Supplementary Material (ESI) for Chemical Communications
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SUPPORTING INFORMATION:
Materials:
Nucleic Acids.
DNA polymers were purchased from Pharmacia Biotech, Inc.
(Piscataway, NJ) and were used without further purification. DNA used include
poly(dA), lot number: 9017836021; poly(dT), lot numbers: 8107834021 and
9107834021; poly(dA)(dT): lot number: 9067860021; Poly(rA):
7104110011,
Poly(rU):
lot number: 9034440021;.
lot number:
The concentrations of all the
polymer solutions were determined spectrophotometrically using the following extinction
coefficients (in units of mol of nucleotide/L)-1 cm-1= 8900 for poly(dA), =
9000 for poly(dT), = 6000 for poly(dA)•poly(dT), ),  = 9800 for poly(rA), 
= 9350 for poly(rU)..
Chemicals: Neomycin B, 1-pyrenebutyric acid N-hydroxysuccinimide ester, 2,4,6Triisopropylbenzenesulfonyl chloride, Di-tert-butyl dicarbonate, 2-aminoethanethiol
hydrochloride, 4-dimethyl-aminopyridine and 1-aminopyrene were purchased from Acros
(New Jersey) and were used without further purification.
4M HCl/disoxane was
purchased from Aldrich and was used without further purification. Methylene chloride,
DMF, dioxane were used as received. Pyridine was purified by CaH2 with distillation
before using.
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
NHR
O
NH2
HO
HO
HO
HO
O
H2 N
NH2
O
HO
O O
OH
O
HO
HO
NHR
HO
(Boc)2 O, DMF/H 2 O
NH2
Et 3N, 5h, 60%
HO
HO
NH2 O OH
H2 N
O
RHN
O
O O
NHR
OH
NHR O OH
RHN
1a
Neomycin B (1)
TIBSCl, pyridine,
rt, 40h, 60%
NHR
O
HO
HO
NHR
S
NH2
HO
HO
RHN
O
HO
HO
NHR
TIBSO
NH2CH 2CH 2SH
RHN
O
O O
NHR
O
NHR
OH
NaOEt/EtOH, 12h, rt.
50%
O
HO
HO
NHR O OH
RHN
O
O O
NHR
OH
NHR O OH
RHN
1c
1b
O
n
NHR
O
O
O
O
H
N
n
n=3
O
HO
HO
RHN
S
O
HO
HO
CH 2Cl 2, rt, overnight,
NHR
OH
NHR O OH
RHN
80%
RHN
O
O O
n=3
1d
4M HCl/dioxane
HSCH 2CH 2SH,
5min., rt, 80%
Abbreviations
R = Boc = di-tert-butyldicarbonate
TPSCl = 2,4,6-triisopropylbenzenesulfonyl chloride
NH2
H
N
n
O
HO
HO
O
HO
HO
H2 N
S
NH2
O
H2 N
O
O
O
OH
NH2 O OH
1e
Figure S1. Synthesis of Pyrene-Neomycin
n=3
NH2
Supplementary Material (ESI) for Chemical Communications
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Pyrene-neomycin Synthesis -Experimental
Compound 1a-1c have previously been reported (Kirk, S. R., Luedtke, N. W., Tor, Y., J.
Am. Chem. Soc., 2000, 122, 980-981).
Compound 1d. Compound 1c (70mg, 0.055mmol) and 4-dimethyl-aminopyridine
(1mg) were dissolved in 5ml anhydrous methylene chloride at room temperature. 1pyrenebutyric acid N-hydroxysuccinimide ester (64mg, 0.165mmol, 3 equiv.) was added
into the solution. The reaction mixture was kept stirring overnight. Organic solvent was
then removed by vacuum.
