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SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25...

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SUPPLEMENTARY INFORMATION Modulation of i-Motif Thermal Stability by Insertion of Anthraquinone Monomers Alaa S. Gouda a, b , Mahasen S. Amine b and Erik B. Pedersen* a a Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark. Fax +45 66158780; *E-mail: [email protected] b Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt13518. Circular Dichroism (CD) spectral analysis of human telomeric DNA (ON1) and anthraquinone-modified i-motif variants (ON2-ON33, Fig. S1-S3): Figure S1. Circular dichroism (CD) spectra of human telomeric i-motif DNA (ON1) and anthraquinone-modified i-motif variants (ON2-ON13) measured at 20 ºC. For sample composition see table 1. 380.2 360.2 340.2 320.2 300.2 280.2 260.2 240.2 220.2 200.2 -6 -4 -2 0 2 4 6 8 10 12 ON1 ON2 ON3 ON4 ON5 ON6 ON7 ON8 ON9 ON10 ON11 ON12 ON13 Wavelength / nm CD / mdeg Electronic Supplementary Material (ESI) for Organic & Biomolecular Chemistry. This journal is © The Royal Society of Chemistry 2017
Transcript
Page 1: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

SUPPLEMENTARY INFORMATIONModulation of i-Motif Thermal Stability by Insertion of Anthraquinone Monomers

Alaa S. Gouda a, b, Mahasen S. Amine b and Erik B. Pedersen*a

aDepartment of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230

Odense M, Denmark. Fax +45 66158780; *E-mail: [email protected] Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt13518.

Circular Dichroism (CD) spectral analysis of human telomeric DNA (ON1) and

anthraquinone-modified i-motif variants (ON2-ON33, Fig. S1-S3):

Figure S1. Circular dichroism (CD) spectra of human telomeric i-motif DNA (ON1) and anthraquinone-modified i-motif variants (ON2-ON13) measured at 20 ºC. For sample composition see table 1.

380.2360.2340.2320.2300.2280.2260.2240.2220.2200.2-6

-4

-2

0

2

4

6

8

10

12ON1ON2ON3ON4ON5ON6ON7ON8ON9ON10ON11ON12ON13

Wavelength / nm

CD

/ m

deg

Electronic Supplementary Material (ESI) for Organic & Biomolecular Chemistry.This journal is © The Royal Society of Chemistry 2017

Page 2: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

380.2360.2340.2320.2300.2280.2260.2240.2220.2200.2-6

-4

-2

0

2

4

6

8

10ON1ON30ON31ON32ON33

Wavelength / nm

CD

\ mde

g

380.2360.2340.2320.2300.2280.2260.2240.2220.2200.2-6

-4

-2

0

2

4

6

8

10ON1ON14ON15ON16ON17ON18ON19ON20ON21ON22ON23ON24ON25ON26ON27ON28ON29

Wavelength / nm

CD

\ m

deg

Figure S2. CD spectra of human telomeric i-motif DNA (ON1) and anthraquinone-modified i-motif variants (ON14-ON29) measured at 20 ºC. For sample composition see table 1.

Figure S3. CD spectra of human telomeric i-motif DNA (ON1) and anthraquinone-modified i-motif variants (ON30-ON33) measured at 20 ºC. For sample composition see table 1.

Page 3: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

25 30 35 40 45 50 55 60 65-0.1

-0.08

-0.06

-0.04

-0.02

0

0.02

0.04ON1ON2ON3ON4ON5ON6ON7ON8ON9ON10ON11ON12ON13

Temperature (ºC)

dA29

5nm

/dT 25 30 35 40 45 50 55 60 65

-0.1

0.1

0.3

0.5

0.7

0.9

1.1

ON1ON2ON3ON4ON5ON6ON7ON8ON9ON10ON11ON12ON13

Temperature (ºC)

Abs

orba

nce

Normalized UV absorption melting curves and first derivatives of human telomeric i-motif

DNA (ON1) and anthraquinone-modified i-motif variants (ON2-ON33, Fig S4-S6):

Figure S4. Normalized UV absorption melting curves (Up) and first derivatives (Down) versus temperature difference (0.5 ºC/min) from 25-65 ºC for i–motifs (ON1-ON13) at 295 nm (4 µM) in potassium buffer (100 mM KCl + 20 mM K2HPO4 (pH= 5.5) and 1 mM K2EDTA). Melting temperatures are within the uncertainty ± 0.5 °C as determined by repetitive experiments and Tm values were calculated taking an average of the two melting curves.

