[show abstract][hide abstract] ABSTRACT: Water-soluble and red-emitting gold nanoclusters (Au NCs) were synthesized with single-stranded DNA as a promising biotemplate and dimethylamine borane as a mild reductant. The fluorescent Au NCs can be formed in a weakly acidic aqueous solution that is free from the simultaneous formation of large nanoparticles. The cluster feature of the formed Au species has been revealed by fluorescence spectra, absorption spectra, and transmission electron microscopy. Additionally, DNA sequences could be used to tune the Au NCs' emissions. The as-prepared Au NCs display high stability at physiological pH condition, and thus, wide potential applications are anticipated for the biocompatible fluorescent Au NCs serving as nanoprobes in bioimaging and related fields.
[show abstract][hide abstract] ABSTRACT: DNA-templated silver nanoclusters (Ag NCs) are emerging sets of fluorophores that are widely applicable because of high brightness, good photostability, and visible to near-infrared emissions tunable using the DNA sequence and length to change the NC size. We find that fluorescent Ag NCs can be size-selectively grown at DNA abasic sites (AP site) using a constrained duplex environment opposed by a cytosine and flanked by two guanines. The size of the AP site-grown Ag NCs is not affected by the increasing Ag(+) concentration. A Job's plot analysis shows that Ag(2) NCs are the species responsible for the observed emissions. Although varying the DNA sequence one base away from the AP site (i.e., the Ag NC growth site) does not alter the size of the fluorescent Ag NCs, the emissions of the formed Ag NCs are still gradually red shifted as the sequence changes from thymine (T) to cytosine (C), adenine (A), and guanine (G). Furthermore, this emission shift is strongly dependent on the base-stacking direction of the 3'-side sequence of the 5'-G stack exactly flanking the AP site, which exhibits a larger emission alteration than altering the 5'-side sequence of the 3'-G stack flanking the AP site on the other side of the site. The excited-state lifetimes of the Ag NCs are inversely proportional to the singlet energies (ΔE(0,0)) of the Ag NCs relative to their ground state and of the vertical ionization potentials of the guanines directly flanking the AP site as determined by the base stacking. All of these results support the conclusion that the Ag NC excited state becomes more stable by interacting with a guanine base because of the larger electronic dipole moment that can be modified by the stacked sequences. Additionally, the size of the formed Ag NCs seems to be dependent on the consecutive AP site number. Thus, the AP site design in this work provides an easy way to shed light on the role of DNA base stacking in the optical properties of Ag NCs.
[show abstract][hide abstract] ABSTRACT: Silver nanoclusters (Ag NCs) templated with DNAs have attracted much attention as novel fluorophores because of their convenient emission tunability by the sequence and length of the template DNAs. However, the precise production of Ag NCs in a site-specific manner still remains a challenge to attain highly selective and label-free DNA recognition. Here we exploited the availability of a gap site in DNA duplexes as a new scaffold for the synthesis of Ag NCs. Compared to the commonly used DNA templates for the creation of Ag NCs, the gap site in DNA duplexes was found to facilitate the rapid formation of the fluorescent Ag NCs without sacrifice of their bright emission and excellent stability. We found that fluorescent Ag NCs were highly selectively formed when cytosine faced toward the gap site in DNA duplexes, and they were in situ utilized as readout by signal-on manner for the DNA mutation assays. This base-selective growth of the fluorescent Ag NCs at the gap site would find promising applications in practical detection of single nucleotide polymorphism (SNP) and construction of DNA-based functional sensors with label-free and cost-effective merits.
[show abstract][hide abstract] ABSTRACT: Due to their good photostability, high quantum yield and low toxicity, fluorescent silver nanoclusters (Ag NCs) have received much attention as novel fluorophores for sensing applications. In this work, we investigate the upconversion emission of Ag NCs templated by single- and double-stranded DNAs. DNA-templated Ag NCs exhibit upconversion emission at wavelengths identical to those observed for the corresponding Stokes emission. Consequently, the Ag NCs' upconversion behavior can be easily tuned by the used DNA sequences. In addition, the Ag NCs are more stable under such an NIR excitation with the upconversion mode relative to the Stokes mode. As a proof-of-concept application, DNA nucleobase recognition with the in situ formed Ag NCs is realized using the Ag NCs' upconversion emission. We expect that the Ag NCs' upconversion emission is more advantageous than the previously used rare-earth materials, at least with respect to easy modulation of the emission energies by DNA sequences, and could find wide application in sensor design.
The Analyst 04/2012; 137(10):2362-6. · 4.23 Impact Factor
[show abstract][hide abstract] ABSTRACT: Label-free DNA nucleobase recognition by fluorescent small molecules has received much attention due to its simplicity in mutation identification and drug screening. However, sequence-dependent fluorescence light-up nucleobase recognition and multicolor emission with individual emission energy for individual nucleobases have been seldom realized. Herein, an abasic site (AP site) in a DNA duplex was employed as a binding field for berberine, one of isoquinoline alkaloids. Unlike weak binding of berberine to the fully matched DNAs without the AP site, strong binding of berberine to the AP site occurs and the berberine's fluorescence light-up behaviors are highly dependent on the target nucleobases opposite the AP site in which the targets thymine and cytosine produce dual emission bands, while the targets guanine and adenine only give a single emission band. Furthermore, more intense emissions are observed for the target pyrimidines than purines. The flanking bases of the AP site also produce some modifications of the berberine's emission behavior. The binding selectivity of berberine at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, excited-state lifetime, DNA melting and fluorescence quenching by ferrocyanide and sodium chloride. It is expected that the target pyrimidines cause berberine to be stacked well within DNA base pairs near the AP site, which results in a strong resonance coupling of the electronic transitions to the particular vibration mode to produce the dual emissions. The fluorescent signal-on and emission energy-modulated sensing for nucleobases based on this fluorophore is substantially advantageous over the previously used fluorophores. We expect that this approach will be developed as a practical device for differentiating pyrimidines from purines by positioning an AP site toward a target that is available for readout by this alkaloid probe.