Flash column chromatography (5% CH3OH in CH2Cl2)
afforded the desired product as a white solid. (62mg, 73%). Rf 0.48 (10% CH3OH in
CH2Cl2); 1HNMR (500MHz, methanol-d4, 25C): 7.9-8.3 (m, 9H, Acr), 5.48 (br, 1H),
5.37 (1H), 5.13 (1H), 4.92 (1H), 4.23 (1H), 4.09(2H), 3.89 (2H), 3.76 (2H), 3.44-3.56
(6H), 3.0-3.3 (9H), 2.86 (2H), 2.7 (4H), 2.38 (2H), 2.18 (2H), 1.94 (1H), 1.4 (m, 54H).
Compound 1e. Compound 1d (10mg) was dissolved in dioxane (0.6ml, treated over
alumina). 1, 2-ethanedithiol (0.002 ml) was added followed by 4M HCl/dioxane (0.6ml).
The solution was swirled for 5 min by hand upon which a pale yellow precipitate formed.
Further precipitation was induced by adding ether and hexane (0.6ml each). Precipitate
was recovered by centrifugation and several washes with ether and hexane. The paleyellow solid was redissolved in water and lyophilized overnight (6mg, 80% yield). max
=342nm; 342 = 16778 cm-1M-1
C45H66N7O13S 944.
HRMS (MALDI) m/z [M+2H]+ 946, calcd for
Supplementary Material (ESI) for Chemical Communications
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1
H NMR of 1a in CD3OD
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1
H NMR of 1b in CDCl3
Supplementary Material (ESI) for Chemical Communications
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1
H NMR of 1c in CD3OD
Supplementary Material (ESI) for Chemical Communications
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1
H NMR of 1d in CD3OD
Supplementary Material (ESI) for Chemical Communications
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NH2
H
N
O
HO
HO
H2 N
9.0
8.5
8.0
7.5
7.0
6.5
6.0
5.5
1
5.0
4.5
4.0
3.5
H NMR of 1e in D2O
3.0
2.5
2.0
O
HO
HO
S
NH2
O
H2 N
O
O O
NH2
OH
NH2 O OH
1.5
1.0
0.5
0.0
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
MS (MALDI) Spectrum of 1e
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
2. 5
2.5
2
2
1. 5
A
1.5
1
1
0. 5
0.5
0
0
20 0
25 0
30 0
35 0
40 0
45 0
50 0
55 0
W av elength (nm)
UV spectrum of Pyrene-neomycin
264 = 10956 cm-1M-1; 275 = 19152 cm-1M-1;
326 = 10663 cm-1M-1; 342 = 16778 cm-1M-1.
Supplementary Material (ESI) for Chemical Communications
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Melting Curves
UV melting profiles of the poly(dA)2poly(dT) in the presence of 150mM KCl at the indicated
ligand concentrations. [DNA]=15M base triplet. Solution conditions: 10 mM sodium
cacodylate buffer, 0.5 mM EDTA, pH 7.2. Samples were heated from 20 to 90C at 5 deg/min,
the annealing(90-5C) and the melting (5-90C) were conducted at 0.2 deg/min, and the samples
were brought back to 20C at a rate of 5 deg/min.
0 M ligand
0.5 M 1-Aminopyrene
0.21
0.23
0.225
0.205
0.22
71
A 26
0
A 26
71
0
0.2
0.195
0.215
0.21
32
0.19
32
0.205
0.185
0.2
0.18
0.195
0
20
40
 60
80
T( C)
100
20
1 M 1-Aminopyrene
30
40
50
60
T( C)
70
90
100
90
100
2 M 1-Aminopyrene
0.215
0.215
0.21
0.21
71.1
71.1
0.205
A 26
0
0
0.205
A 26
80
0.2
0.195
0.2
0.195
32
0.19
32.7
0.19
0.185
0.185
20
30
40
50
60

T( C)
70
80
90
100
20
30
40
50
60
T( C)
70
80
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
4 M 1-Aminopyrene
10 M 1-Aminopyrene
0.205
0.3
0.2
0.29
71.4
71
A 26
0.19
0.27
32.4
32.2
0.185
0.26
0.18
0.25
20
30
40
50
60

70
80
90
100
90
100
T( C)
20 M 1-Aminopyrene
0.31
0.3
0.29
71
0
A 26
0.28
A 26
0
0
0.195
0.28
0.27
32.4
0.26
0.25
20
30
40
50
60
T( C)
70
80
0
20
40
60
T( C)
80
100
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles of the poly(dA)2poly(dT) in the presence of 150mM KCl at the
indicated ligand concentrations. [DNA]=15M base triplet. Solution conditions: 10 mM
sodium cacodylate buffer, 0.5 mM EDTA, pH 7.2. Samples were heated from 20 to 90C
at 5 deg/min, the annealing(90-5C) and the melting (5-90C) were conducted at 0.2
deg/min, and the samples were brought back to 20C at a rate of 5 deg/min.
