Folding Of 16S Rrna In A Signal-Producing Structure For The Detection Of Bacteria

Sixty-four DNA strands hybridize to 16S rRNA to form 32 deoxyribozyme catalytic cores that produce a fluorescent signal. The approach allows detection of 0.6 pM 16S rRNA, or about 3×104 bacterial cells in a PCR-free format. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Towards A Dna Nanoprocessor: Reusable Tile-Integrated Dna Circuits

Modern electronic microprocessors use semiconductor logic gates organized on a silicon chip to enable efficient inter-gate communication. Here, arrays of communicating DNA logic gates integrated on a single DNA tile were designed and used to process nucleic acid inputs in a reusable format. Our results lay the foundation for the development of a DNA nanoprocessor, a small and biocompatible device capable of performing complex analyses of DNA and RNA inputs

Detection Of Bacterial 16S Rrna Using A Molecular Beacon-Based X Sensor

We demonstrate how a long structurally constrained RNA can be analyzed in homogeneous solution at ambient temperatures with high specificity using a sophisticated biosensor. The sensor consists of a molecular beacon probe as a signal reporter and two DNA adaptor strands, which have fragments complementary to the reporter and to the analyzed RNA. One adaptor strand uses its long RNA-binding arm to unwind the RNA secondary structure. Second adaptor strand with a short RNA-binding arm hybridizes only to a completely complementary site, thus providing high recognition specificity. Overall the three-component sensor and the target RNA form a four-stranded DNA crossover (X) structure. Using this sensor, Escherichia coli16. S rRNA was detected in real time with the detection limit of ~0.17. nM. The high specificity of the analysis was proven by differentiating Bacillus subtilis from E. coli 16. S rRNA sequences. The sensor responds to the presence of the analyte within seconds. © 2012 Elsevier B.V

Connectable Dna Logic Gates: Or And Xor Logics

Chalcogenide samples with varying selenium concentrations, As 10Se 90, As 30Se 70, As 40Se 60, and As 50Se 50, were characterized for high power transmission using a Tm:fiber laser system. The Tm:fiber laser oscillator consists of a LMA fiber with 25/400 μm core/cladding diameters pumped by 793 nm diode. The output beam was collimated to a 3 mm beam diameter, and transmitted through the chalcogenide samples at CW powers up to 23 W. We measure the transmission as a function of incident power, as well as some initial characterization of surface damage from nanosecond pulses at 2 μm. Furthermore, we utilize a wavefront sensor to characterized the thermal lens induced by the Tm:fiber laser. © 2012 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE)

Divide And Control: Split Design Of Multi-Input Dna Logic Gates

Logic gates made of DNA have received significant attention as biocompatible building blocks for molecular circuits. The majority of DNA logic gates, however, are controlled by the minimum number of inputs: one, two or three. Here we report a strategy to design a multi-input logic gate by splitting a DNA construct. This journal i

Nucleic Acid Detection Using Mnazymes

Deoxyribozymes are promising biotechnological tools. In a recent JACS article, Mokany et al. reported on the design of multi-component deoxyribozyme (MNAzyme) sensors based on 10-23 and 8-17 DNA enzymes. The sensors can detect down to 5 pM of a specific nucleic acid. The versatility of MNAzyme platform allows the design of catalytic cascades for signal amplification. This work is a step forward to PCR-free molecular diagnostics. © 2010 Elsevier Ltd. All rights reserved

Enzyme-Assisted Target Recycling (Eatr) For Nucleic Acid Detection

Fast, reliable and sensitive methods for nucleic acid detection are of growing practical interest with respect to molecular diagnostics of cancer, infectious and genetic diseases. Currently, PCR-based and other target amplification strategies are most extensively used in practice. At the same time, such assays have limitations that can be overcome by alternative approaches. There is a recent explosion in the design of methods that amplify the signal produced by a nucleic acid target, without changing its copy number. This review aims at systematization and critical analysis of the enzyme-assisted target recycling (EATR) signal amplification technique. The approach uses nucleases to recognize and cleave the probe-target complex. Cleavage reactions produce a detectable signal. The advantages of such techniques are potentially low sensitivity to contamination and lack of the requirement of a thermal cycler. Nucleases used for EATR include sequence-dependent restriction or nicking endonucleases or sequence independent exonuclease III, lambda exonuclease, RNase H, RNase HII, AP endonuclease, duplex-specific nuclease, DNase I, or T7 exonuclease. EATR-based assays are potentially useful for point-of-care diagnostics, single nucleotide polymorphisms genotyping and microRNA analysis. Specificity, limit of detection and the potential impact of EATR strategies on molecular diagnostics are discussed. © The Royal Society of Chemistry 2014

Enzyme-Assisted Binary Probe For Sensitive Detection Of Rna And Dna

The new enzyme-assisted assay for DNA/RNA detection provides real-time fluorescent signal readout along with low limit of detection and high discrimination power toward a single-base substitution. Requiring only two new unmodified DNA oligonucleotides for the detection of each new analyte, the assay is an efficient tool for low-cost analysis of multiple analytes. © The Royal Society of Chemistry 2010

Rna-Cleaving Deoxyribozyme Sensor For Nucleic Acid Analysis: The Limit Of Detection

Along with biocompatibillty, chemical stability, and simplicity of structural prediction and modification, deoxyribozymebased molecular sensors have the potential of an improved detection limit due to their ability to catalytically amplify signal. This study contributes to the understanding of the factors responsible for the limit of detection (LOD) of RNA-cleaving deoxyribozyme sensors. A new sensor that detects specific DNA/ RNA sequences was designed from deoxyribozyme OA-II [Chiuman, W.; Li, Y. (2006) J. Mol. Biol. 357, 748-754]. The sensor architecture allows for a unique combination of high selectivity, low LOD and the convenience of fluorescent signal monitoring in homogeneous solution. The LOD of the sensor was found to be ~1.6x10 -10M after 3 h of incubation. An equation that allows estimation of the lowest theoretical LOD using characteristics of parent deoxyribozymes and their fluorogenlc substrates was derived and experimentally verified. According to the equation, quot;catalytically perfectquot; enzymes can serve as scaffolds for the design of sensors with the LOD not lower than 2x10-15M after 3 h of incubation. A new value termed the detection efficiency (DE) is suggested as a time-independent characteristic of a sensor\u27s sensitivity. The expressions for the theoretical LOD and DE can be used to evaluate nucleic acid and protein enzymes for their application as biosensing platforms. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

Real-Time Snp Analysis In Secondary-Structure-Folded Nucleic Scids

A tricomponent sensor was designed for genotyping stem-loop-structured DNA sequences. DNA adaptor strand f (see picture; red) hybridizes to the analyte (orange) with high affinity and unwinds its secondary structure; strand m (green) forms a stable complex only with the fully complementary analyte sequence. A fluorescing molecular beacon reports complex formation. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim