- Email: [email protected]
Clicked polycyclic aromatic hydrocarbon as a hybridization-responsive fluorescent artificial nucleobase in pyrrolidinyl peptide nucleic acids
1
Supporting information Clicked polycyclic aromatic hydrocarbon as a hybridization-responsive fluorescent artificial nucleobase in pyrrolidinyl peptide nucleic acids Woraluk Mansawat,a Chalothorn Boonlua,a Khatcharin Siriwong,b and Tirayut Vilaivan a,* a
Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand. b Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand. *E-mail: [email protected]
Fig. S1 Fig. S2 Fig. S3 Fig. S4 Fig. S5 Fig. S6 Fig. S7 Fig. S8 Fig. S9 Fig. S10 Fig. S11 Fig. S12 Fig. S13
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H (a) and C (b) NMR spectra of 4 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA1 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA2 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA3 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA1 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA5 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA6 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA7 HPLC chromatogram of crude PNA3 and after click reaction Thermal denaturation curves of hybrids with of PNA1 with DNA1–DNA4 Photographs of PNA1 and its hybrids with DNA1–DNA4 under black light Selected snapshots of MD structures showing the hydrogen-bond formation between TzPy and opposite base Fluorescence spectra of PNA5 (a) and PNA7 (b) in the absence (–) and presence (···) of complementary DNA
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2
9.0
8.0
7.0
6.0
5.0
4.0
3.0
2.0
1.0
ppm (t1)
(a)
150
100
50
ppm (t1)
(b) Fig. S1. 1H (400 MHz, DMSO-d6) (a) and 13C NMR (100 MHz, DMSO-d6) (b) spectra of 4.
3
(a)
(b) Fig. S2. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA1 (BzGCATTAXAGATAC-LysNH2; X = TzPy) obtained by pre-formed TzPy monomer (CCA matrix) (calcd. for [M+H]+: m/z = 4779.2).
4
(a)
(b) Fig. S3. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA2 (BzGCATTAXAGATAC-LysNH2; X = C) (CCA matrix) (calcd. for [M+H]+: m/z = 4621.0).
5
(a)
(b) Fig. S4. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA3 (BzGCATTAXAGATAC-LysNH2; X = N3) (CCA matrix) (calcd. for [M+H]+: m/z = 4552.9).
6
(a)
(b) Fig. S5. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA1 (BzGCATTAXAGATAC-LysNH2; X = TzPy) obtained by post-synthetic click reaction (CCA matrix) (calcd. for [M+H]+: m/z = 4779.2).
7
(a)
(b) Fig. S6. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA5 (BzGCATTTXTGATAC-LysNH2; X = TzPy) (CCA matrix) (calcd. for [M+H]+: m/z = 4761.2).
8
(a)
(b) Fig. S7. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA6 (BzGCATTTXTGATAC-LysNH2; X = TzPh) (CCA matrix) (calcd. for [M+H]+: m/z = 4637.0).
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(a)
(b) Fig. S8. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA7 (BzGCATTTXTGATAC-LysNH2; X = TzAn) (CCA matrix) (calcd. for [M+H]+: m/z = 4737.1).
10
Fig. S9. HPLC chromatogram of crude PNA3 (Bz-GCATTAN3AGATAC-LysNH2) before (top) and after (bottom) click reaction with 1-ethynylpyrene.
11
1.30
Normalized A
260
1.25 1.20
PNA1 + DNA1 (G) PNA1 + DNA2 (A) PNA1 + DNA3 (C) PNA1 + DNA4 (T) PNA3 + DNA4 (T)
1.15 1.10 1.05 1.00 0.95 20
30
40
50
60 o
70
80
90
T ( C) Fig. S10. Thermal denaturation curves of hybrids between PNA1 (TzPy) with DNA1–DNA4 and PNA3 (azide) with DNA4. Conditions: 2.5 µM PNA, 3.0 µM DNA in 10 mM sodium phosphate buffer pH 7.0.
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PNA1 ss
+DNA1 Y=G
+DNA2 Y=A
+DNA3 Y=C
+DNA4 Y=T
Fig. S11. Photographs of PNA1 and its hybrids with DNA1–DNA4 viewed under black light. Conditions: 2.5 µM PNA, 3.0 µM DNA in 10 mM sodium phosphate buffer pH 7.0.
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TzPy-Guanine (PNA1·DNA1)
TzPy-Adenine (PNA1·DNA2)
TzPy-Cytosine (PNA1·DNA3)
TzPy-Thymine (PNA1·DNA4)
Fig. S12. Selected snapshots of MD structures showing the hydrogen-bond formation between TzPy and opposite base for four simulated systems. The hydrogen bond acceptor-donor distances are shown.
14 350
350 PNA PNA+DNA
250 200 150 100 50 0 350
PNA PNA+DNA
300 Fluorescence (Arbitrary unit)
Fluorescence (Arbitrary unit)
300
250 200 150 100 50
400
450
500
Wavelength (nm)
550
600
0 350
400
450
500
550
600
Wavelength (nm)
Fig. S13. Fluorescence spectra of PNA5 (a) and PNA7 (b) in the absence (···) and presence (–) of complementary DNA (5'-GTATCAGAAATGC-3') (conditions: 2.5 µM PNA, 3.0 µM DNA in 10 mM sodium phosphate buffer pH=7.0, λexcit = 350 nm).
