Silver(I)-Induced Conformation Change of DNA: Gold Nanocluster as

Subscriber access provided by University of Newcastle, Australia

Article

Silver (I) Induced Conformation Change of DNA: Gold Nanocluster as Spectroscopic Probe Dipankar Bain, Bipattaran Paramanik, and Amitava Patra J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.6b10560 • Publication Date (Web): 21 Dec 2016 Downloaded from http://pubs.acs.org on December 23, 2016

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

The Journal of Physical Chemistry C is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The Journal of Physical Chemistry

Silver (I) Induced Conformation Change of DNA: Gold Nanocluster as Spectroscopic Probe

Dipankar Bain, Bipattaran Paramanik, and Amitava Patra* Department of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700 032, India

*

Author to whom correspondence should be addressed. Electronic mail: [email protected]

Telephone: (91)-33-2473-4971. Fax: (91)-33-2473-2805

1 ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ABSTRACT DNA based materials are promising avenues for designing optical sensors, light harvesting device, energy conversion device and other potential applications. Therefore, the understanding of DNA conformation is important for designing such materials. Here, we investigate the conformation of DNA by photo excited energy transfer process where 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) acts as acceptor. Spectroscopic studies reveal that Ag+ ions are incorporated into dsDNA to produce 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 Å and 83 Å in absence and presence of Ag+ ion, respectively, indicating the rigid conformation of dsDNA becomes flexible in presence of Ag+ ion. The efficiency of energy transfer increases from 63% to 82% in presence Ag+ ion because the conformation of DNA changes with the formation of DNA-metal base pairs. Analysis suggests that Au cluster is a useful spectroscopic probe to understand the conformation of DNA and other. Furthermore, this energy transfer from dye to Au NCs using DNA scaffold may open up new opportunities in designing artificial light harvesting system.


Page 2 of 27

Page 3 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


INTRODUCTION Recently, DNA-based nanoarchitectures have been attracted as a promising research interest due to its significant applications in medical diagnosis, optical computing, biological probes, light harvesting device, energy conversion device, and DNA photonic wires.1-6 Thus, a great attention has been paid on DNA-hybridization based fluorescence resonance energy transfer (FRET) from donor to acceptor.6-7 FRET is one of the most useful technique to measure the distance between donor-acceptor (D-A) system in the range of 10-100 Å.8-10 In FRET process, the energy is transferred from 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 DNA hybridization technique is to find the donor/acceptor distance with nanoscale accuracy in biological system.14 Hybride DNA base segment has been used as a photonic wire to lock the position of donor fluorophore and acceptor molecule to establish a linear array for efficient photon transfer.2 Combination of two complementary single stranded DNA having less than 100 base pairs results rod like rigid double stranded DNA (length each base pair is 0.34 nm) formation.2 The advantage of using dsDNA as linker between donor and acceptor is to achieve higher energy transfer efficiency in QDs-dye based system.15 Therefore, 18-mer dsDNA is used as a linker between donor and acceptor to understand the change of conformation of dsDNA in the present study. DNA bases can bind with different metal ions such as Hg2+ bind with thymine (T) via strong T-Hg2+ 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, 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, 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 his coworker have synthesized ultrasmall photo emissive Ag cluster using DNA templates.30 Like Ag NC, water soluble luminescent Au NCs can also be synthesized by single stranded DNA.31 Recently, Martinez and his coworker have shown that DNA functionalized gold nanocluster can be used for efficient enzymatic reduction of oxygen.32 Several strategies have also been developed to detect toxic metal ion like Hg2+ and Cu2+ using DNA functionalized Ag NCs.33 Willner et al. have used DNA 3 ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 4 of 27

functionalize QDs for multiplexed optical analysis of Hg2+ and Ag+.34 Recently, we have demonstrated the detection of Hg2+ based on off/on fluorescence probe by switching the DNAmetal base pairs.35 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 nanoclausters use as acceptor. Here, A488 dye is chosen as donor due to its outstanding photo stability and higher quantum yields (92%) in water. On the other hand, Au nanocluster is used as an energy acceptor owing to its size tunable broad absorption over visible region. Both A488 dye and Au NCs are promising choice for photoexcited energy transfer owing to spectral overlap, which is an important requirement for energy transfer. Au nanocluster is attached to dsDNA via thiol modifier. Here, as prepared Au NC is covalently attached to thiol modified dsDNA tagged with A488 dye, which is confirmed from CD spectroscopy. The steady state and time resolve fluorescence spectroscopic studies are being used to investigate the PL quenching and energy transfer process from A488 tagged dsDNA to Au NCs. The Ag+ ion is being incorporated into dsDNA via Ag+-cytosine (Ag+-C) bond formation, resulting change in conformation of native DNA. The conformation of hybrid DNA influences the energy transfer from A488 dye to Au NCs in presence of Ag+ ion.

EXPERIMENTAL SECTION Chemicals Tetrachloroauric acid trihydrate (HAuCl4·3H2O), glutathione reduced (GSH), α-cyano- 4hydroxycinamic 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

dihydrate

(Na2HPO4.2H2O) 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’ -A488-GAAAATTTTGCGGGGGCG-3’. DNA-2: 18 mer, 5 -Thiol Modifier C6-D-CGCCCCCGCAAAATTTTC-3’. DNA-3: (without Thiol Modifier): 18 mer, 5’-CGCCCCCGCAAAATTTTC-3’. Dialysis tube (molecular cut off < 5 KDa) was purchased from Fischer-Chemicals. Throughout the experiment high purity water (≈ 18.2 MΩ) was used. All the chemicals of highest purity 4 ACS Paragon Plus Environment

Page 5 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


grade were used without further purification. Concentration of each ssDNA is calculated from molar extinction coefficient. Characterization The optical absorption spectra at room temperature were recorded with a UV-vis spectrophotometer (Shimadzu) using a cuvette with a path length of 1 cm. The emission spectra of all of the samples were obtained with a Fluoro Max-P (HORIBA Jobin Yvon) luminescence spectrophotometer. The quantum yield (QY) of Au NCs is measured using rhodamine 6G as a reference dye. Transmission electron microscopy (TEM) images were obtained using a JEOLJEM-2100F transmission electron microscope. The mass of the Au NCs were measured by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry on a Bruker Daltonics Autoflex II TOF/TOF system. A pulse laser of 337 nm is used and a saturated CHCA solution is selected as the matrix for the MALDI-TOF measurements. Circular dichroism (CD) spectra were taken by JASCO (J-815-150S). Fourier-transform infrared (FTIR) spectroscopy measurements were performed on a SHIMADZU made FTIR-8300 spectrometer using KBr pellets. For the time-correlated single-photon-counting (TCSPC) measurement, the samples were excited at 405 nm, (picosecond diode laser IBH NANO-LED-07, 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 timeresolved fluorescence decays, P(t):36 n