Page 4: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

25 30 35 40 45 50 55 60 65-0.09

-0.07

-0.05

-0.03

-0.01

0.01

ON1ON14ON15ON16ON17ON18ON19ON20ON21ON22ON23ON24ON25ON26ON27ON28ON29

Temperature (ºC)

dA 2

95nm

/dT

25 30 35 40 45 50 55 60 65-0.1

0.1

0.3

0.5

0.7

0.9

1.1ON1ON14ON15ON16ON17ON18ON19ON20ON21ON22ON23ON24ON25ON26ON27ON28ON29

Temperature (ºC)

Abs

orba

nce

25 30 35 40 45 50 55 60 65-0.1

0.1

0.3

0.5

0.7

0.9

1.1ON1ON30ON31ON32ON33

Temperature (ºC)

Abs

orba

nce

Figure S5. Normalized UV absorption melting curves (Up) and first derivatives (Down) versus temperature difference (0.5 ºC/min) from 25-65 ºC for i–motifs (ON1 and ON14-ON29) at 295 nm (4 µM) in potassium buffer (100 mM KCl + 20 mM K2HPO4 (pH= 5.5) and 1 mM K2EDTA). Melting temperatures are within the uncertainty ± 0.5 °C as determined by repetitive experiments and Tm values were calculated taking an average of the two melting curves.

Page 5: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

25 30 35 40 45 50 55 60 65-0.09

-0.08

-0.07

-0.06

-0.05

-0.04

-0.03

-0.02

-0.01

0

0.01

ON1ON30ON31ON32ON33

Temperature (ºC)

dA 2

95nm

/dT

Figure S6. Normalized UV absorption melting curves (Up) and first derivatives (Down) versus temperature difference (0.5 ºC/min) from 25-65 ºC for i–motifs (ON1 and ON30-ON33) at 295 nm (4 µM) in potassium buffer (100 mM KCl + 20 mM K2HPO4 (pH= 5.5) and 1 mM K2EDTA). Melting temperatures are within the uncertainty ± 0.5 °C as determined by repetitive experiments and Tm values were calculated taking an average of the two melting curves.

Table S1. MALDI-TOF mass spectrometry data (calculated and found mass) of i-Motifs

Page 6: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

Oligo bases replaced Sequence Mcalcd Mfound

ON1 wild type 5'-CCC TAA CCC TAA CCC TAA CCC T-3' 6504.44 6504.13ON2 T10 5'-CCC TAA CCC H18AA CCC TAA CCC T-3' 6617.43 6618.68ON3 A11 5'-CCC TAA CCC TH18A CCC TAA CCC T-3' 6608.43 6608.07ON4 A12 5'-CCC TAA CCC TAH18 CCC TAA CCC T-3' 6608.43 6609.25ON5 T10 5'-CCC TAA CCC H14AA CCC TAA CCC T-3' 6617.43 6617.38ON6 A11 5'-CCC TAA CCC TH14A CCC TAA CCC T-3' 6608.43 6608.94ON7 A12 5'-CCC TAA CCC TAH14 CCC TAA CCC-T-3' 6608.43 6608.07ON8 T10 5'-CCC TAA CCC H15AA CCC TAA CCC T-3' 6617.43 6618.29ON9 A11 5'-CCC TAA CCC TH15A CCC TAA CCC T-3' 6608.43 6609.22

