Colorimetric and ultrasensitive bioassay based on a dual-amplification system using aptamer and DNAzyme.

Rapid detection of ultralow amount of biomarkers in a biologically complex mixture remains a major challenge. Herein, we report a novel aptamer-based protein detection assay that integrates two signal amplification processes, namely, polymerase-mediated rolling-circle amplification (RCA) and DNA enzyme-catalyzed colorimetric reaction. The target biomarker is captured in a sandwich assay by primary aptamer-functionalized microbeads (MBs) and a secondary aptamer that is connected to a RCA primer/circular template complex. RCA reaction, which amplifies the single biomarker binding events by a factor of hundreds to thousands (the first amplification) produces a long DNA molecule containing multiple DNAzyme units. The peroxidase-like DNAzyme catalyzes the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (the second amplification), which generates a blue-green colorimetric signal. This new biosensing platform permits the ultrasensitive, label-free, colorimetric detection of biomarker in real time. Using platelet-derived growth factor B-chain (PDGF-BB) as a model system, we demonstrated that our assay can detect a protein marker specifically in a serum-containing medium, at a concentration as low as 0.2 pg/mL in ∼2 h, which rivals traditional assays such as ELISA. We anticipate this simple methodology for biomarker detection can find utility in point-of-care applications.

DNA stickers promote polymer adsorption onto cellulose.

Adsorption of oligonucleotides onto model cellulose surfaces was investigated by comparing the Boese and Breaker's cellulose binding oligonucleotide (CBO) with a nonspecific oligonucleotide control (NSO). Measurements using the quartz crystal microbalance with dissipation technique confirmed that CBO adsorbed onto cellulose more than NSO, particularly at high ionic strengths (100 mM CaCl(2)). CBO showed a higher maximum adsorption on nanofibrillated and nanocrystalline cellulose than on regenerated cellulose, indicating a preference for the native cellulose I crystal structure under conditions that favored specific adsorption over calcium-mediated electrostatically driven adsorption. In addition, an anionic polyacrylamide (A-PAM) with grafted CBO also adsorbed onto the surface of cellulose in CaCl(2), whereas the unmodified A-PAM did not. This work shows that CBO performs as a "sticker", facilitating the adsorption of polyacrylamide onto cellulose, even under high ionic strength conditions where the adsorption of conventional polyelectrolytes is inhibited.

Characterization of an RNA-cleaving deoxyribozyme with optimal activity at pH 5.

An in vitro selection endeavor previously executed by our laboratory led to the isolation of a set of RNA-cleaving deoxyribozymes that thrive under acidic conditions [Liu, Z., Mei, S. H., Brennan, J. D., and Li, Y. (2003) J. Am. Chem. Soc. 125, 7539-7545]. One of these sequences, coined pH5DZ1, is a 100-nucleotide (nt) cis-acting enzyme that was found to exhibit high cleavage activity near pH 5. Herein, we seek to deduce the properties and sequence requirements of this enzyme. This deoxyribozyme was found to cleave a 23-nt chimeric DNA-RNA substrate, which contains a single ribonucleotide flanked by fluorophore- and quencher-modified nucleotides on each side of the cleavage junction. Extensive nucleotide deletion experiments indicated that only 42 bases within the original enzyme sequence are required for catalysis. Results from a reselection experiment further revealed that 26 of these nucleotides are absolutely conserved. In addition to sequence analysis and minimization studies, we successfully designed a trans-acting variant of this enzyme. Characterization of the cleavage products produced upon pH5DZ1-mediated RNA cleavage and analyses of possible structures of pH5DZ1 provided us with insights into the catalytic mechanism of pH5DZ1 and characteristics of deoxyribozymes that retain their activity under acidic conditions.

Incorporation of an inducible nucleotide analog into DNA by DNA polymerases.