P (t ) = b + ∑ α i exp ( − t / τ i )

(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 following equation. 〈τ 〉 =

n

∑ aτ i

(2)

i

i =1

Where ai = α i / ∑ α i and is the contribution of the decay component. The quantum yield (QY) of Au NCs were obtained by comparison with reference dye, rhodamine 6G (in water), using the following equation.36 QYs = (Fs × Ar × ηs2 × QYs) / (Fr × As × ηr2)

(3) 5

ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Where, Fs and Fr are the integrated fluorescence emission of the sample and the reference. As and Ar are the absorbance at the excitation wavelength of the sample and the reference. QYs and QYr are the quantum yields of the sample and the reference (QYr = 0.95). The refractive index of the solvent is 1.33 for both the sample and reference because water is used for both cases.

Synthesis of gold nanoclusters Glutathione capped luminescent gold nanoclusters were synthesized following an earlier procedure with some modification.37-38 Glutathione reduced, a bio-active tripeptide is used as a surface stabilizing agent (Figure S1).

Preparation of Au nanoparticles The preparation method for gold-glutathione (Au-SG) complex employed here, initially to 100 mL methanol 0.5 mmol HAuCl4 is added. Then reduced glutathione (GSH, 20 mM) is added to the mixture. After that, the mixture is allowed to cooled 0oC in ice bath for 30 minutes. Then a freshly prepared aqueous solution of NaBH4 (25mL, 0.2M), cooled at 0°C, is injected rapidly into the mixture under vagarious stirring, immediately a dark brown precipitate is formed. The reaction mixture is allowed to react for another hour to complete particle formation. The resulting black precipitate is collected using centrifugation at 5000 rpm and washed repeatedly with methanol/water (3:1) mixture to remove the un-reacted precursor. The precipitate is dried for 24 hours to obtain a mixture of small polydisperse nanoparticles and nanoclusters.

Synthesis of luminescent Au NCs Au NC is synthesizing from as prepared Au-SG complex by core etching method. Here, previously prepared Au-SG complex is dissolve in 25 mL ultrapure water. Then, glutathione (614 mg) is added and the mixture is allowed to stir at 55°C. The reaction is monitored by optical absorption spectroscopy. After complete the reaction, the solution is centrifuged and methanol is added to supernatant to precipitate Au NCs. The precipitate is dried and is stored at 4°C for further experiment. The concentration of as-prepared gold nanoclusters is estimated using molar extinction coefficient at 420 nm (ε420 = 112000 cm-1 M-1), reported earlier.26 The synthesis of Au nanoclusters by top down approach is shown in scheme1.


Page 6 of 27

Page 7 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Aurophilic interaction

GSH Core-etching

GSH capped gold nanoclusters (Au NCs)

GSH capped gold nanoparticles (Au NPs)

Scheme 1. Schematic representation of synthesis of gold nanoclusters by top-down approach.

Preparation of double stranded DNA (dsDNA) To prepare double stranded DNA (dsDNA) from single stranded DNA (ssDNA) equal concentration (5.70 µM) of DNA-1 and DNA-2 were mixed and allowed to incubate at 55°C. After 20 min, the solution is cooled to room temperature very slowly to get the perfect double stranded DNA (dsDNA). This dsDNA solution was stored at 4°C for further studies.

RESULTS AND DISCUSSION Size focusing of Au NCs We have synthesized ultrasmall luminescent gold nanoclusters by two step processes. Initially larger size Au NPs were prepared at lower ratio of gold/glutathione and finally larger size Au NPs are converted into Au NCs via “size focusing” in presence of excess glutathione.3940

Transmission electron microscopy (TEM), UV-absorption spectroscopy, Fourier transform

infrared (FTIR) spectroscopy, and matrix-assisted laser desorption ionization (MALDI) are being used to characterize the morphology and optical properties of Au NCs.



6

2.0

1.75x10

(A)

PL Intensity (a.u)

Normalized Absorbance

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 8 of 27

1.5

1.0

0.5

(B)

6

1.40x10

6

1.05x10

a b

5

7.00x10

5

3.50x10 0.0 400

500

600

700

800

0.00 500

900

550

Wavelength (nm)

600

650

700

750

800

Wavelength (nm)

Figure 1. (A) Normalized absorption spectra of glutathione capped Au NPs (red line) and Au NCs (black line). (B) Photoluminescence spectra of Au NPs (red line) and Au NCs (black line) and inset shows digital photographs of Au NCs solution under (a) normal and (b) UV light, respectively.

The absorption spectrum of polydisperse Au NPs exhibits a hump at around 560 nm, which is due to surface plasmon resonance for small gold nanoparticles (Figure 1A, red line). After etching, the disappearance of absorption band at 560 nm is observed (Figure 1A, black line), indicating the formation of Au clusters. A new characteristic absorption band is appeared around 667 nm, which is due to intra-band sp to sp transition (Figure 1A, black line) of Au clusters.37, 41 On the other hand, the optical bands present in higher energy region are due to inter band d to sp transition.

42

The stability of Au NCs is very high because we did not observe any

prominent change in optical properties even after 3 months storage at 4oC. The Au NCs shows a characteristic photoluminescence emission peak at around 680 nm while the larger size polydisperse Au NPs do not show any emission (Figure 1B). The inset of figure 1B shows digital photographs of Au NCs in presence of daylight and under excitation of UV-light at 365 nm. The quantum yield (QY) of nanocluster is found to be 0.2 % (R6G is use as reference dye).37-38 On the other hand, as prepared Au NP does not exhibit any photoemission; the digital photographs are shown in figure S2. TEM image shows the polydisperse nature of Au NPs and the average size is around 4 nm (Figure S3). The HRTEM image of synthesized Au NCs shows polydispersity of spherical 8 ACS Paragon Plus Environment

Page 9 of 27

Au NCs. The size of Au NCs is estimated from particle size distribution plot and the average size of ultrasmall Au NCs is 1.62 ± 0.36 nm. TEM image further clarifies that there is no aggregation present (Figure 2). (A)

25

(B)

(C)

size 1.62 nm SD 0.36 nm

20 No. of Particles

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


15 10 5 0 0.5

1.0

1.5

2.0

2.5

3.0

Diameter (nm)

Figure 2. TEM images of glutathione capped Au NCs; scale bar (A) 50 nm and (B) 10 nm and (C) particle size distribution of Au NCs.

