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Volumn 16, Issue 8, 2010, Pages 2479-2486

An efficient fluorescence resonance energy transfer (FRET) between Pyrene and Perylene assembled in a DNA duplex and its potential for discriminating single-base changes

Author keywords

DNA; Energy transfer, fluorescent probes; Perylene, pyrene

Indexed keywords

BASE PAIRS; DELETION MUTANTS; DNA DUPLEXES; DNA PROBE; EXCIMER EMISSIONS; EXCIPLEXES; FLUORESCENCE INTENSITIES; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT PROBES; MODEL SYSTEM; MONOMER EMISSION; NATURAL BASE; PERYLENES; WILD TYPES;

EID: 77049104967     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.200902078     Document Type: Article
Times cited : (42)

References (56)
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    • The wavelength of UV light for excitation (λ=345 nm) might be too short especially for in vivo analysis because it potentially damages other biomolecules
    • The wavelength of UV light for excitation (λ=345 nm) might be too short especially for in vivo analysis because it potentially damages other biomolecules.
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    • Incorporation of a mismatch into ODN4/C1 lowered the melting temperature although the degree of destabilization was dependent on the position of the mismatch
    • Incorporation of a mismatch into ODN4/C1 lowered the melting temperature although the degree of destabilization was dependent on the position of the mismatch. See Table S3 in the Supporting Information for melting temperatures.
    • See Table S3 in the Supporting Information for Melting Temperatures
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    • Electron transfer between pyrene and perylene is rather unlikely because location of pyrene near the perylene did not quench the fluorescence from perylene. Furthermore, quenching of pyrene was not necessarily facilitated by approximating pyrene to perylene (compare the fluorescence from pyrene (λ=370-430 nm) of ODN8/C2 and ODN9/C2 in Figure 2)
    • Electron transfer between pyrene and perylene is rather unlikely because location of pyrene near the perylene did not quench the fluorescence from perylene. Furthermore, quenching of pyrene was not necessarily facilitated by approximating pyrene to perylene (compare the fluorescence from pyrene (λ=370-430 nm) of ODN8/C2 and ODN9/C2 in Figure 2).
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    • When ODN7 was hybridized with full-matched C2, peaks of pyrene at 330-360 nm showed bathochromicity in absorption spectra, which indicated that pyrenes were intercalated between base pairs. On the other hand, peaks of perylene slightly shifted to shorter wavelength. This shift can be attributed to the change of dimeric perylene in the single-stranded state to monomeric state in the duplex with C2. See Figures S2 and S3 in the Supporting Information for UV/Vis and emission spectra. For the relationship between bathochromicity and intercalation, see: W. Müller, D. M. Crothers, J. Mol. Biol. 1968, 35, 251-290.
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    • Although the change in I550/I461 was not so large, the difference in fluorescence can be discriminated by the naked eye. See Figure S4 in the Supporting Information for the photograph
    • Although the change in I550/I461 was not so large, the difference in fluorescence can be discriminated by the naked eye. See Figure S4 in the Supporting Information for the photograph.
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    • 461 was enhanced with increasing ionic strength. See Figure S5 in the Supporting Information
    • The difference in I550/I461 was enhanced with increasing ionic strength. See Figure S5 in the Supporting Information.
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    • The probe presented in this paper also emits fluorescence even in the single-stranded state. This emission should disturb the detection of the target especially when the amount of the target is small
    • The probe presented in this paper also emits fluorescence even in the single-stranded state. This emission should disturb the detection of the target especially when the amount of the target is small.
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    • 461 ratio by introducing mismatch is attributable to the disordering around the intervening bases that facilitated the dimerization of perylene. These results also support proper base pairing of "full match" even though multiple perylenes and pyrenes were incorporated in the nearest neighboring positions. See Table S4 in the Supporting Information
    • 461 ratio by introducing mismatch is attributable to the disordering around the intervening bases that facilitated the dimerization of perylene. These results also support proper base pairing of "full match" even though multiple perylenes and pyrenes were incorporated in the nearest neighboring positions. See Table S4 in the Supporting Information.
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    • In other reports, chromophores were mainly introduced into grooves or outside duplex. Consequently, this structural problem could be avoided in those reports
    • In other reports, chromophores were mainly introduced into grooves or outside duplex. Consequently, this structural problem could be avoided in those reports.
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    • The distance between the donor and acceptor was about 13 Å, estimated from the energy-minimized structure shown in Figure 5
    • The distance between the donor and acceptor was about 13 Å, estimated from the energy-minimized structure shown in Figure 5.
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    • CD spectra indicated that both ODN2/C1 and ODN3/C1 took similar B-DNA structures. See Figure S7 in the Supporting Information
    • CD spectra indicated that both ODN2/C1 and ODN3/C1 took similar B-DNA structures. See Figure S7 in the Supporting Information.
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    • 0 decreased 25% in the case of q=708
    • 0 decreased 25% in the case of q=708.
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    • Our study, peaks of pyrene were substantially weaker than those of perylene
    • In our study, peaks of pyrene were substantially weaker than those of perylene.
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    • Quenching of pyrene is probably due to electron transfer between pyrene and neighboring bases. For quenching towards pyrene by natural bases, see: M. Manoharan, K. L. Tivel, M. Zhao, K. Nafisi, T. L. Netzel, J. Phys. Chem. 1995, 99, 17461-17472.
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    • Manoharan, M.1    Tivel, K.L.2    Zhao, M.3    Nafisi, K.4    Netzel, T.L.5
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    • 77049085557 scopus 로고    scopus 로고
    • As a result, two pyrenes were required for the efficient energy transfer
    • As a result, two pyrenes were required for the efficient energy transfer.
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    • We believe that all the chromophores were intercalated within the duplex because of the following reasons. No obvious excimer or exciplex emission was observed even with ODN10/C2, which has six chromophores in the nearest-neighboring positions. If the chromophores were flipped out from the duplex, they should form an excimer or exciplex, because flipped out hydrophobic chromophores with flexible ethylene or propylene linkers prefer to be stacked against each other in the aqueous environment. Similar results were also reported by Murakami and Yamana (M. Nakamura, Y. Shimomura, Y. Ohtoshi, K. Sasa, H. Hayashi, H. Nakano, K. Yamana, Org. Biomol. Chem. 2007, 5, 1945-1951
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    • Nakamura, M.1    Shimomura, Y.2    Ohtoshi, Y.3    Sasa, K.4    Hayashi, H.5    Nakano, H.6    Yamana, K.7
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    • They demonstrated that bispyrene flipped out from the duplex was assembled to form an excimer, whereas intercalated bispyrene showed only monomer emission as observed in our case. However, we cannot completely rule out the possibility that some chromophores were flipped out without forming an excimer and exciplex because of the lack of direct evidence of intercalated structure
    • Angew. Chem. Int. Ed. 2002, 41, 3648-3650).They demonstrated that bispyrene flipped out from the duplex was assembled to form an excimer, whereas intercalated bispyrene showed only monomer emission as observed in our case. However, we cannot completely rule out the possibility that some chromophores were flipped out without forming an excimer and exciplex because of the lack of direct evidence of intercalated structure.
    • (2002) Angew. Chem. Int. Ed. , vol.41 , pp. 3648-3650


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