ON10 A12 5'-CCC TAA CCC TAH15 CCC TAA CCC T-3' 6608.43 6609.30ON11 T10 5'-CCC TAA CCC H26AA CCC TAA CCC T-3' 6617.43 6617.49ON12 A11 5'-CCC TAA CCC TH26A CCC TAA CCC T-3' 6608.43 6608.65ON13 A12 5'-CCC TAA CCC TAH26 CCC TAA CCC-T-3' 6608.43 6608.36ON14 A6T16 5'-CCC TAH18 CCC TAA CCC H18AA CCC T-3' 6721.56 6722.74ON15 A6T16 5'-CCC TAH14 CCC TAA CCC H14AA CCC T-3' 6721.56 6722.85ON16 A6T16 5'-CCC TAH15 CCC TAA CCC H15AA CCC T-3' 6721.56 6728.08ON17 A6T16 5'-CCC TAH26 CCC TAA CCC H26AA CCC T-3' 6721.56 6721.66ON18 A6T16 5'-CCC TAH18 CCC TAA CCC H14AA CCC T-3' 6721.56 6723.44ON19 A6T16 5'-CCC TAH18 CCC TAA CCC H15AA CCC T-3' 6721.56 6725.84ON20 A6T16 5'-CCC TAH18 CCC TAA CCC H26AA CCC T-3' 6721.56 6721.66ON21 A6T16 5'-CCC TAH14 CCC TAA CCC H18AA CCC T-3' 6721.56 6722.85ON22 A6T16 5'-CCC TAH14 CCC TAA CCC H15AA CCC T-3' 6721.56 6724.04ON23 A6T16 5'-CCC TAH14 CCC TAA CCC H26AA CCC T-3' 6721.56 6722.76ON24 A6T16 5'-CCC TAH15 CCC TAA CCC H18AA CCC T-3' 6721.56 6723.74ON25 A6T16 5'-CCC TAH15 CCC TAA CCC H14AA CCC-T-3' 6721.56 6722.26ON26 A6T16 5'-CCC TAH15 CCC TAA CCC H26AA CCC T-3' 6721.56 6722.18ON27 A6T16 5'-CCC TAH26 CCC TAA CCC H18AA CCC T-3' 6721.56 6719.88ON28 A6T16 5'-CCC TAH26 CCC TAA CCC H14AA CCC T-3' 6721.56 6722.26ON29 A6T16 5'-CCC TAH26 CCC TAA CCC H15AA CCC T-3' 6721.56 6718.12ON30 A18 5'-CCC TAA CCC TAA CCC TAH18 CCC T-3' 6608.43 6608.28ON31 A18 5'-CCC TAA CCC TAA CCC TAH14 CCC-T-3' 6608.43 6612.98ON32 A18 5'-CCC TAA CCC TAA CCC TAH15 CCC T-3' 6608.43 6608.36ON33 A18 5'-CCC TAA CCC TAA CCC TAH26 CCC T-3' 6608.43 6609.83

Maldi-TOF Mass Spectrometry Data of Oligonucleotides (ON1-ON33)

Page 7: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON1

ON2

ON3

Page 8: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7
Page 9: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON4

ON5

Page 10: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON6

ON7

Page 11: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON8

ON9

Page 12: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON10

ON11

ON1

Page 13: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON12

ON13

Page 14: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON14

ON15

Page 15: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON16

ON17

Page 16: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON18

ON19

Page 17: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON20

ON21

Page 18: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON22

ON23

Page 19: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON24

ON25

Page 20: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON26

ON27

Page 21: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON28

ON29

Page 22: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON30

ON31

Page 23: SUPPLEMENTARY INFORMATION · 2017. 7. 20. · ON10 ON11 ON12 ON13 Temperature (ºC) dA 295nm /dT 25 30 35 40 45 50 55 60 65-0.1 0.1 0.3 0.5 0.7 0.9 1.1 ON1 ON2 ON3 ON4 ON5 ON6 ON7

ON32

ON33


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