A Simple Colorimetric Assay of Bleomycin-Mediated DNA Cleavage Utilizing Double-Stranded DNA-Modified Gold Nanoparticles.

A colorimetric assay of DNA cleavage by bleomycin (BLM) derivatives was developed utilizing high colloidal stability on double-stranded (ds) DNA-modified gold nanoparticles (dsDNA-AuNPs) possessing a cleavage site. The assay was performed using dsDNA-AuNPs treated with inactive BLM or activated BLM (Fe(II)⋅BLM). A 10-min exposure in dsDNA-AuNPs with inactive BLM treatment resulted in a rapid color change from red to purple because of salt-induced non-crosslinking aggregation of dsDNA-AuNPs. In contrast, the addition of active Fe(II)⋅BLM retained the red color, probably because of the formation of protruding structures at the outermost phase of dsDNA-AuNPs caused by BLM-mediated DNA cleavage. Furthermore, the results of our model experiments indicate that oxidative base release and DNA-cleavage pathways could be visually distinguished with color change. The present methodology was also applicable to model screening assays using several drugs with different mechanisms related to antitumor activity. These results strongly suggest that this assay with a rapid color change could lead to simple and efficient screening of potent antitumor agents.

DNA-Programmed Bimodal 2D Assembly of Differently Sized Nanoparticles via Folding of Precursory Circular Chains.

Gold nanoparticle (AuNP) assemblies in two-dimensions (2D) exhibit collective physical/chemical properties that are useful for various devices. However, technical issues still impede the efficient ordering of differently sized AuNPs on solid supports while avoiding phase separation. This paper describes a method to construct binary 2D assemblies by folding precursory circular chains composed of small and large AuNPs. The structural change is caused by a spontaneous, non-cross-linking assembly of fully matched double-stranded DNA-modified AuNPs (dsDNA-AuNPs) at a high ionic strength. Since larger dsDNA-AuNPs have a lower critical coagulation concentration of the supporting electrolyte, the spontaneous assembly of large AuNPs precedes that of small AuNPs in the precursory chain during evaporation. Transmission electron microscopy reveals that alternate-type AuNP chains are folded into a binary 2D structure in a mixed mode, whereas block-type chains are transformed into a binary 2D structure in a core-shell mode. The methodology could potentially be harnessed for the fabrication of binary AuNP arrays for various devices.

Directed Assembly of Gold Nanorods by Terminal-Base Pairing of Surface-Grafted DNA.

Directed assemblies of anisotropic metal nanoparticles exhibit attractive physical and chemical properties. However, an effective methodology to prepare differently directed assemblies from the same anisotropic nanoparticles is not yet available. Gold nanorods (AuNRs) region-selectively modified with different DNA strands can form side-by-side (SBS) and end-to-end (ETE) assemblies in a non-crosslinking manner. When the complementary DNA is hybridized to the surface-bound DNA, stacking interaction between the blunt ends takes place in the designated regions. Such AuNRs assemble into highly ordered structures, assisted by capillary forces emerging on the substrate surface. Moreover, insertion of a mercury(II)-mediated thymine-thymine base pair into the periphery of the DNA layer allows selective formation of the SBS or ETE assemblies from the strictly identical AuNRs with or without mercury(II).

Cross-Linking versus Non-Cross-Linking Aggregation of Gold Nanoparticles Induced by DNA Hybridization: A Comparison of the Rapidity of Solution Color Change.

Gold nanoparticles densely modified with single-stranded DNA (ssDNA-AuNPs) form aggregates with cross-linker ssDNAs via duplex formation. Alternatively, the ssDNA-AuNPs are spontaneously aggregated at high ionic strength in a non-cross-linking manner when complementary ssDNAs are added to form fully matched duplexes. Both aggregation modes are accompanied by a red-to-purple color change, which has been exploited in various bioassays. The current study compares the rapidity of color change between the cross-linking and non-cross-linking aggregation modes under identical conditions. When a small number of cross-linker/complementary DNAs are provided, the cross-linking mode exhibited more rapid color change than the non-cross-linking mode. Conversely, with a large number of the DNAs, the non-cross-linking aggregation occurred more rapidly than the cross-linking counterpart. This finding allows one to select a more appropriate aggregation mode for application of ssDNA-AuNPs to colorimetric assays under given conditions.

