supplementary information · 2017. 7. 20. · on10 on11 on12 on13 temperature (ºc) da 295nm /dt 25...

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: erik@sdu.dkb 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

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.

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.

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.

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

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)

ON1

ON2

ON3

ON4

ON5

ON6

ON7

ON8

ON9

ON10

ON11

ON1

ON12

ON13

ON14

ON15

ON16

ON17

ON18

ON19

ON20

ON21

ON22

ON23

ON24

ON25

ON26

ON27

ON28

ON29

ON30

ON31

ON32

ON33