polydA2polydT with
0.5 M pyrene-7-neo
polydA2polydT with 0 M ligand
0.3
0.32
0.28
0.3
A260
A260
70
0.26
0.24
0.26
36.5
32
0.22
71
0.28
0.24
0.2
0.22
20
30
40
50
o 60
T( C)
70
80
90
20
30
polydA2polydT with
1M pyrene-7-neo
0.32
0.3
0.3
71
A260
A260
60
T( o C)
70
80
90
72.2
0.28
0.26
43.3
0.24
50
polydA2polydT with
2M pyrene-7-neo
0.32
0.28
40
0.26
55.6
0.24
0.22
0.22
0.2
0.2
20
30
40
50
o
60
T( C)
70
80
90
20
polydA2poldT with
4M pyrene-7-neo
30
40
50
60
T( o C)
70
80
90
polydA2polydT with
6M pyrene-7-neo
0.47
0.34
0.46
0.32
0.45
72.6
A260
A260
0.3
0.28
59.1
0.26
74.2
0.44
0.43
0.42
62
0.41
0.24
0.4
0.39
0.22
20
30
40
50
o
60
T( C)
70
80
90
30
40
50
60
T( o C)
70
80
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles of the poly(dA)2poly(dT) in the presence of 150mM KCl at the indicated
ligand concentrations. [DNA]=15M base triplet. Solution conditions: 10 mM sodium
cacodylate buffer, 0.5 mM EDTA, pH 7.2. Samples were heated from 20 to 90C at 5 deg/min,
the annealing(90-5C) and the melting (5-90C) were conducted at 0.2 deg/min, and the samples
were brought back to 20C at a rate of 5 deg/min.
polydA2polydT with
0.5 M neomycin
polydA2polydT with 0 M ligand
0.42
0.44
0.4
0.42
71
0.4
A260
A260
0.38
0.36
71
0.38
0.36
0.34
33
34
0.34
0.32
0.32
0.3
24
32
40
48
56
T ( o C)
64
72
24
80
0.42
0.42
0.4
0.4
71
A260
A260
48
56
T ( o C)
0.38
0.36
0.34
40
64
72
80
polydA2polydT with
2M neomycin
polydA2polydT with
1M neomycin
0.38
32
71
0.36
0.34
35.1
36.5
0.32
0.32
0.3
0.3
24
32
40
48
56
T ( o C)
64
72
80
24
polydA2polydT with
4M neomycin
32
40
48
56
T ( o C)
64
72
80
72
80
polydA2polydT with
6M neomycin
0.36
0.5
0.48
0.34
0.46
72.1
0.44
A260
A 260
0.32
0.3
72.2
0.42
0.4
0.28
0.38
43
0.26
46
0.36
0.24
0.34
24
32
40
48
o 56
T( C)
64
72
80
24
32
40
48
56
T ( o C)
64
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles of the poly(dA)2poly(dT) in the presence of 150mM KCl at the indicated
ligand concentrations. [DNA]=15M base triplet. Solution conditions: 10 mM sodium
cacodylate buffer, 0.5 mM EDTA, pH 7.2. Samples were heated from 20 to 90C at 5 deg/min,
the annealing(90-5C) and the melting (5-90C, curves shown below) were conducted at 0.2
deg/min, and the samples were brought back to 20C at a rate of 5 deg/min.