To investigate the number of gold atom present in the core of Au NCs, we have performed matrix assisted laser desorption ionization-time of flight (MALDI-TOF). The MALDI spectrum of as synthesized Au NCs shows a typical hump rather than a distinctive peak (Figure S4) which is consistent with water soluble Au NCs.43 The MALDI spectrum exhibits a characteristic hump around 10420 KDa with very high intensity. This peak is due to the attribution of mass of 25-gold atom and 18 glutathione molecule and this peak is assigned as Au25(GSH)18, which is consistent with previous reported.13, 37 FTIR study has been used to understand the binding mode of surface protecting ligand. Thiol containing capping ligands bind at the surface of Au NCs through Au-S covalent bond formation that is confirmed by FTIR study. Here, we have compared FTIR spectra of pure capping ligand GSH with GSH capped Au NCs. The peak at around 2525 cm-1 is due to S-H bond stretching of pure GSH (Figure S5).37-38 Interestingly, the S-H bond stretching peak at around 2525 cm-1 is completely disappeared after formation of Au nanoclusters. This disappearance of S-H bond vibration confirms Au-S covalent bond formation because of softsoft interaction, indicating the Au atom interacts with only S-atom of glutathione.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 10 of 27

Attachment of Au NCs with A488 tagged DNA The preparation of dsDNA is confirmed from CD analysis. Figure S6 shows distinctive positive band at around 282 nm, which is due to stacking of purine and pyrimidine bases in dsDNA. On the other hand, the negative valley observed around 248 nm which is due to polynucleotide helicity of phosphate backbones (a curve). In case of ssDNA, a broad positive hump at around 290 nm is observed (b curve of Figure S6). However, no characteristic peak within 230 nm to 257 nm is found for ssDNA, which confirms the absence of double helical conformation. Therefore, the dsDNA formed only after incubation of two complementary ssDNA (DNA-1 and DNA-2), as depicted by CD spectra. The dsDNA-Au NCs conjugates are prepared by mixing 30 µL dsDNA with different amounts of Au NCs separately and then all the solution are diluted up to 550 µL by adding required amount of phosphate buffer (20 mM, pH 7.4). The attachment of Au NCs with A488 tagged dsDNA is further confirmed from CD spectra (Figure 3). To investigate the conformation change of dsDNA in presence of Au NCs, we have carried out circular dichroism (CD) study at a fixed concentration of dsDNA. The characteristic absorption bands found in the region (220-310 nm) are due to backbone conformation of dsDNA.44 The structural changes of dsDNA is caused by Au NCs which is reflected on intrinsic changes of CD spectrum.45 In the CD spectra, we have observed two broad absorption peaks, one present at positive region and another one present at negative region. The absorption peak arises around at 248 nm in negative region is due to the helical ladder conformation of polynucleotide i.e. for pure dsDNA (blue line in Figure 3). The positive band having maxima around 282 nm is due to the stacking of π-π interaction of purine and pyrimidine base pairs.46 Interestingly, both the positive and negative bands are changed in the CD spectra after attachment with Au NC via Au-S bond formation to dsDNA. Negative valley in CD spectra is blue shifted from 248 nm to 240 nm with reduction of its intensity but the positive valley is red shifted from 282 nm to 292 nm with slightly lowering of intensity (black line in Figure 3). The band position shifting and intensity changes are mainly due to the partial denaturation of A488 tagged dsDNA when attached to Au NCs. It reveals that the interaction occurs between gold nanocluster and dsDNA via Au-S bond formation (Figure 3).47


Page 11 of 27

8

4

CD (mdeg)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


0 Pure ds DNA ds DNA-Au NC + ds DNA-Au NC-Ag

-4

-8 225

250

275

300

325

350

Wavelength (nm)

Figure 3. CD spectra of pure A488 tagged dsDNA (blue line), Au NCs attached to A488 tagged dsDNA (black line) and Au NCs attached to A488 tagged dsDNA in presence of silver (I) ion (red line).

Incorporation of Ag+ ion Double stranded DNA is one of the most useful binding blocks that have specific binding capabilities with Ag+ ion at guanine-cytosine rich region (G-C).16 Ihara and co-workers have reported that Ag+ can also bind between two N-atom of cytosine and guanine by replacing hydrogen bonded proton.16 In the present study, Ag+ ion can easily incorporate inside dsDNA owing to its small size and interacts with cytosine via DNA-metal base pairs bond formation. In dsDNA, Ag+ ion specifically bridges C-Ag+-C. Here, the binding of Ag+-ion to GC base pairs inside dsDNA is investigated from CD spectroscopy. Here, we used 0.1 M concentration of Ag+ ion (AgNO3) for incorporation Ag+ ion inside dsDNA. A significant change in CD spectra is observed after incorporation of Ag+ ion inside dsDNA. The shifting of negative valley in CD spectrum is observed from 240 nm to 242 nm, with lowering of intensity in presence of Ag+ (red line in Figure 3).48 This shifting is mainly due to the destruction of helical superstructure of polynucleotide by forming DNA-Ag+ ion base pairs. Again, the broadening of positive valley of dsDNA in presence to Ag+ suggests the conformation change of dsDNA. Owing to small size of Ag+ ion, it can easily incorporate inside dsDNA chain and interacts with cytosine (C) bases 11 ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 12 of 27

which results the destruction of native conformation of dsDNA. Thus, the rigid conformation of dsDNA becomes flexible as a result the Au NCs comes closer to donor A488. Absorption spectroscopic study is done to understand the attachment of Au NCs with A488 tagged dsDNA. Typically the absorption hump of A488 tagged dsDNA is appeared around 494 nm (Figure S7A). Noteworthy, after attachment of Au NCs to dsDNA via Au-S covalent bond formation, a weak hump is appeared at same position as for A488 tagged dsDNA along with other peak (667 nm, characteristic peak for Au NCs) of metal nanoclusters (Figure S7B).47, 49