Non-natural nucleotides with diverse functionalities are highly useful in many areas of basic research and practical applications. We have previously developed an efficient method for post-synthetic modifications of 2-amino-6-vinylpurine (AVP)-containing oligonucleotides, which permits conjugations of a variety of useful functional appendages to the AVP moiety in DNA. Here we report an investigation on the ability of various DNA polymerases to use 5'-triphosphate of 2'-deoxyribosyl-2-amino-6-(2-methylthioethyl)purine (a stable precursor of AVP) as the substrate for templated DNA synthesis.

Microgel-based inks for paper-supported biosensing applications.

As a first step for the development of biosensing inks for inexpensive paper-based biodetection, we prepared paper strips printed with carboxylic poly( N-isopropylacrylamide) microgels that were modified either with an antibody or with a DNA aptamer. We found that the antibody and the DNA aptamer retained their recognition capabilities when coupled to microgel. The printed microgel remains stationary during chromatographic elution while the microgel-supported molecular recognition elements are accessible to their intended targets present in the elution solution. Our work indicates that microgels, large enough to isolate the biosensors from the paper surface, are sufficiently hydrophilic to be wetted during chromatographic elution, exposing the gel-supported affinity probes to their targets.

Enzymatic manipulations of DNA oligonucleotides on microgel: towards development of DNA-microgel bioassays.

We demonstrate that DNA oligonucleotides covalently coupled to colloidal microgel can be manipulated by T4 DNA ligase for DNA ligation and by Phi29 DNA polymerase for rolling circle amplification (RCA). We also show that the long single-stranded RCA product can generate intensive fluorescence upon hybridization with complementary fluorescent DNA probe. We believe DNA-microgel conjugates can be explored for the development of DNA based bioassays and biosensors.

Application of 2-amino-6-vinylpurine as an efficient agent for conjugation of oligonucleotides.

Attempts have been made to conjugate a variety of molecules with oligonucleotides to achieve useful functions. In this study, we have established a new efficient method for post-synthetic conjugation of oligonucleotides with the use of the 2-amino-6-vinylpurine nucleoside. Amino nucleophiles form the corresponding conjugates under acidic conditions, whereas thiol nucleophiles reacted efficiently under alkaline conditions. Thus, glutathione and HS-Cys-(Arg)8 without protecting groups were efficiently conjugated to the 2-amino-6-vinylpurine-bearing ODN under alkaline conditions. The use of 2-amino-6-vinylpurine as an agent for conjugation is advantageous in that it is stable during the reaction and may be applied to conjugation of ODNs with multiple functional molecules.

Cell-surface sensors: lighting the cellular environment.

Cell-surface sensors are powerful tools to elucidate cell functions including cell signaling, metabolism, and cell-to-cell communication. These sensors not only facilitate our understanding in basic biology but also advance the development of effective therapeutics and diagnostics. While genetically encoded fluorescent protein/peptide sensors have been most popular, emerging cell surface sensor systems including polymer-, nanoparticle-, and nucleic acid aptamer-based sensors have largely expanded our toolkits to interrogate complex cellular signaling and micro- or nano-environments. In particular, cell-surface sensors that interrogate in vivo cellular microenvironments represent an emerging trend in the development of next generation tools which biologists may routinely apply to elucidate cell biology in vivo and to develop new therapeutics and diagnostics. This review focuses on the most recent development in areas of cell-surface sensors. We will first discuss some recently reported genetically encoded sensors that were used for monitoring cellular metabolites, proteins, and neurotransmitters. We will then focus on the emerging cell surface sensor systems with emphasis on the use of DNA aptamer sensors for probing cell signaling and cell-to-cell communication.

Enzymatic incorporation of 2-amino-6-vinylpurine derivative.

Modified nucleotides are incorporated by enzymatic reactions into a DNA oligonulceotide to provide additional functionalities, which has shown potential applications in a wide variety of fields. A large number of modified nucleotide triphosphates have been incorporated to DNA or RNA by polymerases. We have previously described that the sulfide derivatives (1) of 2-amino-6-vinyl purine nucleoside (2, AVP) are activated within duplex to form cross-link toward cytidine selectively at the target site. In this paper, we describe the preparation of the triphosphate derivative of 2'-deoxyribosyl-2-amino-6-(2-methylthioethyl) purine nucleoside (5, dAVP(S Me)-TP), and its enzymatic incorporation to DNA.

