Accessibility of Densely Localized DNA on Soft Polymer Nanoparticles

The dense localization of DNA on soluble nanoparticles can lead to effects distinct from equivalent amounts of the DNA in solution. However, the specific effect may depend on the nature of the assembly and the nanoparticle core. Here we examine the accessibility of densely packed DNA duplexes that extend from a bottle-brush polymer core. We find that unlike spherical nucleic acids, the DNA duplex bristles on the bottle-brush polymer remain accessible to sequence-specific cleavage by endonucleases. In addition, the hybridized strand of the duplex can be displaced through a toehold-mediated strand exchange even at the polymer interface. These results demonstrate that the DNA on bottle-brush polymer remains sufficiently flexible to allow enzymatic degradation or DNA hybridization.

Bright Fluorescent Nanotags from Bottlebrush Polymers with DNA-Tipped Bristles

Bright signal outputs are needed for fluorescence detection of biomolecules at their native expression levels. Increasing the number of labels on a probe often results in crowding-induced self-quenching of chromophores, and maintaining the function of the targeting moiety (e.g., an antibody) is a concern. Here we demonstrate a simple method to accommodate thousands of fluorescent dye molecules on a single antibody probe while avoiding the negative effects of self-quenching. We use a bottlebrush polymer from which extend hundreds of duplex DNA strands that can accommodate hundreds of covalently attached and/or thousands of noncovalently intercalated fluorescent dyes. This polymer-DNA assembly sequesters the intercalated fluorophores against dissociation and can be tethered through DNA hybridization to an IgG antibody. The resulting fluorescent nanotag can detect protein targets in flow cytometry, confocal fluorescence microscopy, and dot blots with an exceptionally bright signal that compares favorably to commercially available antibodies labeled with organic dyes or quantum dots.

Iron-Based ICAR ATRP of Styrene with ppm Amounts of FeIIIBr3 and 1,1'-Azobis(cyclohexanecarbonitrile)

A successful ICAR (initiators for continuous activator regeneration) ATRP (atom transfer radical polymerization) of styrene was conducted with iron(III) bromide and 1,1'-azobis(cyclohexanecarbonitrile) (ACHN) as the thermal initiator. A polymerization, started with 50 ppm of FeBr₃ and 50 mol equivalents of ACHN in 33% (v/v) anisole at 90 °C, reached 70% conversion in 24 h and was well controlled, giving a polymer with a narrow molecular weight distribution (M_w/M_n = 1.15). The number average molecular weight (M_n) corresponded well to theoretical values, as conversion increased. The rate of polymerization was dependent on the amount of ACHN initially added to the reaction. A polymer with a relatively narrow molecular weight distribution, M_w/M_n = 1.29 at 65% of conversion, was obtained with 5 ppm of FeBr₃ and the appropriate amount of ACHN. This procedure therefore provides an efficient controlled polymerization in addition to creating a robust, cheap, and environmentally friendly catalytic system. Control of polymerization with ACHN was better than with tert-butyl peracetate as a thermal initiator or tin(II) 2-ethylhexanoate, Fe⁰, or Zn⁰ wire as reducing agents.

Reliable ferrocenyloligonucleotide-immobilized electrodes and their application to electrochemical DNase I assay

A ferrocenyloligonucleotide (FcODN) having contiguous cytosine bases was immobilized effectively and reproducibly on a gold electrode furnished with a self-assembled monolayer (SAM) having an N-hydroxysuccinimide-activated carboxylic acid. The resulting electrode was used as a sensor chip in DNase I assay. Thus, the current response of the modified electrode decreased upon addition of DNase I, demonstrating that the phosphodiester bonds of FcODN were cleaved. The DNase I activity assessed by Deltai defined as (i0-i)/i0, where i0 and i represent the current before and after DNase I treatment, respectively, was found to be reproducible with a standard deviation not greater than 9%. The DNase I can be quantitated in the range of 10(-5) to 10(-3) units microL(-1) with a detection limit of 10(-5) units microL(-1) with this sensor chip. The current signal of the FcODN electrode was stable to storage in Biopak water up to 16 days with a 30% signal decrease over this period. DNase I activity in human sera was also determined successfully with this sensor chip.

