I in the absence and presence of a) Cu II, b) Cu II and Na 2SO 3 (reducing agent, R.A), c) Cu I and KNO 3 (oxidizing agent, O.A). Conditions: 1 M duplex, 20 mm NaClO 4, 50 mm ACN, 5 mm MOPS (ph 6.8).4 Figure S12. HPLC traces of purified oligonucleotides a) ODN1 and b) ODN2. An RP 18 column (250 mm, 10 m) was used in combination with the following eluents at a flow rate of 0.75 ml min 1. Gradient applied for oligonucleotides: 0 3 min, 10 15% A; 3 15 min, 15 50% A; 15 20 min, 50 10% A. Solvent A represents acetonitrile and solvent B represent 0.1 M aqueous triethylammonium acetate (ph 7.0). 8

Figure S13. 1 H NMR spectrum of the GNA based phosphoramidite. Figure S14. 31 P NMR spectrum of the GNA based phosphoramidite. 9

Figure S15. ESI MS of the GNA based phosphoramidite (top: experimental; bottom: computed for [M+H] + ). S2. References [1] a) B. Jash, P. Scharf, N. Sandmann, C. Fonseca Guerra, D. A. Megger, J. Müller, Chem. Sci. 2017, 8, 1337; b) P. Scharf, B. Jash, J. A. Kuriappan, M. P. Waller, J. Müller, Chem. Eur. J. 2016, 22, 295; c) B. Jash, J. Neugebauer, J. Müller, Inorg. Chim. Acta 2016, 452, 181. [2] D. K. Johnson, M. J. Stevenson, Z. A. Almadidy, S. E. Jenkins, D. E. Wilcox, N. E. Grossoehme, Dalton Trans. 2015, 44, 16494. 10