Substituent effects on the in situ activation of the double activated cross-linking reaction.

We have previously reported that the oligonucleotides (ODN) containing 2-amino-6-(1-ethylsulfinyl)vinyl purine derivatives (2) exhibit selective and efficient cross-linking to a cytidine at the target site under neutral conditions. In addition, bis-alkylsulfinyl derivative (3b) as the stable precursor of 2 showed the moderate reactivity. In this study, we have searched other bis-alkylsulfinyl precursors to achieve higher cross-linking ability, and found that acetamidoethyl and hydroxyethyl derivatives showed highly efficient and selective reactivity.

Hybridization-promoted and cytidine-selective activation for cross-linking with the use of 2-amino-6-vinylpurine derivatives.

Recently, we have proposed a new concept for cross-linking agents with inducible reactivity, in which the highly reactive cross-linking agent, the 2-amino-6-vinylpurine nucleoside analogue (1), can be regenerated in situ from its stable precursors, the phenylsulfide (4) and the phenylsulfoxide (3) derivatives, by a hybridization-promoted activation process with selectivity to cytidine. The phenylsulfide precursor (4) exhibited cross-linking ability despite its high stability toward strong nucleophiles such as amines and thiols. In this study, we investigated the substituent effects of the phenylsulfide group on the cross-linking reaction, and determined the 2-carboxy substituent of the phenylsulfide derivative (11k) as an efficient cross-linking agent with inducible reactivity. Detailed investigations have shown that the phenylsulfoxide (3) and phenylsulfide (4) precursors produce the 2-amino-6-vinylpurine nucleoside (1) as the common reactive species. It has been concluded that the nature of the inducible reactivity of the precursors (3 and 4) is acceleration of their elimination to the 2-amino-6-vinylpurine nucleoside (1) through the selective process in the duplex with the ODN having cytidine at the target site.

2-Amino-6-vinyl purine as a tool for post synthetic conjugation of DNA with radio-, spin-, fluorescence labels and peptides.

We have previously demonstrated that 2-amino-6-vinylpurine is an efficient cross-linking agent with high selectivity towards cytidine. In this study, we applied this nucleobase analog to versatile conjugation of oligodeoxynucleotides with radio-, spin-, fluorescence- and peptide labels. The oligodeoxynucleotides incorporating 2-amino-6-vinylpurine nucleoside were reacted with amino- bearing nucleophies in an excess amount to give the corresponding conjugates in good yield.

Sequence- and base-specific delivery of nitric oxide to cytidine and 5-methylcytidine leading to efficient deamination.

Nitric oxide (NO) is an important endogenous regulatory molecule, and S-nitrosothiols are believed to play a significant role in NO storage, transport, and delivery. On the basis of their ability to generate NO in vivo, S-nitrosothiols can be used as therapeutic drugs. In this study, we have developed an innovative method for sequence- and base-specific delivery of NO to a specific site of DNA followed by specific deamination. We designed a NO transfer reaction from S-nitroso thioguanine to an imino tautomer of cytosine. Nitrosation of the thioguanosine-containing ODN 1 was carried out with S-nitroso-N-acetylpenicillamine (SNAP) to produce ODN 2. An interstrand NO transfer reaction was performed using ODN 2 and its complementary ODN 3 having dC or dmC at the target site, and a rapid NO transfer reaction was observed. In contrast, a transfer reaction was not observed either with ODN 3 having dT, dA, or dG at the target site or with ODN 5-7 having dC at a nontarget site. In the analysis of deaminated products of the NO-transferred ODN 4, it was found that the transformation ratio from dmC to dT was as high as 42% together with the dmC-diazoate (13%). In conclusion, we have demonstrated the innovative method of sequence- and base-specific delivery of nitric oxide to cytidine and 5-methylcytidine. The selectivity and efficiency of NO transfer followed by deamination exhibited in this study are extremely high compared to those of the conventional methods.