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ABSTRACT: We describe an aptamer-based surface enhanced resonance Raman scattering (SERRS) sensor with high sensitivity, specificity, and stability for the detection of a coagulation protein, human alpha-thrombin. The sensor achieves high sensitivity and a limit of detection of 100 pM by monitoring the SERRS signal change upon the single-step of thrombin binding to immobilized thrombin binding aptamer. The selectivity of the sensor is demonstrated by the specific discrimination of thrombin from other protein analytes. The specific recognition and binding of thrombin by the thrombin binding aptamer is essential to the mechanism of the aptamer-based sensor, as shown through measurements using negative control oligonucleotides. In addition, the sensor can detect 1 nM thrombin in the presence of complex biofluids, such as 10% fetal calf serum, demonstrating that the immobilized, 5'-capped, 3'-capped aptamer is sufficiently robust for clinical diagnostic applications. Furthermore, the proposed sensor may be implemented for multiplexed detection using different aptamer-Raman probe complexes.
Nano Letters 01/2009; 8(12):4386-90. · 13.20 Impact Factor
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ABSTRACT: We report a sensitive and efficient magnetic bead-based assay for viral DNA identification using isothermal amplification of a reporting probe.
Bioorganic & medicinal chemistry letters 08/2008; 18(22):5871-4. · 2.65 Impact Factor
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ABSTRACT: An efficient and easy-to-execute single microbead SELEX approach is developed to generate high affinity ssDNA aptamers against botulinum neurotoxin.
Chemical Communications 05/2008; · 6.17 Impact Factor
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ABSTRACT: Metallic nanoparticles suspended in aqueous solutions and functionalized with chemical and biological surface coatings are important elements in basic and applied nanoscience research. Many applications require an understanding of the electrokinetic or colloidal properties of such particles. We describe the results of experiments to measure the zeta potential of metallic nanorod particles in aqueous saline solutions, including the effects of pH, ionic strength, metallic composition, and surface functionalization state. Particle substrates tested include gold, silver, and palladium monometallic particles as well as gold/silver bimetallic particles. Surface functionalization conditions included 11-mercaptoundecanoic acid (MUA), mercaptoethanol (ME), and mercaptoethanesulfonic acid (MESA) self-assembled monolayers (SAMs), as well as MUA layers subsequently derivatized with proteins. For comparison, we present zeta potential data for typical charge-stabilized polystyrene particles. We compare experimental zeta potential data with theoretically predicted values for SAM-coated and bimetallic particles. The results of these studies are useful in predicting and controlling the aggregation, adhesion, and transport of functionalized metallic nanoparticles within microfluidic devices and other systems.
Electrophoresis 04/2008; 29(5):1131-9. · 3.30 Impact Factor
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ABSTRACT: Aptamers are single-stranded nucleic acids that fold into defined tertiary structures to bind target molecules with high specificities and affinities. DNA aptamers have garnered much interest as recognition elements for biodetection and diagnostic applications due to their small size, ease of discovery and synthesis, and chemical and thermal stability. Here we describe the design and application of a short DNA molecule capable of both protein target binding and amplifiable bioreadout processes. Because both recognition and readout capabilities are incorporated into a single DNA molecule, tedious conjugation procedures required for protein-DNA hybrids can be omitted. The DNA aptamer is designed to be amplified directly by either polymerase chain reaction (PCR) or rolling circle amplification (RCA) processes, taking advantage of real-time amplification monitoring techniques for target detection. A combination of both RCA and PCR provides a wide protein target dynamic range (1 microM to 10 pM).
Analytical Biochemistry 03/2008; 373(1):121-8. · 3.00 Impact Factor
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ABSTRACT: We report a versatile biofunctional subwavelength photonic device platform for real-time detection of biological molecules. Our devices contain lipid bilayer membranes fused onto metal oxide nanowire waveguides stretched across polymeric flow channels. The lipid bilayers incorporating target receptors are submersed in the propagating evanescent field of the optical cavity. We show that the lipid bilayers in our devices are continuous, have very high mobile fraction, and are resistant to fouling. We also demonstrate that our platform allows rapid membrane exchange. Finally, we use this device to detect the hybridization of specific DNA target sequences in solution to complementary probe DNA strands anchored to the lipid bilayer. This evanescent wave sensing architecture holds great potential for portable, all-optical detection systems.
ACS Nano 03/2008; 2(2):255-62. · 10.77 Impact Factor
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ABSTRACT: Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules.
High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and inter-chip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array.
The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.
PLoS ONE 01/2008; 3(7):e2720. · 4.09 Impact Factor
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ABSTRACT: Nucleic acid (aptasensors) have found steadily increased utility and application over the past decade. In particular, aptamers have been touted as a valuable complement to and, in some cases, replacement for antibodies owing to their structural and functional robustness as well as their ease in generation and synthesis. They are thus attractive for biosecurity applications (e.g. pathogen detection) and are especially well suited because their in vitro generation process does not require infection of any host systems. Herein we provide a brief overview of the aptamers generated against pathogens and toxins over the past few years. In addition, a few recently described detection platforms using aptamers and potentially suitable applications for biosecurity will be discussed.
Current Opinion in Chemical Biology 07/2007; 11(3):316-28. · 9.85 Impact Factor
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ABSTRACT: Rapid and efficient sensors are essential for effective defense against the emerging threat of bioterrorism and biological warfare. This review article describes several recent immunosensing advances that are relevant to biothreat detection. These highly diverse examples are intended to demonstrate the breadth of these immunochemical sensing systems and platforms while highlighting those technologies that are suitable for pathogen detection.
