S-1

Supporting information for:

Targeting of parallel c-myc G-quadruplex by dimeric

cyanine dye supramolecular assembly: dependence on

the linker length

Lijia Yu, a,b

Qianfan Yang, *a Junfeng Xiang,

*

a Hongxia Sun,

a Lixia Wang,

a Qian Li,

a Aijiao Guan,

a and Yalin Tang*

a

a Beijing National Laboratory for Molecular Sciences, Centre for

Molecular Science, State Key Laboratory for Structural Chemistry for

Unstable and Stable Species, Institute of Chemistry, Chinese Academy of

Sciences (ICCAS), Beijing, 100190, P.R. China.

b University of Chinese Academy of Sciences, Beijing, China

Email: tangyl@iccas.ac.cn, jfxiang@iccas.ac.cn and

yangqf@iccas.ac.cn; Tel: 86 10 62558322 or 86 1 0 82617304.

Electronic Supplementary Material (ESI) for Analyst.This journal is © The Royal Society of Chemistry 2015

S-2

1. The spectra characteristics of TC and TC-P3-7.

Table S1. Absorption and emission maxima (λmax), Stokes’s shifts (∆νst) and quantum yields (Φ) of dyes TC

and TC-P3-7.

Complex λmax(Abs) (nm) λmax(Em)

(nm)

Stoke shift

∆νst (nm)

Φ

TC 586 607 21 0.17a

TC-P3 586 609 23 0.21 a

TC-P4 587 610 23 0.11 a

TC-P5 586 611 23 0.21 a

TC-P6

TC-P7

587

590

611

625

24

35

0.13 a

0.13 a

a The fluorescence quantum yield (Φ) were measured in DMSO solution using crystal violet in methanol as the reference.

2. Absorption and fluorescence spectra of TC-P4

400 500 600 700 8000.0

0.2

0.4

0.6

Abs

orba

nce

Wavlength(nm)

H-aggregate

Dimer

monomer

600 650 700 7500

40

80

120

160

Fluo

resc

ence

Inte

nsity

Wavelength(nm)

H-aggregate

Dimer

monomer

604 nm

597.8nm

587 nm

Figure S1. The absorbance (left) and fluorescence emission (right) of TC-P4 in MeOH (red), CH2Cl2

(blue) and water (black).

As shown in Figure S1, TC-P4 shows different assembly in different solvents. TC-P4

shows strong enhancement fluorescence intensity around 604 nm assigned to monomer in

CH2Cl2, moderate enhancement fluorescence intensity around 597.8 nm assigned to dimer in

MeOH, and strongly quenched around 587 nm assigned to H-aggregates in PBS. It is well

documented that the fluorescence of H-aggregates is strong quenched in aqueous solution1.

3. The stability of TC-P3-7

S-3

20 30 40 50 60 70 80 90 100Temperature(oC)

TC-P3

TC-P4

TC-P5

TC-P6

TC-P7

Figure S2. The stability of dyes TC-P3-7 was carried out in PBS. The absorbance spectra of these dyes were

normalized at 470 nm.

4. The sequence and origin of 4 oligonucleotides in the study

Table S2. Sequence and origin of 4 oligomers

Sequence (from 5 to 3) Motifs Origin

c-myc 22 TGAGGGTGGGTAGGGTGGGTAA Parallel G-quadruplex Oncogenic promoter

c-myc TGAGGGTGGGGAGGGTGGGGAA Parallel G-quadruplex Oncogenic promoter

CT Linear double-stranded Calf thymus

S17 CCAGTTCGTAGTAACCC Single-Stranded

5. The Structure identification of 4 sequences by CD spectroscopy.

240 260 280 300 320-20

-10

0

10

20

30

40

CD

(mdg

ree)

Wavelength(nm)

c-myc c-myc22 CT S17

Figure S3. The CD spectra for 4 oligomers in 10 mM PBS (K+).

6. UV titration spectra of c-myc with TC-P3, TC-P5, TC-P6 and TC-P7.

400 500 600 700 8000.0

0.2

0.4

0.6

Abs

orba

nce

(AU

)

Wavelength (nm)

[TC-P3]=5 M

[c-myc]:[TC-P3] 0

0.25

0.5

0.75

1

2

4

6

8

400 500 600 700 8000.0

0.1

0.2

0.3

0.4

0.5

Abs

orba

nce

(AU

)

Wavelength (nm)

[TC-P3]=5 M

[CT]:[TC-P3]

0

1

2

4

8

400 500 600 700 800

0.0

0.1

0.2

0.3

0.4

0.5

Abs

orba

nce

(AU

)