polydA2polydT with 0.5 M neo
+ 0.5 M1-aminopyrene
polydA2polydT with 0 M ligand
0.42
0.42
0.4
0.4
71
0.38
A260
A260
0.38
0.36
0.34
71
0.36
0.34
33
34.5
0.32
0.32
0.3
0.3
24
32
40
48
o
56
64
72
80
24
32
40
48
56
64
72
80
T ( C)
T ( o C)
polydA2polydT with 1 M neo
+ 1 M 1-aminopyrene
polydA2polydT with 2 M neo
+ 2 M 1-aminopyrene
0.42
0.5
0.48
0.4
0.46
71
72.8
0.44
A260
A260
0.38
0.36
0.42
0.4
0.34
36
0.38
40
0.32
0.36
0.3
0.34
24
32
40
48
56
T ( o C)
64
72
80
24
32
40
48
56
T ( o C)
64
72
80
polydA2polydT with 6 M neo
+ 6 M 1-aminopyrene
polydA2polydT with 4 M neo
+4 M 1-aminopyrene
0.42
0.42
0.4
0.4
71
71
A260
0.38
A260
0.38
0.36
53
0.36
49
43
49
0.34
0.34
0.32
0.32
24
32
40
48
56
T ( o C)
64
72
80
24
32
40
48
56
T ( o C)
64
72
80
Supplementary Material (ESI) for Chemical Communications
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UV melting profiles (287nm) of the poly(rA)poly(rU) and poly(rA)2poly(rU) in the presence
of 35mM NaCl at the indicated ligand concentrations. [RNA]=30M base triplet. Solution
conditions: 10 mM sodium cacodylate buffer, 0.1 mM EDTA, pH 6.8. Samples were heated
from 20 to 90C at 0.2 deg/min.
polyrApolyrU with 0 M ligand
polyrA2polyrU with 0 M ligand
0. 32
0. 35
0. 315
0. 31
A 287
48
A 287
48.0
0. 305
0. 3
0. 295
0. 29
0. 285
0. 28
0. 3
20
25
30
35
40
45
o
50
55
60
20
25
30
35
40
o
45
50
55
60
T( C)
T( C)
polyrApolyrU with 1 M pyrene-7-neo
polyrA2polyrU with 1 M pyrene-7-neo
0. 33
0. 35
0. 325
0. 34
0. 32
A 287
A 287
48
0. 315
0. 31
0. 305
48
0. 33
0. 32
0. 3
0. 31
0. 295
0. 29
0. 3
20
25
30
35
40
o
45
50
55
60
20
25
30
35
T( C)
40
45
T( oC)
50
55
60
polyrA2polyrU with 2 M pyrene-7-neo
polyrApolyrU with 2 M pyrene-7-neo
0. 33
0. 35
0. 345
0. 32
49.2
0. 31
A 287
A 287
0. 34
50
0. 335
0. 3
0. 33
0. 325
0. 32
0. 29
0. 315
0. 28
0. 31
20
25
30
35
40
45
T( oC)
50
55
60
20
25
30
35
40
45
T( oC)
50
55
60
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
polyrA2polyrU with 4 M pyrene-7-neo
polyrApolyrU with 4 M pyrene-7-neo
0. 35
0. 37
0. 34
0. 36
54.7
0. 35
A 287
A 287
0. 33
55.2
0. 32
0. 34
0. 31
0. 33
0. 3
0. 32
0. 29
0. 31
20
30
40
o50
T( C)
60
70
20
30
40
o
50
T( C)
60
70
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles (280nm) of the poly(rA)poly(rU) and poly(rA)2poly(rU) in the presence
of 35mM NaCl at the indicated ligand concentrations. [RNA]=30M base triplet. Solution
conditions: 10 mM sodium cacodylate buffer, 0.1 mM EDTA, pH 6.8. Samples were heated
from 20 to 90C at 0.2 deg/min.