The Analyst 04/2007; 132(3):187-91. · 4.23 Impact Factor
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Angewandte Chemie International Edition 11/2006; 45(41):6900-4. · 13.45 Impact Factor
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ABSTRACT: We report the generation of peptide ligands for silver nanowires using a linear 12-mer peptide phage display random library technique. Phage clones that specifically bind the silver nanowires are sequenced after three rounds of biopanning, and obtained DNA sequences suggest that there are a few conserved amino acid residues which may be critical for binding. A selected binding peptide, together with two mutant peptide sequences, were subsequently synthesized on Tentagel resins to examine the importance of both the identities and positions of the conserved amino acid residues.
Bioorganic & Medicinal Chemistry Letters 11/2006; 16(20):5261-4. · 2.55 Impact Factor
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ABSTRACT: A new approach to construct a single dual-acting agent is described. Compounds 6a-c are potent free radical scavengers as demonstrated by the EC(50) values in PC12 cell survival assay in term of NO, H(2)O(2), and ()OH scavenging activity. The Ach-induced vaso-relaxation assay further confirms the potent NO scavenging activity of compounds 6a-c. In addition, 6a-c are efficacious in a rat arterial thrombosis, and are active in ADP- or PAF-induced in vitro platelet aggregation assay, suggesting that compounds 6a-c also possess anti-thrombotic activities. Since both free radical and thrombogenesis are important risk factors in myocardial ischemic/reperfusion injuries, these dual-acting agents having both free radical scavenging and antithrombolic activities may potentially be beneficial toward their treatment.
Bioorganic & Medicinal Chemistry Letters 10/2006; 16(17):4523-7. · 2.55 Impact Factor
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ABSTRACT: A class of 5-trifluoroacetylamino-1,3-dioxacycloalkanes, 5-benzoylamino-1,3-dioxacycloalkanes, and 5-amino-1,3-dioxacycloalkane compounds were stereoselectively synthesized as potential anti-inflammatory drug candidates. The anti-inflammatory activities of these compounds were tested using the xylene-induced mouse ear edema model, from which multiple compounds possessing anti-inflammatory properties which surpass aspirin were identified; these compounds were then compared to establish structure-activity relationships.
Bioorganic & Medicinal Chemistry 04/2006; 14(5):1339-47. · 2.92 Impact Factor
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ABSTRACT: A novel stereospecific synthetic route to obtain a series of 2,5-disubstituted-dioxacycloalkanes is reported. Using an in vivo inhibition assay by monitoring xylene-induced ear edema in mice, the structure-activity relationship of the dioxacycloalkane compounds was studied, and compounds possessing high anti-inflammatory activity were identified.
Bioorganic & Medicinal Chemistry 11/2005; 13(19):5640-6. · 2.92 Impact Factor
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ABSTRACT: Mismatched bulges in nucleic acid constructs are important in the recognition event between biological molecules. Herein, it is observed that napthyridine dimer 2 is able to specifically bind G-G mismatches in all nucleic acid constructs comprising of RNA-RNA, RNA-DNA and DNA-DNA duplexes. However, the binding affinity of 2 is strongest toward DNA duplex, followed by RNA-DNA heteroduplex and RNA duplex being the weakest binding partner. Nonetheless, this binding behavior suggests that the binding process primarily occurs between the guanine base pairs and the napthyridine moiety, and is independent of the tertiary structure of the nucleic acid duplexes.
Bioorganic & Medicinal Chemistry Letters 03/2005; 15(3):827-31. · 2.55 Impact Factor
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ABSTRACT: Association between RNA and DNA strands to form RNA-DNA heteroduplex is important in many biological processes such as transcription, DNA replication and reverse transcription. Herein, binding affinities of a 17-mer BIV Tat peptide is compared with TAR DNA duplex, TAR RNA-DNA heteroduplex and TAR RNA duplex. It was observed that binding affinities of Tat peptide is comparable against DNA-RNA heteroduplex and RNA duplex, whereas DNA duplex binding is decidedly poor.
Bioorganic & Medicinal Chemistry Letters 02/2005; 15(1):129-33. · 2.55 Impact Factor
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ABSTRACT: Besides generating novel binding peptides or small molecules to their RNA target, successful design of chemically modified RNA constructs capable of tighter binding with their binding peptides is also of significant importance. Herein, the synthesis and binding studies of a series of both wt and mutant bovine immunodeficiency virus (BIV) TAR RNA constructs against its Tat peptide are reported. Understanding the requirements that enable RNA construct binding properties, especially at the hairpin loop or internal bulge, would afford potential therapeutic approaches to control the BIV life cycle.
Bioorganic & Medicinal Chemistry Letters 01/2005; 14(24):6101-5. · 2.55 Impact Factor
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ABSTRACT: Protein synthesis is a central function in cellular physiology, and this important process is the target of many naturally occurring antibiotics and toxins. One such antibiotic is the aminoglycoside, which has been widely utilized in the clinical in the last fifty years due to their low cost and reliable activities. However the usage and applications of aminoglycosides have been severely limited due to their numerous side effects and resistance mechanism acquired by bacteria. Advances in understanding their mechanism of action have led to attempts in developing novel aminoglycoside-derivatives that would potentially eliminate harmful side effects and be resistant to aminoglycoside-modifying enzymes. This account provides a brief introduction to the various classes of antibiotics that target the ribosome, and also provide highlights in recent advancement of the synthesis of aminoglycoside analogs.
Current Topics in Medicinal Chemistry 02/2003; 3(9):1001-19. · 4.17 Impact Factor
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ABSTRACT: The design and synthesis of synthetically modified cyclic A-site 16S rRNA construct is reported. The binding characteristics of several members of the aminoglycoside antibiotics with this novel class of synthetically modified A-site 16S rRNA constructs were subsequently investigated.
Bioorganic & Medicinal Chemistry Letters 03/2002; 12(3):365-70. · 2.55 Impact Factor