Rapid Non-Crosslinking Aggregation of DNA-Functionalized Gold Nanorods and Nanotriangles for Colorimetric Single-Nucleotide Discrimination.

Gold nanoparticles modified with DNA duplexes are rapidly and spontaneously aggregated at high ionic strength. In contrast, this aggregation is greatly suppressed when the DNA duplex has a single-base mismatch or a single-nucleotide overhang located at the outermost surface of the particle. These colloidal features emerge irrespective of the size and composition of the particle core; however, the effects of the shape remain unexplored. Using gold nanorods and nanotriangles (nanoplatelets), we show herein that both remarkable rapidity in colloidal aggregation and extreme susceptibility to DNA structural perturbations are preserved, regardless of the shape and aspect ratio of the core. It is also demonstrated that the DNA-modified gold nanorods and nanotriangles are applicable to naked-eye detection of a single-base difference in a gene model. The current study corroborates the generality of the unique colloidal properties of DNA-functionalized nanoparticles, and thus enhances the feasibility of their practical use.

Modulation of Interparticle Distance in Discrete Gold Nanoparticle Dimers and Trimers by DNA Single-Base Pairing.

Self-assembled structures of metallic nanoparticles with dynamically changeable interparticle distance hold promise for the regulation of collective physical properties. This paper describes gold nanoparticle dimers and trimers that exhibit spontaneous and reversible changes in interparticle distance. To exploit this property, a gold nanoparticle is modified with precisely one long DNA strand and approximately five short DNA strands. The long DNA serves to align the nanoparticles on a template DNA via hybridization, while the short DNAs function to induce the interparticle distance changes. The obtained dimer and trimer are characterized with gel electrophoresis, dynamic light scattering measurements, and transmission electron microscopy (TEM). When the complementary short DNA is added to form the fully matched duplexes on the particle surface in the presence of MgCl2 , spontaneous reduction of the interparticle distance is observed with TEM and cryo-electron microscopy. By contrast, when the terminal-mismatched DNA is added, no structural change occurs under the same conditions. Therefore, the single base pairing/unpairing at the outermost surface of the nanoparticle impacts the interparticle distance. This unique feature could be applied to the regulation of structures and properties of various DNA-functionalized nanoparticle assemblies.

DNA dangling-end-induced colloidal stabilization of gold nanoparticles for colorimetric single-nucleotide polymorphism genotyping.

A single-nucleotide polymorphism (SNP) detection method was developed by combining single-base primer extension and salt-induced aggregation of gold nanoparticles densely functionalized with double-stranded DNA (dsDNA-AuNP). The dsDNA-AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single-base protrusion at the outermost surface disperse stably, allowing detection of a single-base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single-stranded DNA on the AuNP surface, the resulting dsDNA-AuNP works as a visual indicator of single-base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single-base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.

Facile Preparation of a Hairpin DNA-Gold Nanoparticle Monoconjugate with a Single-Dye Molecule and Lactobionic Acid as Targeting Ligand.

We established a new design for a single molecular beacon-conjugated gold nanoparticle, named monoMB-GNP, which showed enhanced fluorescence emission only in the presence of the complementary DNA sequence. MonoMB-GNP also showed no apparent toxicity to NIH/3T3 cells at 1 nM, as determined by the water-soluble tetrazolium assay. Importantly, the lactobionic acid was successfully modified on the surface of monoMB-GNP. The proposed nanoparticle has prospects for use in several applications for targetable molecular beacon strategies.

Preparation of Spherical Nucleic Acid Nanoparticles Containing a Self-immolative Poly(carbamate) Core.

We prepared a novel spherical nucleic acid, containing a core structure of self-immolative poly(carbamate) (PC), with aminobenzyl alcohol as a repeating unit, by conjugating an end-activated PC derivative with an amine-terminated oligoDNA on a solid support for PC-oligoDNA. Dynamic light-scattering measurements revealed a hydrodynamic diameter of 107 nm with a narrow size distribution. A fluorescent monomer with aminobenzyl alcohol is available for PC-oligoDNA synthesis to enhance the fluorescence emission by a domino-like disassembly of PC in response to various external stimuli.

Multiplex MicroRNA Detection on a Surface-Functionalized Power-Free Microfluidic Chip.