Supporting information Clicked polycyclic aromatic hydrocarbon as a hybridization-responsive fluorescent artificial nucleobase in pyrrolidinyl peptide nucleic acids Woraluk Mansawat,a Chalothorn Boonlua,a Khatcharin Siriwong,b and Tirayut Vilaivan a,* a
Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand. b Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand. *E-mail: [email protected]
Fig. S1 Fig. S2 Fig. S3 Fig. S4 Fig. S5 Fig. S6 Fig. S7 Fig. S8 Fig. S9 Fig. S10 Fig. S11 Fig. S12 Fig. S13
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H (a) and C (b) NMR spectra of 4 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA1 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA2 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA3 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA1 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA5 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA6 Analytical HPLC chromatogram and MALDI-TOF mass spectrum of PNA7 HPLC chromatogram of crude PNA3 and after click reaction Thermal denaturation curves of hybrids with of PNA1 with DNA1–DNA4 Photographs of PNA1 and its hybrids with DNA1–DNA4 under black light Selected snapshots of MD structures showing the hydrogen-bond formation between TzPy and opposite base Fluorescence spectra of PNA5 (a) and PNA7 (b) in the absence (–) and presence (···) of complementary DNA
Page 2 3 4 5 6 7 8 9 10 11 12 13 14
2
9.0
8.0
7.0
6.0
5.0
4.0
3.0
2.0
1.0
ppm (t1)
(a)
150
100
50
ppm (t1)
(b) Fig. S1. 1H (400 MHz, DMSO-d6) (a) and 13C NMR (100 MHz, DMSO-d6) (b) spectra of 4.
3
(a)
(b) Fig. S2. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA1 (BzGCATTAXAGATAC-LysNH2; X = TzPy) obtained by pre-formed TzPy monomer (CCA matrix) (calcd. for [M+H]+: m/z = 4779.2).
4
(a)
(b) Fig. S3. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA2 (BzGCATTAXAGATAC-LysNH2; X = C) (CCA matrix) (calcd. for [M+H]+: m/z = 4621.0).
5
(a)
(b) Fig. S4. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA3 (BzGCATTAXAGATAC-LysNH2; X = N3) (CCA matrix) (calcd. for [M+H]+: m/z = 4552.9).
6
(a)
(b) Fig. S5. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA1 (BzGCATTAXAGATAC-LysNH2; X = TzPy) obtained by post-synthetic click reaction (CCA matrix) (calcd. for [M+H]+: m/z = 4779.2).
7
(a)
(b) Fig. S6. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA5 (BzGCATTTXTGATAC-LysNH2; X = TzPy) (CCA matrix) (calcd. for [M+H]+: m/z = 4761.2).
8
(a)
(b) Fig. S7. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA6 (BzGCATTTXTGATAC-LysNH2; X = TzPh) (CCA matrix) (calcd. for [M+H]+: m/z = 4637.0).
9
(a)
(b) Fig. S8. Analytical HPLC chromatogram (a) and MALDI-TOF mass spectrum (b) of PNA7 (BzGCATTTXTGATAC-LysNH2; X = TzAn) (CCA matrix) (calcd. for [M+H]+: m/z = 4737.1).
10
Fig. S9. HPLC chromatogram of crude PNA3 (Bz-GCATTAN3AGATAC-LysNH2) before (top) and after (bottom) click reaction with 1-ethynylpyrene.
11
1.30
Normalized A
260
1.25 1.20
PNA1 + DNA1 (G) PNA1 + DNA2 (A) PNA1 + DNA3 (C) PNA1 + DNA4 (T) PNA3 + DNA4 (T)
1.15 1.10 1.05 1.00 0.95 20
30
40
50
60 o
70
80
90
T ( C) Fig. S10. Thermal denaturation curves of hybrids between PNA1 (TzPy) with DNA1–DNA4 and PNA3 (azide) with DNA4. Conditions: 2.5 µM PNA, 3.0 µM DNA in 10 mM sodium phosphate buffer pH 7.0.
12
PNA1 ss
+DNA1 Y=G
+DNA2 Y=A
+DNA3 Y=C
+DNA4 Y=T
Fig. S11. Photographs of PNA1 and its hybrids with DNA1–DNA4 viewed under black light. Conditions: 2.5 µM PNA, 3.0 µM DNA in 10 mM sodium phosphate buffer pH 7.0.
13
TzPy-Guanine (PNA1·DNA1)
TzPy-Adenine (PNA1·DNA2)
TzPy-Cytosine (PNA1·DNA3)
TzPy-Thymine (PNA1·DNA4)
Fig. S12. Selected snapshots of MD structures showing the hydrogen-bond formation between TzPy and opposite base for four simulated systems. The hydrogen bond acceptor-donor distances are shown.
14 350
350 PNA PNA+DNA
250 200 150 100 50 0 350
PNA PNA+DNA
300 Fluorescence (Arbitrary unit)
Fluorescence (Arbitrary unit)
300
250 200 150 100 50
400
450
500
Wavelength (nm)
550
600
0 350
400
450
500
550
600
Wavelength (nm)
Fig. S13. Fluorescence spectra of PNA5 (a) and PNA7 (b) in the absence (···) and presence (–) of complementary DNA (5'-GTATCAGAAATGC-3') (conditions: 2.5 µM PNA, 3.0 µM DNA in 10 mM sodium phosphate buffer pH=7.0, λexcit = 350 nm).