Electrochemical assay for deoxyribonuclease I activity

A thiolated oligonucleotide having three ferrocenes was immobilized on a gold electrode through the sulfur-gold linkage. This electrode showed a current response based on the redox reaction of the ferrocene moieties and this response was decreased after treatment with deoxyribonuclease I (DNase I), suggesting the disappearance of the ferrocene moieties on the electrode by the DNase I digestion. A linear correlation between i(0) and i, which are current peaks before and after DNase I treatment, respectively, was observed and this slope was decreased with increase in the amount of DNase I. No current decrease was observed in the presence of EDTA or RNase A instead of DNase I. These results suggested that the current decrease responded specifically to the amount of DNase I and this electrode could be used for an electrochemical DNase I assay. Under the optimum conditions of DNase I digestion at 37 degrees C for 30 min, a quantitative analysis could be achieved in the range of 10(-4)-10(-2)units/microl of DNase I.

Electrochemical detection of DNase I activity

DNase I in one microl of the water could quantitate electrochemically with the detection limit of 0.01 units (ca. 20 pg) by using the ferrocenyl oligonucleotide-immobilized electrode prepared by thiolated oligonucleotide and ferrocenyl carbodiimide as a simple labeling reagent of redox unit.

Preparation of carbodiimide-terminated dithiolane self-assembly monolayers as a new DNA-immobilization method

A carbodiimide derivative having a dithiolane part at its terminus was designed and synthesized for use to construct carbodiimide-coated self-assembly monolayers (SAMs) on a gold surface with 6-mercaptohexanol (6MH). When treated with poly(dT), poly(dA), or poly(dA)poly(dT), only poly(dT) was immobilized on the surface of the SAMs through a specific reaction of the free imino moiety of thymine (T) with the carbodiimide moiety. The carbodiimide-covered SAM treated with probe DNA was tested in hybridization with sample DNA. Its hybridization efficiency was estimated by ferrocenylnaphthalene diimide (FND), described previously and the result revealed that the carbodiimide-covered SAM electrode can immobilize a DNA probe through the thymine moiety not involved in base pairing. The resulting electrode was capable of hybridizing with the target DNA, as proven by an increased current response of FND.

Synthesis of ferrocenyl carbodiimide as a novel ferrocenyl reagent of single stranded DNA

Ferrocenyl carbodiimide (FcCDI) was newly synthesized as a ferrocenylation reagent for single stranded DNA. FcCDI could attach to oligodeoxyribonucleotides (ODN) through a covalent bond with thymine and guanine bases. The reactivity of thymine with FcCDI was higher than that of guanine, but independent of their location on the DNA sequence. After a single stranded DNA was treated with FcCDI, resulting ODN could be detected electrochemically by a redox signal deriving from the ferrocenyl moiety with a DNA probe-immobilized electrode. These results suggest that the labeling of DNA with FcCDI can be applied to rapid analysis of electrochemical genosensors.

Investigation of ferrocenyl carbodiimide (FCDI) in the modification reaction of nucleic acids

Ferrocenyl carbodiimide (FCDI) was allowed to react with thymine or guanine bases of single stranded DNA in borate buffer (pH 9.5) at 37 degrees C for a short period of time. The reactivity of FCDI with the guanine bases was smaller than that with the thymine ones and the prolongation of the reaction time resulted in a lower yield. The reactivity for double stranded oligonucleotide was extremely decreased from that for the single stranded one. One base mismatched double stranded oligonucleotides could react with FCDI, albeit slowly. These results suggested that the reactivity of FCDI was variable depending on the kind of bases and the oligonucleotide structure.