Circulating microRNAs (miRNAs) have emerged as promising cancer biomarkers because their concentration profiles in body fluids are associated with the type and clinical stage of cancer. For multiplex miRNA detection, a novel surface-functionalized power-free microfluidic chip (SF-PF microchip) has been developed. The inner surface of the SF-PF microchip microchannels was functionalized via electron beam-induced graft polymerization and immobilization of capture probe DNAs. Simultaneous and specific duplex miRNA detection was achieved on the line-type SF-PF microchip with detection limits of 19.1 and 47.6 nmol L-1 for hsa-miR-16 and hsa-miR-500a-3p, respectively. Moreover, simultaneous and specific triplex miRNA detection was achieved on the stripe-type SF-PF microchip. The sample volume required for this microchip was 0.5 µL, and the time required for detection was 17 min. These results indicate that up to six types of miRNAs could be detected without compromising the advantages of the previous SF-PF microchips for cancer point-of-care testing.

The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern.

Transcriptional regulation of the bcl-2 proto-oncogene is highly complex, with the majority of transcription driven by the P1 promoter site and the interaction of multiple regulatory proteins. A guanine- and cytosine-rich (GC-rich) region directly upstream of the P1 site has been shown to be integral to bcl-2 promoter activity, as deletion or mutation of this region significantly increases transcription. This GC-rich element consists of six contiguous runs of guanines and cytosines that have the potential to adopt DNA secondary structures, the G-quadruplex and i-motif, respectively. Our laboratory has previously demonstrated that the polypurine-rich strand of the bcl-2 promoter can form a mixture of three different G-quadruplex structures. In this current study, we demonstrate that the complementary polypyrimidine-rich strand is capable of forming one major intramolecular i-motif DNA secondary structure with a transition pH of 6.6. Characterization of the i-motif folding pattern using mutational studies coupled with circular dichroic spectra and thermal stability analyses revealed an 8:5:7 loop conformation as the predominant structure at pH 6.1. The folding pattern was further supported by chemical footprinting with bromine. In addition, a novel assay involving the sequential incorporation of a fluorescent thymine analog at each thymine position provided evidence of a capping structure within the top loop region of the i-motif. The potential of the GC-rich element within the bcl-2 promoter region to form DNA secondary structures suggests that the transition from the B-DNA to non-B-DNA conformation may play an important role in bcl-2 transcriptional regulation. Furthermore, the two adjacent large lateral loops in the i-motif structure provide an unexpected opportunity for protein and small molecule recognition.

Identification and cleavage site analysis of DNA sequences bound strongly by bleomycin.

A hairpin DNA library containing an 8-base pair sequence-randomized region was employed in a SELEX-type procedure to identify DNAs that bound strongly to bleomycin A(5), the latter of which was immobilized on a solid support. Ten hairpin DNAs that bound BLM A(5) strongly were identified and sequenced, and used to characterize DNA binding by the antitumor antibiotic. While all 10 selected hairpin DNAs bound to BLM strongly, they did exhibit a range of binding specificities. Further, while the binding specificity was generally the greatest for hairpin DNAs that contained at least one of the sequences (5'-GC-3' and 5'-GT-3') cleaved most frequently by Fe(II).bleomycin, the hairpin DNA exhibiting the poorest binding specificity also contained a 5'-GT-3' site. Four of the hairpin DNA substrates were 5'-(32)P end-labeled and used to assess the preferred sites of cleavage by Fe(II).BLM. The substrate DNAs included two lacking any 5'-GT-3' or 5'-GC-3' site; these were cleaved at 5'-AA-3' and (more strongly) at 5'-AT-3' and 5'-GA-3' sequences. For two hairpin DNAs containing 5'-GT-3' or 5'-GC-3' sequences, cleavage was observed at these sequences as well, but the three aforementioned sequences were also cleaved efficiently. For hairpin DNA 3, which was bound the least well of the 10 DNAs studied, a 5'-TA-3' site was also cleaved efficiently. Thus, the pattern and intensities of cleavage of the four DNAs studied were not entirely consistent with the preferred pattern of DNA cleavage reported for Fe(II).BLM in numerous published studies that have employed arbitrarily chosen DNA substrates. Also studied were the chemistry of DNA cleavage for one of the hairpin DNAs, and competition experiments in which the diminution of cleavage was measured following admixture of a molar excess of a smaller hairpin DNA shown to be an exceptionally good substrate for cleavage by Fe(II).BLM. In the aggregate, the data indicate that the relationship between DNA binding and degradation by Fe.BLM, as well as the chemistry leading to DNA degradation, are more complex than suggested by earlier studies that employed only DNA degradation product analysis as an end point.