This confirms the successful attachment of Au NCs with A488 tagged dsDNA. In control experiment, a dsDNA is prepared by mixing DNA-1 (A488 tagged DNA) with

DNA-3 (complementary of DNA-1), having no thiol modification. Interestingly, this newly prepared dsDNA does not exhibit any fluorescence quenching in presence of Au NCs. As, there is no thiol moiety present in newly prepared dsDNA, thus Au NCs cannot interact with this dsDNA (Figure S8). Therefore, we have chosen one thiol modified ssDNA to prepared dsDNA so that Au NCs can covalently bind with dsDNA via Au-S bond formation.47 The exact orientation of donor and acceptor is an important factor for PL quenching, energy transfer etc which is not possible in former case. Again, we have performed control experiment to investigate any fluorescence quenching of Au clusters or A488 tagged dsDNA in presence of Ag+ ion. No significant fluorescence quenching of Au clusters or A488 tagged dsDNA is observed in presence of Ag+ ion (Figure S9).

Steady state spectroscopic study To further investigate the photophysical property changes of Au NCs attached A488 tagged dsDNA in presence Ag+; we have carried out steady state spectroscopic study. The photoluminescence (PL) intensity of A488 tagged dsDNA is decreased in presence of Au NCs. The PL quenching efficiency (E) is calculated from the steady state fluorescence spectroscopy, using the following equation.

E = 1−

FDA FD

(4)

FDA is florescence intensity of donor in presence of acceptor and FD is fluorescence intensity of donor without acceptor.


Page 13 of 27

6

5

(A) PL Intensity (a.u)

a 6

2.8x10

6

2.1x10

5

2.25x10

4

5

1.50x10

4

7.50x10

0.00 600

g

6

1.4x10

650

700

750

800

3 2

Wavelength (nm)

5

1

7.0x10

0.0 500

(B)

5

3.00x10

F0/F

3.5x10

PL Intensity (a.u)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


0 550

600

650

700

750

800

0

1

Wavelength (nm)

2 3 4 [Au NCs], µΜ

5

6

Figure 4. (A) Photoluminescence spectra of A488 tagged dsDNA in presence of Au NCs having concentration ratio of A488/Au NCs (a) 1:0, (b) 1:10, (c) 1:12, (d) 1:15, (e) 1:20, (f) 1:25 and (g) 1:30, inset shows enhancement of the emission intensity of Au NCs and (B) corresponding Stern-Volmer plot, respectively.

The PL quenching efficiency increases with increasing the concentration of Au NCs and the quenching efficiency is found to be 63% where the ratio of A488/Au NCs is 1:20 (Figure 4A). The emission spectra of A488 tagged dsDNA in presence of Au NCs intersect at a single point, which implies the direct correlation between lowering of fluorescence intensity of A488 dye and the enhancement of fluorescence intensity of Au NCs (inset of figure 4A).50 This is also probably due to energy transfer from A488 tagged dsDNA to Au NCs in conjugate system. To understand the PL quenching mechanism of A488 tagged dsDNA in presence of Au NCs, we have used the Stern-Volmer study. The Stern-Volmer plot shows the typical linear behavior of steady state quenching and the Stern-Volmer constant is calculated using the following equation (Figure 4B). F0 = 1 + k sv [Q ] F

(5)

Here, F0 is initial fluorescence intensity of A488 tagged dsDNA, F is fluorescence intensity of A488 dye donor in presence Au nanoclusters,

K sv is Stern-Volmer constant and Q is the

concentration of Au NCs. The Stern-Volmer constant can be measured from the slope of the plot 13 ACS Paragon Plus Environment


and it is found to be (1.04 ± 0.02) x 106 M-1. This large value of Stern-Volmer constant demonstrates the strong binding of Au nanoclusters with dsDNA through strong Au-S covalent bond formation. The decrease of PL intensity of A488 tagged dsDNA in presence of Au NCs is due to energy transfer.

6

4x10

5

2.0x10

(A)

(B)

f

PL Intensity (a.u)

a

PL Intensity (a.u)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 14 of 27

6

3x10

6

f

2x10

6

1x10

0 500

550

600

650

700

750

5

1.5x10

a

5

1.0x10

4

5.0x10

0.0 600

800

Wavelength (nm)

650

700

750

800

Wavelength (nm)

Figure 5. (A) PL spectra of (a) pure A488 tagged dsDNA (control), (b) Au NCs attached to A488 tagged dsDNA and in presence of (c) 54 µM, (d) 90 µM, (e) 127 µM and (f) 181 µM of Ag+ ion, respectively and (B) Enhancement of the emission intensity of Au NCs due to the incorporation of Ag+ ion inside the dsDNA. The photophysical interaction of Ag+ ion to Au NCs attached A488 tagged dsDNA is studied from PL quenching analysis. PL quenching efficiency of A488 tagged dsDNA to Au NCs increases from 63 % to 79 % in presence of 90 µM Ag+ when the ratio of A488/Au NCs is 1:20 (Figure 5A). Interestingly, the PL intensity of acceptor Au NCs simultaneously increases up to 59 % in presence of 90 µM Ag+ ion (Figure 5B). The drastic enhancement of PL intensity of Au NCs is due to the incorporation Ag+ ion inside dsDNA, which facilitates the energy transfer from A488 tagged dsDNA to Au NCs. Again the PL emission of acceptor Au NCs is red shifted from 680 nm to 700 nm in presence of Ag+ ion. This red shifting (20 nm) of emission maxima of Au NCs confirms the interaction of Ag+ to A488 tagged dsDNA attached to Au NCs (Figure 6). The energy transfer process is further investigated by decay time measurement. 14 ACS Paragon Plus Environment

1.2 b

f

0.9

0.6

0.3 600

650

700

750

800

Wavelength (nm) Figure 6. Spectral shifting of emission maxima of Au NCs with increasing the concentration of Ag+ ions from 54 µM to 181 µM (b to f).

Time resolved spectroscopic study Time resolved spectroscopic study is undertaken to understand the excited state dynamics of A488 tagged dsDNA, in absence and presence of Au NCs ( λex = 489 nm and λem = 518 nm). The experimental data is fitted using the equation 1 and the average decay time is calculated by equation 2. The average decay times are summarized in Table 1.