polyrApolyrU with 0 M ligand
polyrA2polyrU with 0 M ligand
0. 354
0. 45
0. 352
0. 445
31
A 260
A 280
0. 35
0. 348
0. 346
0. 44
0. 435
0. 344
0. 43
0. 342
0. 34
0. 425
20
25
30
35
o
40
45
50
20
25
30
35
40
45
50
T( C)
T( oC)
polyrApolyrU with 1 M pyrene-7-neo
polyrA2polyrU with 1 M pyrene-7-neo
0. 364
0. 445
0. 362
0. 44
A 280
A 280
0. 36
0. 358
34.1
0. 435
0. 356
0. 43
0. 354
0. 352
0. 425
20
25
30
35
o
40
45
50
20
25
30
35
o
40
45
50
T( C)
T( C)
polyrApolyrU with 2 M pyrene-7-neo
polyrA2polyrU with 2 M pyrene-7-neo
0. 36
0. 46
0. 455
0. 358
A 280
A 280
0. 45
0. 356
0. 354
0. 445
36.1
0. 44
0. 435
0. 352
0. 43
0. 35
0. 425
20
25
30
35
o
T( C)
40
45
50
20
25
30
35
o
T( C)
40
45
50
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
polyrA2polyrU with 4 M pyrene-7-neo
polyrApolyrU with 4 M pyrene-7-neo
0. 39
0. 49
0. 48
A 280
A 280
0. 385
0. 38
0. 47
40.1
0. 46
0. 375
0. 45
0. 37
0. 44
20
25
30
35
40
o
T( C)
45
50
55
60
20
25
30
35
40
o
T( C)
45
50
55
60
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles (284nm) of the poly(rA)poly(rU) and poly(rA)2poly(rU) in the presence
of 35mM NaCl at the indicated ligand concentrations. [RNA]=30M base triplet. Solution
conditions: 10 mM sodium cacodylate buffer, 0.1 mM EDTA, pH 6.8. Samples were heated
from 20 to 90C at 0.2 deg/min.
polyrA2polyrU with 0 M ligand
0. 35
0. 4
0. 34
0. 39
0. 33
0. 38
A 284
A 284
polyrApolyrU with 0 M ligand
48
0. 32
48
0. 37
0. 31
0. 36
0. 3
0. 35
0. 29
31.7
0. 34
20
25
30
35
o
40
T( C)
45
50
55
60
20
polyrApolyrU with 1 M pyrene-7-neo
25
30
35
40
T( oC)
45
50
55
60
polyrA2polyrU with 1 M pyrene-7-neo
0. 35
0. 39
0. 385
34.9
0. 38
48
48.0
A 284
A 284
0. 375
0. 37
0. 365
0. 36
0. 355
0. 3
0. 35
20
25
30
35
40
45
o
50
55
60
20
25
30
35
40
45
o
50
55
60
T( C)
T( C)
polyrApolyrU with 2 M pyrene-7-neo
polyrA2polyrU with 2 M pyrene-7-neo
0. 35
0. 395
0. 39
36.1
0. 385
A 284
A 284
0. 38
50
50.4
0. 375
0. 37
0. 365
0. 36
0. 3
0. 355
20
30
40
o
50
T( C)
60
70
20
30
40
o
50
T( C)
60
70
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
polyrA2polyrU with 4 M pyrene-7-neo
polyrApolyrU with 4 M pyrene-7-neo
0. 37
0. 42
0. 36
0. 41
40.1
55
55.2
0. 4
A 284
A 284
0. 35
0. 34
0. 39
0. 33
0. 38
0. 32
0. 37
0. 31
0. 36
20
30
40
o
50
T( C)
60
70
20
30
40
o
50
T( C)
60
70
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles (280nm) of the poly(rA)poly(rU) and poly(rA)2poly(rU) in the presence
of 35mM NaCl at the indicated ligand concentrations. [RNA]=30M base triplet. Solution
conditions: 10 mM sodium cacodylate buffer, 0.1 mM EDTA, pH 6.8. Samples were heated
from 20 to 90C at 0.2 deg/min.