Identification of strong DNA binding motifs for bleomycin.

The bleomycins (BLMs) are clinically used antitumor antibiotics. Their mechanism of action is believed to involve oxidative cleavage of DNA and possibly also RNA degradation. DNA degradation has been studied extensively and shown to involve binding of an activated metallobleomycin to DNA, followed by abstraction of C4'-H from deoxyribose in the rate-limiting step for DNA degradation. It is interesting that while DNA and RNA degradation by activated Fe.BLM has been studied extensively, much less is known about the actual binding selectivity of BLM, that is, the obligatory step that precedes cleavage. Thus it is unclear whether cleavage specificity is defined by the binding event or whether cleavage occurs at a subset of preferred binding sites. With only a few exceptions, NMR binding studies have employed metalloBLMs such as Co.BLM and Zn.BLM whose therapeutic relevance is uncertain. A single biochemical study that compared DNA binding and cleavage directly also employed Co.BLM. It is logical to anticipate that preferred sites of DNA cleavage will occur at sites that are (a subset of) preferred DNA binding sites, but there are currently no data available relevant to this issue. Herein, we describe the development and implementation of a novel strategy to identify DNA motifs that bind BLM strongly.

A novel DNA hairpin substrate for bleomycin.

A 16-nucleotide DNA hairpin containing 4-aminobenzo[g]quinazoline-2-one 2'-deoxyribose at position 15 has been prepared and found to lack significant fluorescence. When treated with Fe(II).BLM, the hairpin was found to undergo oxidative transformation selectively at position 15. The predominant fluorescent product was characterized and quantified. The pro-fluorescent DNA hairpin was used as a substrate for 15 bleomycin congeners, and the results were compared with those obtained following cleavage of a radiolabeled DNA duplex and PAGE analysis.

Reversible Shrinkage of DNA-Functionalized Gold Nanoparticle Assemblies Revealed by Surface Plasmon Resonance.

A technique for tuning interparticle distance in plasmonic gold nanoparticle (AuNP) assemblies has shown great potential for the development of optoelectronic nanodevices. However, it still remains a challenge to reversibly alter the distance in a facile manner. DNA-templated AuNP assemblies are among the mostly investigated plasmonic nanomaterials. In previous work, salt-induced structural shrinkage of DNA-templated AuNP (5 nm in diameter) dimers/trimers is demonstrated only by electron microscopic analyses. In the present study, interparticle distance is modulated in larger AuNP (15 nm or 20 nm in diameter) dimers that exhibit strong surface plasmon resonance (SPR). The reversible SPR shift is achieved by using the temperature-dependent shrinkage/extension of the DNA-templated AuNP dimers. The present proof-of-concept study suggests a potential application of the reversible structural change to optical switching.

Rapid Naked-Eye Discrimination of Cytochrome P450 Genetic Polymorphism through Non-Crosslinking Aggregation of DNA-Functionalized Gold Nanoparticles.

The front cover artwork is provided by the group of Tohru Takarada at RIKEN (Japan). The image shows a colorimetric single-nucleotide polymorphism (SNP) genotyping method that uses spontaneous aggregation of DNA-modified gold nanoparticles (DNA-AuNPs) for the simple and rapid SNP genotyping of the human cytochrome P450 2C19 monooxygenase gene. For more details, read the full text of the Full Paper at p. 508.

Rapid Naked-Eye Discrimination of Cytochrome P450 Genetic Polymorphism through Non-Crosslinking Aggregation of DNA-Functionalized Gold Nanoparticles.

Involvement of single-nucleotide polymorphism (SNP) genotyping in healthcare should allow for more effective use of pharmacogenomics. However, user-friendly assays without the requirement of a special instrument still remain unavailable. This study describes naked-eye SNP discrimination in exon 5 of the human cytochrome P450 2C19 monooxygenase gene, CYP2C19*1 (the wild-type allele) and CYP2C19*2 (the variant allele with G681A point mutation). The present assay is composed of allele-specific single-base primer extension and salt-induced aggregation of DNA-modified gold nanoparticles (DNA-AuNPs). Genetic samples extracted from human hair roots are subjected to this assay. The results are verified by direct sequencing. This study should promise the prospective use of DNA-AuNPs in gene diagnosis.

