Article pubs.acs.org/JPCC
Silver(I)-Induced Conformation Change of DNA: Gold Nanocluster as a Spectroscopic Probe Dipankar Bain, Bipattaran Paramanik, and Amitava Patra* Department of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700 032, India
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S Supporting Information *
ABSTRACT: DNA-based materials are promising avenues for designing optical sensors, light-harvesting devices, energy conversion devices, and other potential applications. Therefore, the understanding of DNA conformation is important for designing such materials. Here, we investigate the conformation of DNA by a photoexcited energy transfer process where the Au cluster is covalently attached with AlexaFluor 488 (A488) dye tagged DNA. Fluorescence resonance energy transfer (FRET) is a well-known method to determine the donor−acceptor distance where A488 acts as donor and the gold nanoclusters (Au NCs) act as acceptor. Spectroscopic studies reveal that Ag+ ions are incorporated into dsDNA to produce a Ag+-C (cytosine) metal base pair bond as the used DNA contains 55.6% G-C base pairs. Steady-state and time-resolved spectroscopic studies reveal that the distances between donor and acceptor are found to be 98 and 83 Å in the absence and presence of Ag+ ion, respectively, indicating the rigid conformation of dsDNA becomes flexible in the presence of a Ag+ ion. The efficiency of energy transfer increases from 63% to 82% in the presence of the Ag+ ion because the conformation of DNA changes with the formation of DNA-metal base pairs. Analysis suggests that the Au cluster is a useful spectroscopic probe to understand the conformation of DNA and others. Furthermore, this energy transfer from dye to Au NCs using the DNA scaffold may open up new opportunities in designing an artificial light-harvesting system.
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ions such as Hg2+ which binds with thymine (T) via strong THg2+ bond formation, whereas Ag+ binds with cytosine (C) via Ag+−C bond formation.16−21 Therefore, to investigate the effect of conformation change of dsDNA on energy transfer, the Ag+ ion is being used because it can strongly interact with cytosine bases of dsDNA and destroy the native conformation. The ultrasmall metal nanoclusters (Au NCs, Ag NCs, and Cu NCs) exhibit molecular-like properties such as d−sp and sp−sp transitions, broad absorption, and intense fluorescence properties.22−25 Earlier studies reveal that an ultrasmall metal nanocluster acts as an efficient energy quencher of dyes and QDs.26−29 Recently, Dickson and co-workers have synthesized an ultrasmall photoemissive Ag cluster using DNA templates.30 Like Ag NCs, water-soluble luminescent Au NCs can also be synthesized by single-stranded DNA.31 Recently, Martinez and co-workers have shown that a DNA-functionalized gold nanocluster can be used for efficient enzymatic reduction of oxygen.32 Several strategies have also been developed to detect toxic metal ions like Hg2+ and Cu2+ using DNA-functionalized Ag NCs.33 Willner et al. have used DNA-functionalized QDs for multiplexed optical analysis of Hg2+ and Ag+.34 Recently, we have demonstrated the detection of Hg2+ based on an off/on fluorescence probe by switching the DNA−metal base pairs.35
INTRODUCTION Recently, DNA-based nanoarchitectures have been attracting attention as a promising research interest due to their significant applications in medical diagnosis, optical computing, biological probes, light-harvesting devices, energy conversion devices, and DNA photonic wires.1−6 Thus, great attention has been paid to DNA-hybridization-based fluorescence resonance energy transfer (FRET) from donor to acceptor.6,7 FRET is one of the most useful techniques to measure the distance between the donor−acceptor (D−A) system in the range of 10−100 Å.8−10 In the FRET process, the energy is transferred from a photoexcited chromophore to its nearby acceptor in a nonradiative pathway via dipole−dipole interaction.11,12 FRET is a 1/r6 distance-dependent photophysical process.13 The advantage of using a DNA hybridization technique is