Direct Modification of mRNA by Ferrocenyl Carbodiimide and Its Application to Electrochemical Detection of mRNA

Ferrocenyl carbodiimide (1) could be used for the direct labeling of synthetic RNA and expressed mRNA in vitro with the electrochemically active ferrocene moieties. These RNAs modified by 1 could be detected electrochemically coupled with a DNA probe-immobilized electrode. After hybridization of 1.1 Kb mRNA modified by 1 with the DNA probe-immobilized electrode, the peak charge observed by an Osteryoung square wave voltammetry (SWV) measurement correlated well with the concentration of mRNA, having a detection limit at the sub nanogram level.

Reactivity of Ferrocenylcarbodiimide with DNA Duplex Containing Single-mismatched Base Pairs

Ferrocenylcarbodiimide (1), which is known to react with a guanine (G) or thymine (T) base of single stranded DNA, was allowed to react with DNA duplex having a single mismatched base pair of G-T, T-T, or T-cytosine (C). Electrophoreograms of the reaction mixture showed that 1 could react with G or T base of the mismatched sites on the DNA duplex. However, 1 also reacted with the G base of the terminal site on the DNA duplex. This showed that 1 can react with an unpaired base or unstable base pair such as a terminal or mismatched base on the DNA duplex. Electrochemical mismatch detection could be achieved after hybridization of the ferrocenylated mismatched DNA duplex with a selected DNA probe-immobilized electrode. These results revealed that 1 has a potentiality of serving as a labeling reagent of mismatched bases on the DNA duplex, which is important in the search for heterozygous single nucleotide polymorphisms (SNPs).

Electrochemical SNP detection

Detection of mismatched base on a DNA duplex, which is important for the search of the heterozygote, achieved by the comparison with the reactivity of ferrocenylcarbodiimide (1) developed by our group. Mismatched thymine base on the 30-meric DNA duplex as a model of SNPs in lipoprotein lipase (LPL) gene, could react with 1 in 20 mM borate buffer (pH 8.5) and 0.1 M NaCl containing 20% DMSO at 37 degrees C. DNA duplex modified by 1 in the mismatched thymine bases could be detected by its shifted migration time in microTAS electrophoresis.

Development of a novel genosensor based on ferrocenyl oligonucleotides

Two types of ferrocenyl oligonucleotides, Fc1-ODN and Fc2-ODN, carrying a 5'-ATT GCT CAG GGG TAA GGT CAT TAG TTG GAA-3' sequence were allowed to hybridize with the DNA probe carrying a complementary sequence immobilized on the gold electrode to give rise to a redox signal deriving from their ferrocenyl moieties. When a mixture of these oligonucleotides in a proper ratio was used as a model of DNA samples, two redox peaks were observed in one differential pulse voltammogram. The peak currents varied depending on the initial ratio of the two oligonucleotides, suggesting a possibility that this technique may be applied to electrochemical monitoring of gene expression by, for example, the electrochemical differential hybridization, EDH.

[Progression and recurrence in the prostate and upper urinary tract following intravesical bacillus Calmette-Guerin therapy for superficial bladder cancer]

A total of 13 patients received intravesical bacillus Calmette-Guerin (BCG) therapy for superficial bladder cancer and were followed for at least 6 months (range 6 to 50 months). Of the patients 7 had carcinoma in situ and 6 had recurrent tumors following intravesical mitomycin C therapy. Of the 7 patients who had carcinoma in situ, 4 (57%) are free of disease and 3 (43%) have required cystectomy for recurrence or progression. Of the 6 patients who had recurrent tumors following intravesical mitomycin C therapy, 3 (50%) remain free of tumor after BCG therapy alone, 2 (33%) had superficial recurrences but no progression and 1 (17%) has required cystectomy for prostatic involvement. After intravesical BCG therapy, transitional cell carcinoma of the prostate was identified in 4 of the 13 patients, and tumors in the upper urinary tract were detected in 2 of the 4 patients with prostatic involvement. Of the 4 patients 2 have local recurrence or distant metastasis. In patients treated with BCG therapy the prostate and upper urinary tract represent a potential site of progression or recurrence. Patients treated with intravesical BCG therapy for superficial bladder cancer should be monitored closely for the development of transitional cell carcinoma of the prostate and upper urinary tract.