Colloidal Au replacement assay for highly sensitive quantification of low molecular weight analytes by surface plasmon resonance.

A novel sensing method based on surface plasmon resonance (SPR) was developed for the highly sensitive quantification of low molecular weight (LMW) analytes (colloidal Au replacement assay). Gold nanoparticles (diameter = 20 nm) functionalized with lactosyl-poly(ethylene glycol) (PEG) were prepared and were specifically adsorbed onto a Ricinus communis agglutinin (RCA120)-immobilized SPR sensor chip surface. Subsequent injection of free d-galactose elicited the elution of the preadsorbed lactosyl-PEGylated gold nanoparticles in a manner proportional to the galactose concentration, achieving a substantial and quantitative analysis over a wide range of galactose concentrations (0.1-50 ppm). This method of d-galactose sensing through the substituted elution of preadsorbed nanoparticles from the sensor chip surface would be applicable for the highly sensitive SPR quantification of various LMW analytes, which are known to be difficult to detect by the conventional SPR sensing regime.

Preparation and characterization of polyion complex micelles with a novel thermosensitive poly(2-isopropyl-2-oxazoline) shell via the complexation of oppositely charged block ionomers.

Novel thermosensitive polyion complex (PIC) micelles were prepared in an aqueous medium based on the complexation of a pair of oppositely charged block ionomers, poly(2-isopropyl-2-oxazoline)-b-poly(amino acid)s (PiPrOx-b-PAA), containing thermosensitive PiPrOx segments. The controlled synthesis of PiPrOx-b-PAA was achieved via the ring-opening anionic polymerization of N-carboxyanhydrides (NCA) of either eta-benzyloxycarbonyl-l-lysine (Lys(Z)-NCA) or beta-benzyl-l-aspartate (BLA-NCA) with omega-amino-functionalized PiPrOx macroinitiators and the subsequent deprotection reaction under acidic or basic conditions. Gel permeation chromatography (GPC) and 1H NMR spectroscopy revealed that the syntheses of two block ionomers, poly(2-isopropyl-2-oxazoline)-b-poly(l-lysine) [PiPrOx-P(Lys)] and poly(2-isopropyl-2-oxazoline)-b-poly(aspartic acid) [PiPrOx-P(Asp)], proceeded almost quantitatively to give samples with a narrow molecular weight distribution (Mw/Mn

Ligand density effect on biorecognition by PEGylated gold nanoparticles: regulated interaction of RCA120 lectin with lactose installed to the distal end of tethered PEG strands on gold surface.

PEGylated gold nanoparticles (diameter: 20 nm) possessing various functionalities of lactose ligand on the distal end of tethered PEG ranging from 0 to 65% were prepared to explore the effect of ligand density of the nanoparticles on their lectin binding property. UV-visible spectra of the aqueous solution of the nanoparticles revealed that the strong steric stabilization property of the PEG layer lends the nanoparticles high dispersion stability even under the physiological salt concentration (ionic strength, I = 0.15 M). The number of PEG strands on a single particle was determined to be 520 from thermogravimetric analysis (TGA). Scanning electron microscopy (SEM) observation under controlled acceleration voltage revealed the thickness of the PEG layer on the nanoparticle to be approximately 7 nm. The area occupied by a single lactose molecule on the surface of PEGylated gold nanoparticles was then calculated based on TGA and SEM results and was varied in the range of 10-34 nm2 depending on the lactose functionality (65 approximately 20%). PEGylated gold nanoparticles with 40% and 65% lactose functionality showed a selective and time-dependent aggregation in phosphate buffer with the addition of Ricinus communis agglutinin (RCA120) lectin, a bivalent galactose-specific protein. The aggregates can be completely redispersed by adding an excess amount of galactose. Time-lapse monitoring of UV-visible spectra at 600-750 nm revealed that the aggregation of PEGylated gold nanoparticles was accelerated with an increase in both RCA120 concentration in the solution and the lactose density of the nanoparticles. Furthermore, the sensitivity of lectin detection could be controlled by the regulation of lactose density on the particle surface. Interestingly, there was a critical lactose density (>20%) observed to induce detectable particle aggregation, indicating that the interaction between the particles is triggered by the multimolecular bridging via lectin molecules.