polyrA2polyrU with 0 M ligand
0. 36
0. 45
0. 355
0. 445
A 280
A 280
polyrApolyrU with 0 M ligand
0. 35
0. 345
35
0. 44
0. 435
0. 34
0. 43
20
25
30
35
40
o
45
50
20
25
30
35
40
o
T( C)
45
50
T( C)
polyrApolyrU with 1 M neomycin
polyrA2polyrU with 1 M neomycin
0. 358
0. 445
0. 356
0. 44
A 280
A 280
0. 354
0. 352
0. 35
0. 348
41
0. 435
0. 43
0. 346
0. 344
0. 425
20
24
28
32
36
40
o
44
48
52
20
24
28
32
T( C)
polyrApolyrU with 2 M neomycin
40
o
44
48
52
polyrA2polyrU with 2 M neomycin
0. 375
0. 46
0. 37
0. 45
0. 365
0. 44
A 280
A 280
36
T( C)
0. 36
0. 355
43.6
0. 43
0. 42
0. 35
0. 41
20
25
30
35
o
40
T( C)
45
50
55
20
25
30
35
o
40
T( C)
45
50
55
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
polyrA2polyrU with 4 M neomycin
0. 344
0. 44
0. 342
0. 435
0. 34
0. 43
A 280
A 280
polyrApolyrU with 4 M neomycin
0. 338
0. 336
0. 334
0. 425
0. 42
46
0. 415
0. 332
0. 41
0. 33
0. 405
20
25
30
35
40
o
T( C)
45
50
55
60
30
35
40
45
o
T( C)
50
55
60
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles (284nm) of the poly(rA)poly(rU) and poly(rA)2poly(rU) in the presence
of 35mM NaCl at the indicated ligand concentrations. [RNA]=30M base triplet. Solution
conditions: 10 mM sodium cacodylate buffer, 0.1 mM EDTA, pH 6.8. Samples were heated
from 20 to 90C at 0.2 deg/min.
polyrA2polyrU with 0 M ligand
0.4
0. 33
0.39
48
0. 32
A284
A 284
polyrApolyrU with 0 M ligand
0. 34
0. 31
34.5
0.38
48.8
0.37
0.36
0. 3
0.35
0. 29
20
25
30
35
40
o
45
50
55
20
60
25
30
35
T( C)
40
45
T( o C)
50
55
60
polyrA2polyrU with 1 M neomycin
polyrApolyrU with 1 M neomycin
0.395
0. 35
41
0.39
0. 34
51.2
0.38
51.2
0. 33
A284
A 284
0.385
0. 32
0.375
0.37
0.365
0. 31
0.36
0.355
0. 3
20
25
30
35
40
45
o
50
55
20
60
25
30
35
T( C)
polyrApolyrU with 2 M neomycin
40
45
T( o C)
50
55
60
polyrA2polyrU with 2 M neomycin
0.36
0.39
42.6
0.385
0.35
A284
A284
0.38
52
0.34
0.33
51.6
0.375
0.37
0.365
0.32
0.36
0.31
0.355
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
30
35
40
45
T( o C)
50
55
60
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
polyrApolyrU with 4 M neomycin
polyrA2polyrU with 4 M neomycin
0.335
0.4
0.33
53.2
0.325
0.39
A284
A284
0.32
0.315
0.31
0.38
53.2
0.37
0.305
0.36
0.3
0.295
0.35
20
25
30
35
40
o
45
T( C)
50
55
60
28
32
36
40
44
48
T( o C)
52
56
60
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles (287nm) of the poly(rA)poly(rU) and poly(rA)2poly(rU) in the presence
of 35mM NaCl at the indicated ligand concentrations. [RNA]=30M base triplet. Solution
conditions: 10 mM sodium cacodylate buffer, 0.1 mM EDTA, pH 6.8. Samples were heated
from 20 to 90C at 0.2 deg/min.