1000

Counts (log)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Normalized PL Intensity (a.u)

Page 15 of 27

a

100

c 10 IRF 0

5

10

15

20

25

Time (ns) 15 ACS Paragon Plus Environment

30


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 16 of 27

Figure 7. Time-resolved decay curves of (a) pure A488 tagged dsDNA, (b) in presence of Au NCs where the ratio of A488/Au NCs 1:20, (c) 90 µM Ag+ ion with A488/Au NCs and the black curve is IRF of the LED source, respectively.

The average decay time of A488 tagged dsDNA is found to be 3.72 ns with single exponential fitting.2 In presence of Au NCs, the average decay time of A488 tagged dsDNA is shortening to 1.37 ns with component of 0.83 ns (82%) and 3.83 ns (18%) when the concentration ratio of A488/Au NCs is fixed to 1:20. Interestingly, one new faster component is appeared in the conjugate system, which implies that A488 tagged dsDNA molecules interact with Au NCs in excited state (Figure 7). However, the decay time of A488 tagged dsDNA attached to Au NCs is further decreased from 1.37 ns to 0.64 ns in presence of Ag+ ion (Figure 7). This drastic change in the decay time is due to the increasing contribution of faster component from 0.83 ns (82%) to 0.17 ns (87%). The faster component 0.17 ns is due to fast energy transfer from A488 dye to Au NCs in presence of Ag+ ion. Static quenching is a ground state interaction that does not influence the decay time of donor. Thus, the excited state interaction is responsible for decay time shortening. The shortening of decay time of A488 tagged dsDNA in presence of Au NCs is owing to the energy transfer.51 Therefore, to understand the mechanism of energy transfer, we have measured the decay time for estimating the energy transfer efficiency and the rate of energy transfer. The efficiency of energy transfer is calculated from decay time measurement using following equation.36

τ  Φ ET = 1 −  DA   τD 

(6)

Here ΦET is efficiency of energy transfer, τ DA and τ D are the decay time of donor in presence and absence of acceptor (Au NCs). The calculated efficiency of energy transfer from A488 dye to Au NCs is found to be 63% when the concentration ratio of A488/Au NCs is fixed to 1:20. However, the energy transfer is significantly raised from 63% to 82% in presence of Ag+ ion (Table 1). The energy transfer efficiency can also be calculated using the enhancement of acceptor emission.52 The lifetime of acceptor Au cluster increases in presence of A488 tagged dsDNA. We have excited the sample at 405 nm and measured the decay time of acceptor Au NCs in presence and absence of A488. The decay time of pure Au NCs is found to be 0.76 µs with 16 ACS Paragon Plus Environment

Page 17 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


components of 0.02 µs (35%), 0.23 µs (31%) and 2.03 µs (34%). However, in presence of donor A488, the decay time is increased to 1.17 µs with components of 0.03 µs (31%), 0.41 µs (22%) and 2.28 µs (47%). This significant enhancement of acceptor decay time in presence of donor confirms the energy transfer from A488 tagged dsDNA to Au NCs (Figure S10). Again, we have estimated the number of acceptors per donor from PL efficiency (E) versus CD/CA plot (ratio between molar concentration of donor and acceptor).53-54 It is clearly seen from the figure S11 that the quenching efficiency increases with decreasing CD/CA ratio. We have observed E=0.66 when the CD/CA ratio is 0.049. It suggested that 20 acceptor Au NCs binds with one A488 tagged dsDNA. The efficiency of energy transfer ( E ), is very sensitive to the average distance between donor and acceptor. Therefore, the distance between donor and acceptor is measured by using the following equation.14, 50-51, 55 56

E=

(7)

nR06 nR06 + rn6

Here, E is energy transfer efficiency, R0 is Förster distance and rn is the average distance between donor-acceptor and n is the acceptor/donor ratio. The Förster distance can be calculated using following equation.36

[

R0 = 0.211 k 2η −4φD J (λ )

]

1/ 6

(in angstroms)

(8)

Where, k 2 is the dipole orientation factor between donor and acceptor, usually the value of < k 2 > is 2/3 for random orientation,

φD is the quantum yield of donor, η (1.33) is the refractive

index of solvent and J (λ ) is the overlap integral between the absorption of Au NCs and the emission of A488 tagged dsDNA. The value of J (λ ) has been estimated by following equation.36



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 18 of 27

Figure 8. The overlap plot between absorption spectrum of Au NCs (a) and emission spectrum of A488 tagged dsDNA (b).

∫ J (λ ) =

∞

0

FD (λ )ε A (λ )λ4 dλ

∫

∞

0

(9)

FD (λ ) dλ

Where, FD (λ) is the corrected fluorescence intensity of donor in the range of wavelength λ to

λ + ∆λ with a total normalized intensity and ε A (λ) is the extinction coefficient of the acceptor at wavelength λ . Figure 8 displays the overlap between the absorption spectrum of Au NCs (acceptor) and emission spectrum of A488 tagged dsDNA (donor). The calculated value of overlap integral is found to be 6.810 x 1015 M-1 cm-1 nm4. Thus, there is very good overlap between donor emission and acceptor absorption further indicating the efficient energy transfer from A488 tagged dsDNA to Au NCs. The calculated Förster distance is found to be 65 Å. The distance between the A488 dye and Au NCs is found to be 98 Å.


Page 19 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Table 1. Time resolved fluorescence data for A488 tagged dsDNA in different systems.

Emission (nm)

τ1a (ns)

τ2a (ns)

(a1)

(a2)

A488 tagged dsDNA

518

--

3.72

--

A488/Au NCs (1:20)

518

63

518

3.83 (0.18) 3.84 (0.13)

1.37

A488/Au NCs (1:20) + 90 µM Ag+

3.72 (1.00) 0.83 (0.82) 0.17 (0.87)

0.64

82

System

a

± 3%

a(ns)

Energy Transfer (%)

(error).

Again, the distance between donor and acceptor is reduced from 98 Å to 83 Å in presence of Ag+ due to conformational change of native dsDNA. This tremendous enhancement in energy transfer efficiency is owing to proximal distance between A488 dye and Au NCs in presence of Ag+ ion. Furthermore, we have estimated rate of energy transfer ( kT ) using following equation.36

1 R  kT =  0  τ D  rn 

6

(10)

Where, τ D is decay time of donor in absence of acceptor, R0 is the Förster distance and r is the distance between donor and acceptor. The rate of energy transfer from A488 tagged dsDNA to Au NCs is found to be 2.28 x 107 sce-1. Interestingly, the rate of energy transfer increases almost three times in presence of Ag+ and is found to be 6.20 x 107 sec-1. Time resolved anisotropy decay further confirms the proximity of Au NCs to A488 tagged dsDNA in presence of Ag+ ion (details study given in supporting information, Figure S12).35, 57 A schematic diagram represents the attachment of Au NCs to dsDNA and incorporation of Ag+ ion inside dsDNA (Scheme 2).