Wavelength (nm)

[TC-P3]=5 M

[S17]:[TC-P3]

0

1

2

4

8

S-4

400 500 600 700 8000.0

0.1

0.2

0.3

0.4

Abs

orba

nce

(AU

)

Wavelength (nm)

[TC-P5]=5 M

[c-myc]:[TC-P5]

0

0.25

0.5

0.75

1

2

4

6

8

400 500 600 700 8000.00

0.04

0.08

0.12

0.16

0.20

Abs

orba

nce

(AU

)

Wavelength (nm)

[TC-P5]=5 M

[CT]:[TC-P5] 0

1

2

4

8

400 500 600 700 8000.00

0.05

0.10

0.15

0.20[TC-P5]=5 M

[S17]:[TC-P5]

0

1

2

4

8

Abs

orba

nce

(AU

)

Wavelength (nm)

400 500 600 700 8000.0

0.1

0.2

0.3

0.4

Abs

orba

nce

(AU

)

Wavelength (nm)

[TC-P6]=5 M

[c-myc]:[TC-P6]

0

0.25

0.5

0.75

1

2

4

6

8

400 500 600 700 8000.0

0.1

0.2

0.3[TC-P6]=5 M

[CT]:[TC-P6]

0

1

2

4

8A

bsor

banc

e (A

U)

Wavelength (nm)400 500 600 700 800

0.00

0.05

0.10

0.15

0.20

Abs

orba

nce

(AU

)

Wavelength (nm)

[TC-P6]=5 M

[S17]:[TC-P6]

0

1

2

4

8

400 500 600 700 8000.00

0.05

0.10

0.15

Abs

orba

nce

(AU

)

Wavelength (nm)

[TC-P7]=5

[c-myc]:[TC-P7]

0

0.25

0.5

0.75

1

2

4

6

8

400 500 600 700 800

0.00

0.05

0.10

Abs

orba

nce

(AU

)

Wavelength (nm)

[TC-P7]=5 M

[CT]:[TC-P7]

0

1

2

4

8

400 500 600 700 800

0.00

0.04

0.08

Ab

so

rba

nce

(A

U)

Wavelength (nm)

[TC-P7]=5

[S17]:[TC-P7]

0

1

2

4

8

Figure S4. The UV titration spectra of 5 μM TC-P3 and TC-P5-7 in 10 mM PBS with parallel G-quadruplex

c-myc, duplex CT and single-stranded S17.

7. The FL titration spectra of c-myc with TC-P3, TC-P5, TC-P6 and TC-P7.

600 650 700 7500

30

60

90

Fluo

resc

ence

Inte

nsity

Wavelenth(nm)

[TC-P3]=5 M

[c-myc]:[TC-P3]

0

0.25

0.5

0.75

1

2

4

6

8

600 650 700 7500

4

8

12 [TC-P3]=5 M

[CT]:[TC-P3]

0

1

2

4

8

Fluo

resc

ence

Inte

nsity

Wavelength(nm)600 650 700 750

0

2

4

6

8

10

Fluo

resc

ence

Inte

nsity

Wavelength(nm)

[TC-P3]=5 M

[S17]:[TC-P3]

0

1

2

4

8

600 650 700 7500

40

80

120

160

Fluo

resc

ence

Inte

nsity

Wavelength(nm)

[TC-P5]=5

[c-myc]:[TC-P5]

0

0.25

0.5

0.75

1

2

4

6

8

600 650 700 7500

5

10

15

20

25 [TC-P5]=5 M

[CT]:[TC-P5] 0

1

2

4

8

Fluo

resc

ence

Inte

nsity

Wavelength(nm)600 650 700 750

0

3

6

9

12

15

18

Fluo

resc

ence

Inte

nsity

Wavelength(nm)

[TC-P5]=5 M

[S17]:[TC-P5]

0

1

2

4

8

S-5

600 650 700 7500

40

80

120Fl

uore

scen

ce In

tens

ity

Wavelength(nm)

[TC-P6]=5 M

[c-myc]:[TC-P6]

0

0.25

0.5

0.75

1

2

4

6

8

600 650 700 7500

5

10

15

20

25

Fluo

resc

ence

Inte

nsity

Wavelength(nm)

[TC-P6]=5 M

[CT]:[TC-P6]

0

1

2

4

8

600 650 700 7500

3

6

9

12

15

[TC-P6]=5 M

[S17]:[TC-P6]

0

1

2

4

8

Fluo

resc

ence

Inte

nsity

Wavelength(nm)

600 650 700 7500

30

60

90

120

150

Flu

ore

scen

ce In

ten

sity

Wavelength(nm)