polyrA2polyrU with 0 M ligand
polyrApolyrU with 0 M ligand
0.32
0.35
0.315
0.34
0.31
A287
A287
0.305
48
0.3
0.295
48.8
0.33
0.32
0.29
0.31
0.285
0.28
0.3
20
25
30
35
40
o
45
50
55
60
20
25
30
35
T( C)
0.325
0.345
0.32
0.34
0.315
0.335
A287
A287
0.35
51.2
0.31
45
50
55
60
polyrA2polyrU with 1 M neomycin
polyrApolyrU with 1 M neomycin
0.33
0.305
40
T( o C)
0.33
0.325
0.3
0.32
0.295
0.315
0.29
51.2
0.31
20
25
30
35
40
o
45
T( C)
50
55
60
20
polyrApolyrU with 2 M neomycin
25
30
35
40
45
T( o C)
50
55
60
polyrA2polyrU with 2 M neomycin
0.34
0.35
0.345
52
0.34
51.2
0.335
0.32
A287
A287
0.33
0.31
0.33
0.325
0.32
0.3
0.315
0.29
0.31
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
30
35
40
45
T( o C)
50
55
60
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
polyrApolyrU with 4 M neomycin
polyrA2polyrU with 4 M neomycin
0.32
0.37
0.315
0.36
0.31
0.35
53
0.3
A287
A287
0.305
0.295
53.1
0.34
0.33
0.29
0.32
0.285
0.28
0.31
20
30
40
o
50
T( C)
60
70
30
35
40
45
50
55
T( o C)
60
65
70
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles (280nm) of the poly(rA), poly(rU) and poly(rA)2poly(rU) in the presence
of 35mM NaCl at the indicated ligand concentrations. [RNA]=30M base triplet. Solution
conditions: 10 mM sodium cacodylate buffer, 0.1 mM EDTA, pH 6.8. Samples were heated
from 20 to 90C at 0.2 deg/min.
polyrA2polyrU with 0 M ligand
polyrApolyrU with 0 M ligand
0.33
0.435
0.329
48
0.328
0.43
A280
A280
0.327
0.326
0.325
35
0.425
0.42
0.324
0.415
0.323
0.322
0.41
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
polyrApolyrU with
1M 1-aminopyrene
30
35
40
45
T( o C)
50
55
60
55
60
55
60
polyrA2polyrU with
1M 1-aminopyrene
0.35
0.445
0.348
0.44
48
0.346
A280
A280
0.344
0.342
0.34
35.7
0.435
0.43
0.338
0.425
0.336
0.334
0.42
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
polyrApolyrU with
2M 1-aminopyrene
30
35
40
45
T( o C)
50
polyrA2polyrU with
2M 1-aminopyrene
0.355
0.445
0.44
49
0.435
A280
A280
0.35
0.345
35.7
0.43
0.425
0.34
0.42
0.335
0.415
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
30
35
40
45
T( o C)
50
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
polyrApolyrU with
4M 1-aminopyrene
0.35
0.48
0.345
0.47
35.4
48
A280
0.34
A280
polyrA2polyrU with
4M 1-aminopyrene
0.335
0.46
0.45
0.33
0.44
0.325
0.32
0.43
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
30
35
40
45
T( o C)
50
55
60
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles (284 nm) of the poly(rA), poly(rU) and poly(rA)2poly(rU) in the presence
of 35mM NaCl at the indicated ligand concentrations. [RNA]=30M base triplet. Solution
conditions: 10 mM sodium cacodylate buffer, 0.1 mM EDTA, pH 6.8. Samples were heated
from 20 to 90C at 0.2 deg/.