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 20 of 27

Scheme 2. Schematic representation of attachment of Au NCs to dsDNA and incorporation of Ag+ ion inside dsDNA

CONCLUSION In this report, we have synthesized GSH-capped Au NCs via “top-down” approach. Au NCs is attached to dsDNA (one end thiol modified) tagged with A488 dye. 18 mer dsDNA is chosen as a linker between donor and acceptor to understand the effect of conformation change of dsDNA on photo excited energy transfer. The covalent attachment of Au NCs with thiol modified dsDNA is confirmed by CD and PL studies. The PL intensity and decay time of A488 dye is continuously quenched with increasing the ratio of A488/Au NCs tagged dsDNA, indicating the energy transfer. Interestingly, the efficiency of energy transfer drastically increases from 63 % to 82% in presence of Ag+ ion for a fixed ratio of A488/Au NCs tagged dsDNA. CD spectra clarifies that Ag+ ion helps to make closer distance between Au NCs and A488 by incorporating inside dsDNA. The Ag+ ion interacts with cytosine bases of G-C rich region of dsDNA; as a result the rigidity of dsDNA breaks down. The enhancement of the rate of energy transfer is due to shorting of distance between Au NCs and A488 dye in presence of Ag+ ion. Analysis reveals Study reveals that Au nanocluster is an efficient spectroscopic probe to understand the conformation of DNA.


Page 21 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Supporting Information Molecular structure of glutathione reduced, digital photographs of Au NPs solution under normal and UV light, TEM image of glutathione capped gold nanoparticles, MALDI-TOF spectrum of glutathione capped Au NCs, FTIR spectra of pure glutathione and glutathione capped Au NCs, CD spectra of ssDNA and dsDNA, absorption spectra of pure A488 tagged dsDNA and A488 tagged dsDNA attached with Au NC, PL quenching of A488 tagged dsDNA in presence of Au NCs, PL spectra of Au NCs in presence of Ag+ ion and A488 in presence of Ag+ ion, Time-resolved decay of pure Au NCs and Au NCs in presence of A488, PL efficiency as a function of the ratio of molar concentration between the donor and acceptor, CD/CA, timeresolved anisotropy decay. This material is available free of charge via the Internet at http://pubs.acs.org.

ACKNOWLEDGMENTS “DAE-SRC Outstanding Investigator Award” is gratefully acknowledged for financial support. DB and BP thank CSIR for awarding fellowship. We thank Mr. Gopal Krishna Manna, IACS, for the graphic design.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 22 of 27

REFERENCES (1)

Hildebrandt, N.; Spillmann, C. M.; Algar, W. R.; Pons, T.; Stewart, M. H.; Oh, E.;

Susumu, K.; Díaz, S. A.; Delehanty, J. B.; Medintz, I. L., Energy Transfer with Semiconductor Quantum Dot Bioconjugates: A Versatile Platform for Biosensing, Energy Harvesting, and Other Developing Applications. Chem. Rev. 2016, DOI: 10.1021/acs.chemrev.6b00030. (2)

Massey, M.; Ancona, M. G.; Medintz, I. L.; Algar, W. R., Time-Gated DNA Photonic

Wires with Förster Resonance Energy Transfer Cascades Initiated by a Luminescent Terbium Donor. ACS Photonics 2015, 2, 639-652. (3)

Trifonov, A.; Sharon, E.; Tel-Vered, R.; Kahn, J. S.; Willner, I., Application of the

Hybridization Chain Reaction on Electrodes for the Amplified and Parallel Electrochemical Analysis of DNA. J. Phys. Chem. C 2016, 120, 15743-15752. (4)

Pinheiro, A. V.; Han, D.; Shih, W. M.; Yan, H., Challenges and Opportunities for

Structural DNA Nanotechnology. Nat. Nanotechnol. 2011, 6, 763-772. (5)

Tinnefeld, P.; Heilemann, M.; Sauer, M., Design of Molecular Photonic Wires Based on

Multistep Electronic Excitation Transfer. ChemPhysChem 2005, 6, 217-222. (6)

Börjesson, K.; Tumpane, J.; Ljungdahl, T.; Wilhelmsson, L. M.; Nordén, B.; Brown, T.;

Mårtensson, J.; Albinsson, B., Membrane-Anchored DNA Assembly for Energy and Electron Transfer. J. Am. Chem.Soc. 2009, 131, 2831-2839. (7)

Spillmann, C. M.; Medintz, I. L., Use of Biomolecular Scaffolds for Assembling

Multistep Light Harvesting and Energy Transfer Devices. J. Photochem. and Photobiol. C:

Photochem. Rev. 2015, 23, 1-24. (8)

Singh, M. P.; Jennings, T. L.; Strouse, G. F., Tracking Spatial Disorder in an Optical

Ruler by Time-Resolved NSET. J. Phys. Chem. B 2009, 113, 552-558. (9)

Clapp, A. R.; Medintz, I. L.; Mattoussi, H., Förster Resonance Energy Transfer

Investigations Using Quantum-Dot Fluorophores. ChemPhysChem 2006, 7, 47-57. (10)

Jennings, T. L.; Singh, M. P.; Strouse, G. F., Fluorescent Lifetime Quenching near D =

1.5 nm Gold Nanoparticles: Probing NSET Validity. J. Am. Chem. Soc. 2006, 128, 5462-5467. (11)

Kundu, S.; Patra, A., Nanoscale Strategies for Light Harvesting. Chem. Rev. 2016, DOI:

10.1021/acs.chemrev.6b00036. (12)

Sen, T.; Patra, A., Recent Advances in Energy Transfer Processes in Gold-Nanoparticle-

Based Assemblies. J. Phys. Chem. C 2012, 116, 17307-17317. 22 ACS Paragon Plus Environment

Page 23 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(13)

Bain, D.; Paramanik, B.; Sadhu, S.; Patra, A., A Study into the Role of Surface Capping

on Energy Transfer in Metal Cluster-Semiconductor Nanocomposites. Nanoscale 2015, 7, 20697-20708. (14)