[TC-P7]=5

[c-myc]:[TC-P7]

0

0.25

0.5

0.75

1

2

4

6

8

600 650 700 7500

4

8

12

16

Fluo

resc

ence

Inte

nsity

Wavelength(nm)

[TC-P7]=5

[CT]:[TC-P7]

0

1

2

4

8

600 650 700 7500

2

4

6

Fluo

resc

ence

Inte

nsity

Wavelength(nm)

[TC-P7]=5 M

[S17]:[TC-P7]

0

1

2

4

8

Figure S5. The FL titration spectra of 5 μM TC-P3 and TC-P5-7 in 10 mM PBS with parallel G-quadruplex

c-myc, duplex CT and single-stranded S17.

0.0 0.2 0.4 0.6 0.8 1.00

10

20

30

40

50

(F/(F

0-1)

)*([T

C-P

3]/([

TC-P

3]+[

c-m

yc]))

[TC-P3]/([TC-P3]+[c-myc])0.0 0.2 0.4 0.6 0.8 1.0

0

4

8

12

16

(F/(F

0-1)

)*([T

C-P

4]/([

TC-P

4]+[

c-m

yc]))

[TC-P4]/([TC-P4]+[c-myc])

0.0 0.2 0.4 0.6 0.8 1.00

2

4

6

8

10

12

(F/(F

0-1)

)*([T

C-P

5]/([

TC-P

5]+[

c-m

yc]))

[TC-P5]/([TC-P5]+[c-myc])0.0 0.2 0.4 0.6 0.8 1.0

0

4

8

12

(F/(F

0-1)

)*([T

C-P

6]/([

TC-P

6]+[

c-m

yc]))

[TC-P6]/([TC-P6]+[c-myc])

0.0 0.2 0.4 0.6 0.8 1.00

4

8

12

16

F/(F

0-1)

)*([T

C-P

7]/([

TC-P

7]+[

c-m

yc]))

[TC-P7]/([TC-P7]+[c-myc]) Figure S6. Job plot analysis2. TC-P3 and TC-P5-7 were mixed with c-myc at different ratio in 10 mM PBS.

S-6

8．Inhibition activity of TC-P3 and TC-P5-7 on the peroxidase activity of G4/hemin

complexes.

Figure S7. Inhibition of activity of TC-P3 (a) and TC-P5-6 (b-d) on the peroxidase activity of G4/Hemin

complexes. The curves represent the changes of the product concentration (absorbance at 415 nm) of peroxidase

reaction with 2 min. The G4/hemin peroxidase reaction in the absence of dyes was used as a control.

9. Molecular docking experiment

S-7

Figure S8. Molecular models showing interaction of TC-P3-7 (a-f) with G-quadruplex (PDB: 2L7V).

TC-P3-7 could stack on both ends of G-quadruplex.

10. The flow cytometric analysis. Table S3. Flow cytometric analysis of CRL 2614 and Hela cells by TC-P3

Cell Cell No. TC-P3 Uptake( /105 cell)

control stained control stained Δ/ uptake

No.

CRL2614 30059 100000 585 79716 79131

Hela 100000 100000 99 11475 11376

Table S4. Flow cytometric analysis of CRL 2614 and Hela cells by TC-P4

Cell Cell No. TC-P4 Uptake( /105 cell)

control stained control stained Δ/ uptake

S-8

No.

CRL2614 100000 100000 102 51601 51499

Hela 100000 100000 265 91235 90970

Table S5. Flow cytometric analysis of CRL 2614 and Hela cells by TC-P5

Cell Cell No. TC-P5 Uptake( /105 cell)

control stained control stained Δ/ uptake

No.

CRL2614 100000 100000 109 3665 3556

Hela 100000 100000 94 51012 50918

Table S6. Flow cytometric analysis of CRL 2614 and Hela cells by TC-P6

Cell Cell No. TC-P6 Uptake( /105 cell)

control stained control stained Δ/ uptake No.

CRL2614 100000 100000 109 867 758

Hela 100000 100000 94 47654 47560

Table S7. Flow cytometric analysis of CRL 2614 and Hela cells by TC-P7

Cell Cell No. TC-P7 Uptake( /105 cell)

control stained control stained Δ/ uptake No.

CRL2614 100000 100000 109 2103 1994

Hela 100000 100000 94 13341 13247

Reference

1. U. Rösch, S. Yao, R. Wortmann and F. Würthner, Angewandte Chemie, 2006, 118, 7184-7188.

2. P. Job, Annali di Chimica Applicata, 1928, 9, 113-203.