polyrA2polyrU with 0 M ligand
0.38
0.31
0.37
48
0.3
A284
A284
polyrApolyrU with 0 M ligand
0.32
0.29
0.28
34
48
0.36
0.35
0.34
0.27
0.33
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
polyrApolyrU with
1M 1-aminopyrene
30
35
40
45
T( o C)
50
60
polyrA2polyrU with
1M 1-aminopyrene
0.34
0.39
0.33
0.38
34.5
48
0.37
0.32
A284
A284
55
0.31
0.36
0.35
0.3
0.34
0.29
0.33
20
25
30
35
40
45
T( o C)
50
55
60
20
25
polyrApolyrU with
2M 1-aminopyrene
30
35
40
45
T( o C)
50
55
60
55
60
polyrA2polyrU with
2M 1-aminopyrene
0.34
0.39
0.33
0.38
0.32
0.37
A284
A284
35
0.31
0.3
48
0.36
0.35
0.29
0.34
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
30
35
40
45
T( o C)
50
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
polyrA2polyrU with
4M 1-aminopyrene
polyrApolyrU with
4M 1-aminopyrene
0.34
0.43
35
0.42
0.33
0.41
48
0.4
A284
A284
0.32
48.1
0.31
0.3
0.39
0.38
0.37
0.29
0.36
0.28
0.35
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
30
35
40
45
T( o C)
50
55
60
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
UV melting profiles (287 nm)of the poly(rA), poly(rU) and poly(rA)2poly(rU) in the presence
of 35mM NaCl at the indicated ligand concentrations. [RNA]=30M base triplet. Solution
conditions: 10 mM sodium cacodylate buffer, 0.1 mM EDTA, pH 6.8. Samples were heated
from 20 to 90C at 0.2 deg/min and the samples were brought back to 5C at a rate of 5 deg/min.
polyrA2polyrU with 0 M ligand
0.33
0.295
0.325
0.29
0.32
0.285
0.315
0.28
A287
A287
polyrApolyrU with 0 M ligand
0.3
48
0.275
0.305
0.27
0.3
0.265
0.295
0.26
48.8
0.31
0.29
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
35
40
45
T( o C)
50
55
60
55
60
55
60
polyrA2polyrU with
1M 1-aminopyrene
0.32
0.34
0.31
0.33
0.3
A287
A287
polyrApolyrU with
1M 1-aminopyrene
30
48.1
0.29
0.28
48.4
0.32
0.31
0.3
0.27
0.29
20
25
30
35
40
o
45
50
55
60
20
25
30
35
T( C)
polyrApolyrU with
2M 1-aminopyrene
40
45
T( o C)
50
polyrA2polyrU with
2M 1-aminopyrene
0.315
0.34
0.31
0.33
0.305
48.1
A287
A287
0.3
0.295
0.29
0.32
49
0.31
0.285
0.3
0.28
0.275
0.29
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
30
35
40
45
T( o C)
50
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
polyrApolyrU with
4M 1-aminopyrene
polyrA2polyrU with
4M 1-aminopyrene
0.31
0.37
0.36
0.3
A287
A287
0.35
48
0.29
0.28
48.4
0.34
0.33
0.32
0.27
0.31
0.26
0.3
20
25
30
35
40
o
45
T( C)
50
55
60
20
25
30
35
40
45
T( o C)
50
55
60
Supplementary Material (ESI) for Chemical Communications
This journal is © The Royal Society of Chemistry 2001
Computer Modeling
Step I: DNA (TAT) triplex conformation
The original structure of dT10dA10dT10 triplex was obtained from the NMR structure
reported by Feigon (Biochemistry 1998). 27 sodium ions were added to neutralize the
structure. The conformation was then optimized by AMPER* force field, in water, to
within a gradient of 0.5 kJ/molÅ. The movements of the atoms of the external bases
were restricted during minimization.
Step II: Neomycin conformation
Neomycin structure was built and optimized with MacroModel and SYBYL programs
using AMBER* force field. The all atom AMBER* force field has been used since it
contains parameters for both neomycin and the DNA triplex. In accordance with NMR
experiments, five of the six-neomycin amines were protonated. Conformational
searching was done with Monte Carlo routine from MacroModel, using all atom
AMBER* force field, the force field charges, and the continuum GB/SA model of water
as implemented in MacroModel. All the flexible bonds were selected.
Conformation of neomycin bound to W-H groove.
Step III Pyrene-neomycin conformation
Pyrene-neomycin conformation was generated based on neomycin conformation. The
generated conformation was then optimized by AMPER* force field and water as a
solvent.
Step IV Docking
After optimizing the pyrene-neomycin conformation, the structure was docked into
Waston-Hoogsteen groove of TAT triplex in different orientations. Restricting the
movement of the triplex, the structure of the complex was optimized using AMBER*
force field and water as a solvent.