to find the donor/acceptor distance with nanoscale accuracy in a biological system.14 The hybrid DNA base segment has been used as a photonic wire to lock the position of the donor fluorophore and acceptor molecule to establish a linear array for efficient photon transfer.2 The combination of two complementary single-stranded DNAs having less than 100 base pairs results in rodlike rigid double-stranded DNA (length of each base pair is 0.34 nm) formation.2 The advantage of using dsDNA as a linker between the donor and acceptor is to achieve higher energy transfer efficiency in QD-dye-based systems.15 Therefore, 18-mer dsDNA is used as a linker between the donor and acceptor to understand the change of conformation of dsDNA in the present study. DNA bases can bind with different metal © 2016 American Chemical Society
Received: October 19, 2016 Revised: December 21, 2016 Published: December 21, 2016 4608
DOI: 10.1021/acs.jpcc.6b10560 J. Phys. Chem. C 2017, 121, 4608−4617
Article
The Journal of Physical Chemistry C
urements were performed on a SHIMADZU made FTIR-8300 spectrometer using KBr pellets. For the time-correlated singlephoton-counting (TCSPC) measurement, the samples were excited at 405 nm (picosecond diode laser IBH NANO-LED07, fwhm = 90 ps) and 489 nm (NANO-LED IBH-489, fwhm = 1.4 ns). The fluorescence decays were collected on a Hamamatsu MCP photomultiplier. Equation 1 is used to analyze the experimental time-resolved fluorescence decays, P(t)36
In the present report, we investigate the change of DNA conformation by using FRET-based energy transfer. To serve this purpose, we use A488-tagged dsDNA which acts as a fluorescence donor and luminescent Au nanoclusters as acceptor. Here, A488 dye is chosen as a donor due to its outstanding photostability and higher quantum yields (92%) in water. On the other hand, the Au nanocluster is used as an energy acceptor owing to its size-tunable broad absorption over the visible region. Both A488 dye and Au NCs are a promising choice for photoexcited energy transfer owing to spectral overlap, which is an important requirement for energy transfer. The Au nanocluster is attached to dsDNA via a thiol modifier. Here, the as-prepared Au NC is covalently attached to thiolmodified dsDNA tagged with A488 dye, which is confirmed from CD spectroscopy. The steady-state and time-resolved fluorescence spectroscopic studies are being used to investigate the PL quenching and energy transfer process from A488tagged dsDNA to Au NCs. The Ag+ ion is being incorporated into dsDNA via Ag+−cytosine (Ag+−C) bond formation, resulting in a change in conformation of native DNA. The conformation of hybrid DNA influences the energy transfer from A488 dye to Au NCs in the presence of Ag+ ion.
n
P(t ) = b +
∑ αi exp(−t /τi)
(1)
i
Here, n is the number of emissive species; b is the baseline correction (“DC” offset); and αi and τi are, respectively, the pre-exponential factor and the excited-state fluorescence decay time associated with the ith component. The average decay time, ⟨τ⟩, is calculated from the following equation. n
⟨τ ⟩ =
∑ βτi i
(2)
i=1
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where βi = ai/∑ai and βi is the contribution of the decay component. The quantum yield (QY) of Au NCs was obtained by comparison with reference dye, rhodamine 6G (in water), using the following equation.36
EXPERIMENTAL SECTION Chemicals. Tetrachloroauric acid trihydrate (HAuCl4· 3H2O), glutathione reduced (GSH), and α-cyano-4-hydroxycinnamic acid (CHCA) were obtained from Sigma-Aldrich. Other chemicals such as sodium chloride (NaCl), sodium borohydride (NaBH4), methanol (MeOH), sodium phosphate dibasic heptahydrate (Na2HPO4·7H2O), and sodium dihydrogen phosphate dehydrate (NaH2PO4·2H2O) were received from Merck. All the solvents used were of analytical grade. The oligonucleotides were purchased from Integrated DNA technology, having sequence as follows: DNA-1: 18 mer, 5′-A488GAAAATTTTGCGGGGGCG-3′. DNA-2: 18 mer, 5-thiol modifier C6-DCGCCCCCGCAAAATTTTC-3′. DNA-3 (without thiol modifier): 18 mer, 5′CGCCCCCGCAAAATTTTC-3′. A dialysis tube (molecular cutoff