[show abstract][hide abstract] ABSTRACT: DNA-templated fluorescent silver nanoclusters (Ag NCs) composed of several or tens of atoms are gaining much interest because of their unique properties and convenient emission tunability by DNA sequence and length. However, the modulation by other factors other than DNA is also dependent on the special DNA secondary structure formation such as i-motif or G-quadruplex that is stimulated by pH or K+. One main observation considered in this work is emission modulation of Ag NCs by divalent Mg2+ during or after the clusters' creation. Tuning the emitting intensities and band positions can be realized by Mg2+ addition for the examined single-stranded DNA (ss-DNA) templates, which is dependent on the addition moment of Mg2+, while only intensity modulation should be achieved for the used double-stranded DNA (ds-DNA). Despite of this discrepancy, Mg2+ addition always induces a lifetime-varied emission state of Ag NCs. The modulated emission still follows the common nature of the previously used DNA sequence- and length-dependent emitting. Efficient screening the negative charges of DNA backbone upon addition of the divalent ion is responsible for the modulation by adaptively accommodating the formed Ag NCs. This strategy could be more advantageous over the emission modulation by DNA sequence and length because a desired emitting could be achieved only by alteration of the electrolyte conditions during or after the Ag NCs' creation.
Journal of Nanoscience and Nanotechnology 02/2012; 12(2):861-9. · 1.15 Impact Factor
[show abstract][hide abstract] ABSTRACT: DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation-related diseases. Various fluorescence methods for SNP detection have been proposed and many are already in use. However, fluorescence enhancement for signal-on SNP identification without label modification still remains a challenge. Here, we find that the abasic site (AP site) in a DNA duplex can be developed as a binding pocket favorable for the occurrence of the excited-state intramolecular proton transfer (ESIPT) of a 3-hydroxyflavone, fisetin, which is used as a proof of concept for effective SNP identification. Fisetin binding at the AP site is highly selective for target thymine or cytosine facing the AP site by observation of a drastic increase in the ESIPT emission band. In addition, the target recognition selectivity based on this ESIPT process is not affected by flanking bases of the AP site. The binding selectivity of fisetin at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, emission lifetime and DNA melting. The fluorescent signal-on sensing for SNP based on this fluorophore is substantially advantageous over the previously used fluorophores such as the AP site-specific signal-off organic ligands with a similar fluorescing mechanism before and after binding to DNA with hydrogen bonding interaction. We expect that this approach will be employed to develop a practical SNP detection method by locating an AP site toward a target and employing an ESIPT probe as readout.
The Analyst 09/2011; 136(21):4480-5. · 4.23 Impact Factor
[show abstract][hide abstract] ABSTRACT: DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation related diseases. Various methods for SNP detection have been proposed and many are already in use. Here, we find that the abasic site (AP site) in the DNA duplex can be developed as a capping scaffold for the generation of fluorescent silver nanoclusters (Ag NCs). As a proof of concept, the DNA sequences from fragments near codon 177 of cancer supression gene p53 were used as a model for SNP detection by in situ formed Ag NCs. The formation of fluorescent Ag NCs in the AP site-containing DNA duplex is highly selective for cytosine facing the AP site and guanines flanking the site and can be employed in situ as readout for SNP detection. The fluorescent signal-on sensing for SNP based on this inorganic fluorophore is substantially advantageous over the previously reported signal-off responses using low-molecular-weight organic ligands. The strong dependence of fluorescent Ag NC formation on the sequences surrounding the AP site was successfully used to identify mutations in codon 177 of cancer supression gene p53. We anticipate that this approach will be employed to develop a practical SNP detection method by locating an AP site toward the midway cytosine in a target strand containing more than three consecutive cytosines.
[show abstract][hide abstract] ABSTRACT: Many efforts have been made for the developments of aptamers due to their wide applications for various targets. In this work, we tried to use an abasic site (AP site) that was embeded in a double-stranded DNA as a binding pocket for fisetin. With the AP site being wholly opposed and flanked by thymines (named T-T aptamer), the aptamer exhibits high binding selectivity and sensitivity for fisetin over the other flavonoids such as morin, rutin, apigenin, kaempferol, myricetin, quercetin, luteolin, baicalin, naringenin, genistein, chrysin, and galangin. Upon binding to the AP site, fisetin experiences a significant enhancement in fluorescence emisson by favoring the occurrence of its excited-state intramolecular proton transfer (ESIPT) reaction. The detection limit is about 50 nM at a signal-to-noise ratio of 3. Therefore, the realization for fisetin's selective analysis is beneficial from the novel aptamer design without any fluorophore modification. Thus, the almost negligible fluorescence background from the aptamer is achieved in our method.
Sensors and Actuators B: Chemical. s 171–172:666–671.