Kukolka, F.; Müller, B. K.; Paternoster, S.; Arndt, A.; Niemeyer, C. M.; Bräuchle, C.;

Lamb, D. C., A Single-Molecule Förster Resonance Energy Transfer Analysis of Fluorescent DNA–Protein Conjugates for Nanobiotechnology. Small 2006, 2, 1083-1089. (15)

Zhou, D.; Piper, J. D.; Abell, C.; Klenerman, D.; Kang, D.-J.; Ying, L., Fluorescence

Resonance Energy Transfer between a Quantum Dot Donor and a Dye Acceptor Attached to DNA. Chem. Commun.2005, 4807-4809. (16)

Ihara, T.; Ishii, T.; Araki, N.; Wilson, A. W.; Jyo, A., Silver Ion Unusually Stabilizes the

Structure of a Parallel-Motif DNA Triplex. J. Am. Chem. Soc. 2009, 131, 3826-3827. (17)

Burda, J. V.; Šponer, J.; Leszczynski, J.; Hobza, P., Interaction of DNA Base Pairs with

Various Metal Cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): Nonempirical Ab Initio Calculations on Structures, Energies, and Nonadditivity of the Interaction. J. Phys. Chem. B 1997, 101, 9670-9677. (18)

Miyake, Y., et al., MercuryII-Mediated Formation of Thymine−HgII−Thymine Base Pairs

in DNA Duplexes. J. Am. Chem. Soc. 2006, 128, 2172-2173. (19)

Li, D.; Wieckowska, A.; Willner, I., Optical Analysis of Hg2+ Ions by Oligonucleotide–

Gold-Nanoparticle Hybrids and DNA-Based Machines. Angew. Chem. Int. Ed. 2008, 47, 39273931. (20)

Clever, G. H.; Kaul, C.; Carell, T., DNA–Metal Base Pairs. Angew. Chem. Int. Ed. 2007,

46, 6226-6236. (21)

Tanaka, Y.; Kondo, J.; Sychrovsky, V.; Sebera, J.; Dairaku, T.; Saneyoshi, H.; Urata, H.;

Torigoe, H.; Ono, A., Structures, Physicochemical Properties, and Applications of T-HgII-T, CAgI-C, and Other Metallo-Base-Pairs. Chem. Commun. 2015, 51, 17343-17360. (22)

Yuan, X.; Luo, Z.; Zhang, Q.; Zhang, X.; Zheng, Y.; Lee, J. Y.; Xie, J., Synthesis of

Highly Fluorescent Metal (Ag, Au, Pt, and Cu) Nanoclusters by Electrostatically Induced Reversible Phase Transfer. ACS Nano 2011, 5, 8800-8808. (23)

Xie, J.; Zheng, Y.; Ying, J. Y., Protein-Directed Synthesis of Highly Fluorescent Gold

Nanoclusters. J. Am. Chem. Soc. 2009, 131, 888-889.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

(24)

Page 24 of 27

Jin, R.; Eah, S.-K.; Pei, Y., Quantum-Sized Metal Nanoclusters. Nanoscale 2012, 4,

4026-4026. (25)

Goswami, N.; Yao, Q.; Chen, T.; Xie, J., Mechanistic Exploration and Controlled

Synthesis of Precise Thiolate-Gold Nanoclusters. Coord. Chem. Rev. 2016, 329, 1-15. (26)

Aldeek, F.; Ji, X.; Mattoussi, H., Quenching of Quantum Dot Emission by Fluorescent

Gold Clusters: What It Does and Does Not Share with the Förster Formalism. J. Phys. Chem. C

2013, 117, 15429-15437. (27)

Paramanik, B.; Kundu, S.; De, G.; Patra, A., Structural Evolution, Photoinduced Energy

Transfer in Au Nanocluster-CdTe QD Nanocomposites and Amino Acid Sensing. J. Mater.

Chem. C 2016, 4, 486-496. (28)

Barman, M. K.; Paramanik, B.; Bain, D.; Patra, A., Light Harvesting and White-Light

Generation in a Composite of Carbon Dots and Dye-Encapsulated BSA-Protein-Capped Gold Nanoclusters. Chem. Eur. J. 2016, 22, 11699-11705. (29)

Chowdhury, S.; Wu, Z.; Jaquins-Gerstl, A.; Liu, S.; Dembska, A.; Armitage, B. A.; Jin,

R.; Peteanu, L. A., Wavelength Dependence of the Fluorescence Quenching Efficiency of Nearby Dyes by Gold Nanoclusters and Nanoparticles: The Roles of Spectral Overlap and Particle Size. J. Phys. Chem. C 2011, 115, 20105-20112. (30)

Petty, J. T.; Zheng, J.; Hud, N. V.; Dickson, R. M., DNA-Templated Ag Nanocluster

Formation. J. Am. Chem. Soc. 2004, 126, 5207-5212. (31)

Liu, G.; Feng, D.-Q.; Zheng, W.; Chen, T.; Li, D., An Anti-Galvanic Replacement

Reaction of DNA Templated Silver Nanoclusters Monitored by the Light-Scattering Technique.

Chem. Commun. 2013, 49, 7941-7943. (32)

Chakraborty, S.; Babanova, S.; Rocha, R. C.; Desireddy, A.; Artyushkova, K.; Boncella,

A. E.; Atanassov, P.; Martinez, J. S., A Hybrid DNA-Templated Gold Nanocluster for Enhanced Enzymatic Reduction of Oxygen. J. Am. Chem. Soc. 2015, 137, 11678-11687. (33)

Su, Y.-T.; Lan, G.-Y.; Chen, W.-Y.; Chang, H.-T., Detection of Copper Ions through

Recovery of the Fluorescence of DNA-Templated Copper/Silver Nanoclusters in the Presence of Mercaptopropionic Acid. Anal. Chem. 2010, 82, 8566-8572. (34)

Freeman, R.; Finder, T.; Willner, I., Multiplexed Analysis of Hg2+ and Ag+ Ions by

Nucleic Acid Functionalized Cdse/Zns Quantum Dots and Their Use for Logic Gate Operations.

Angew. Chem. Int. Ed. 2009, 48, 7818-7821. 24 ACS Paragon Plus Environment

Page 25 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(35)

Paramanik, B.; Bain, D.; Patra, A., Making and Breaking of DNA-Metal Base Pairs: Hg2+

and Au Nanocluster Based Off/on Probe. J. Phys. Chem. C 2016, 120, 17127-17135. (36)

J. R. Lakowicz, Principles of Fluorescence Spectroscopy, Springer, 3rd edn, 2006.

(37)

Negishi, Y.; Nobusada, K.; Tsukuda, T., Glutathione-Protected Gold Clusters Revisited:

Bridging the Gap between Gold(I)−Thiolate Complexes and Thiolate-Protected Gold Nanocrystals. J. Am.Chem. Soc. 2005, 127, 5261-5270. (38)

Muhammed, M. A. H.; Verma, P. K.; Pal, S. K.; Kumar, R. C. A.; Paul, S.; Omkumar, R.

V.; Pradeep, T., Bright, NIR-Emitting Au23 from Au25: Characterization and Applications Including Biolabeling. Chem. Eur. J. 2009, 15, 10110-10120. (39)

Muhammed, M. A. H.; Aldeek, F.; Palui, G.; Trapiella-Alfonso, L.; Mattoussi, H.,

Growth of in Situ Functionalized Luminescent Silver Nanoclusters by Direct Reduction and Size Focusing. ACS Nano 2012, 6, 8950-8961. (40)

Lin, C.-A. J., et al., Synthesis, Characterization, and Bioconjugation of Fluorescent Gold

Nanoclusters toward Biological Labeling Applications. ACS Nano 2009, 3, 395-401. (41)

Zhu, M.; Aikens, C. M.; Hollander, F. J.; Schatz, G. C.; Jin, R., Correlating the Crystal

Structure of a Thiol-Protected Au25 Cluster and Optical Properties. J. Am. Chem. Soc. 2008, 130, 5883-5885. (42)

Dreaden, E. C.; Alkilany, A. M.; Huang, X.; Murphy, C. J.; El-Sayed, M. A., The Golden

Age: Gold Nanoparticles for Biomedicine. Chem. Soc. Rev. 2012, 41, 2740-2779. (43)

Chaudhari, K.; Xavier, P. L.; Pradeep, T., Understanding the Evolution of Luminescent

Gold Quantum Clusters in Protein Templates. ACS Nano 2011, 5, 8816-8827. (44)

Grueso, E.; Perez-Tejeda, P.; Prado-Gotor, R.; Cerrillos, C., DNA Strand Elongation

Induced by Small Gold Nanoparticles at High Ethanol Content. J. Phys. Chem. C 2014, 118, 4416-4428. (45)

Garbett, N. C.; Ragazzon, P. A.; Chaires, J. B., Circular Dichroism to Determine Binding

Mode and Affinity of Ligand-DNA Interactions. Nat. Protoc. 2007, 2, 3166-3172. (46)

Rajendran, A.; Nair, B. U., Unprecedented Dual Binding Behaviour of Acridine Group of

Dye: A Combined Experimental and Theoretical Investigation for the Development of Anticancer Chemotherapeutic Agents. Biochim. Biophys. Acta 2006, 1760, 1794-1801. (47)

Sandström, P.; Boncheva, M.; Åkerman, B., Nonspecific and Thiol-Specific Binding of

DNA to Gold Nanoparticles. Langmuir 2003, 19, 7537-7543. 25 ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

(48)

Page 26 of 27

Zheng, Y.; Yang, C.; Yang, F.; Yang, X., Real-Time Study of Interactions between

Cytosine–Cytosine Pairs in DNA Oligonucleotides and Silver Ions Using Dual Polarization Interferometry. Anal. Chem. 2014, 86, 3849-3855. (49)

Rahul, C.; Jaswinder, S.; Haining, W.; Shengli, Z.; Su, L.; Hao, Y.; Stuart, L.; Yan, L.,

Distance-Dependent Interactions between Gold Nanoparticles and Fluorescent Molecules with DNA as Tunable Spacers. Nanotechnology 2009, 20, 485201. (50)

Flehr, R.; Kienzler, A.; Bannwarth, W.; Kumke, M. U., Photophysical Characterization

of a FRET System Using Tailor-Made DNA Oligonucleotide Sequences. Bioconjugate Chem.

2010, 21, 2347-2354. (51)

Beane, G.; Boldt, K.; Kirkwood, N.; Mulvaney, P., Energy Transfer between Quantum

Dots and Conjugated Dye Molecules. J. Phys. Chem. C 2014, 118, 18079-18086. (52)

Raut, S.; Rich, R.; Fudala, R.; Butler, S.; Kokate, R.; Gryczynski, Z.; Luchowski, R.;

Gryczynski, I., Resonance Energy Transfer between Fluorescent BSA Protected Au Nanoclusters and Organic Fluorophores. Nanoscale 2014, 6, 385-391. (53)

Sadhu, S.; Patra, A., Donor–Acceptor Systems: Energy Transfer from CdS Quantum

Dots/Rods to Nile Red Dye. ChemPhysChem 2008, 9, 2052-2058. (54)

Medintz, I. L.; Clapp, A. R.; Brunel, F. M.; Tiefenbrunn, T.; Tetsuo Uyeda, H.; Chang, E.

L.; Deschamps, J. R.; Dawson, P. E.; Mattoussi, H., Proteolytic Activity Monitored by Fluorescence Resonance Energy Transfer through Quantum-Dot-Peptide Conjugates. Nat. Mater

2006, 5, 581-589. (55)

Medintz, I. L.; Sapsford, K. E.; Clapp, A. R.; Pons, T.; Higashiya, S.; Welch, J. T.;

Mattoussi, H., Designer Variable Repeat Length Polypeptides as Scaffolds for Surface Immobilization of Quantum Dots. J. Phys. Chem. B 2006, 110, 10683-10690. (56)

Sahoo, H.; Roccatano, D.; Hennig, A.; Nau, W. M., A 10-Å Spectroscopic Ruler Applied

to Short Polyprolines. J. Am. Chem. Soc. 2007, 129, 9762-9772. (57)

Jana, B.; Bhattacharyya, S.; Patra, A., Functionalized Dye Encapsulated Polymer

Nanoparticles Attached with a BSA Scaffold as Efficient Antenna Materials for Artificial Light Harvesting. Nanoscale 2016, 8, 16034-16043.


Page 27 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


TOC Graphic


Silver(I)-Induced Conformation Change of DNA: Gold Nanocluster as

Recommend Documents