Development of a Novel Stem-loop-type Molecular Beacon Probe Possessing Polyamine-connected Deoxyuridine and Silylated Pyrene

2014 ◽  
Vol 43 (12) ◽  
pp. 1915-1917 ◽  
Author(s):  
Jakir Ahmed Chowdhury ◽  
Tomohisa Moriguchi ◽  
Kazuo Shinozuka
Keyword(s):  
Molecular Beacon ◽  
Stem Loop

scholarly journals Rationally Manipulating Aptamer Binding Affinities in a Stem-Loop Molecular Beacon

2014 ◽  
Vol 25 (10) ◽  
pp. 1769-1776 ◽  
Author(s):  
Rachel E. Armstrong ◽  
Geoffrey F. Strouse
Keyword(s):  
Molecular Beacon ◽  
Binding Affinities ◽  
Stem Loop

scholarly journals DNA Detection ofToxoplasma gondiiwith a Magnetic Molecular Beacon Probe via CdTe@Ni Quantum Dots as Energy Donor

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Shichao Xu ◽  
Chen Zhang ◽  
Lei He ◽  
Tongyao Wang ◽  
Liusong Ni ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Toxoplasma Gondii ◽  
Molecular Beacon ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Xrd Analysis ◽  
Stem Loop ◽  
Current Sensing ◽  
Energy Donor ◽  
Base Pair Mismatch

A new method for detection ofToxoplasma gondiivia DNA sensing technology was developed in this study. It was based on the mechanism of fluorescence resonance energy transfer (FRET) in which multifunctional and magnetic-fluorescent CdTe@Ni quantum dots (mQDs) were utilized as energy donor and a commercial BHQ2as acceptor. The sensing probe was fabricated by labeling a stem-loopToxoplasma gondiiDNA oligonucleotide with CdTe@Ni mQDs at the 5′ end and BHQ2at 3′ end, respectively. The surface assembly of CdTe on Ni core and the formation of CdTe@Ni were confirmed by XRD analysis. The sizes of CdTe, Ni nanoparticles, and CdTe@Ni were measured via TEM and XRD methods and estimated to be~3 nm,~15 nm, and~20 nm, respectively. The sensing ability was investigated by the fluorescence spectrum (FS). An obvious fluorescence recovery was observed when the complete complimentary targetToxoplasma gondiiDNA was introduced, which did not happen in the case of the target DNA with one-base pair mismatch. Our research indicates that the current sensing probe is sensitive and specific in detection ofToxoplasma gondiiDNA and has great potential in Toxoplasmosis diagnosis.

scholarly journals Molecular Beacons: A New Approach to Plant Virus Detection

2000 ◽  
Vol 90 (3) ◽  
pp. 269-275 ◽  
Author(s):  
Alvin Jin-Cherng Eun ◽  
Sek-Man Wong
Keyword(s):  
Molecular Beacon ◽  
Virus Detection ◽  
Plant Viruses ◽  
Molecular Beacons ◽  
Cymbidium Mosaic Virus ◽  
Stem Loop ◽  
Chain Reactions ◽  
Plant Virus Detection ◽  
Virus Indexing ◽  
Fluorescent Moiety

Molecular beacons are single-stranded nucleic acid molecules with a stem-loop conformation. The stem portion consists of complementary sequences at the 5′ and 3′ terminals of the molecule, while the loop portion consists of probe sequences that are complementary to the target sequences of choice. A fluorescent moiety is attached to one end, while a quenching moiety is attached to the opposite end. Reverse transcription-polymerase chain reactions are carried out with primers that amplify specific genome sequences of interest, yielding targets complementary to their respective molecular beacons for subsequent detection. Here, we have designed four molecular beacons specific to the RNA-dependent RNA polymerase and coat protein genes of two orchid viruses, namely Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV). This technology is successfully applied to detect as little as 0.5 ng of viral RNA of both orchid viruses simultaneously in 100 mg of coinfected Oncidium orchid leaves. This rapid and specific technique is applicable to the orchid industry, which routinely carries out virus indexing and screening for virus-resistant cultivars. We belief that use of this molecular beacon approach can be extended to the detection of multiple plant viruses in various crops.

scholarly journals An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

Scientifica ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Dmitry M. Kolpashchikov
Keyword(s):  
Molecular Beacon ◽  
Signal To Noise Ratio ◽  
Probe Design ◽  
Rna Sequences ◽  
Molecular Sensing ◽  
Stem Loop ◽  
Nucleic Acid Analysis ◽  
Loop Shape ◽  
Folded Rna ◽  
Rna And Dna

Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.

Synthesis and Properties of Molecular Beacon DNA Probe Bearing Novel Silylated Pyrene Derivative

2011 ◽  
Vol 497 ◽  
pp. 47-50 ◽  
Author(s):  
M. Gias Uddin ◽  
Tomohisa Moriguchi ◽  
Mayumi Ichimura ◽  
Kazuo Shinozuka
Keyword(s):  
Molecular Beacon ◽  
Dna Probe ◽  
Stem Segment ◽  
Excimer Emission ◽  
Stem Loop ◽  
Complementary Dna ◽  
Single Base ◽  
Fluorescent Signal ◽  
Modified Dna ◽  
Dna Strand

A novel stem-loop structured fluorescent oligoDNA probe (molecular beacon probe) bearing a silylated pyrene derivative at C-5 position of deoxyuridine has been synthesized. The fluorescently labeled modified nucleoside has been incorporated into two consecutive positions in the stem segment of the DNA using an automated DNA synthesizer. The resulting modified DNA exhibited an excimer fluorescent signal upon binding to the fully matched complementary DNA strand. The excimer emission was, however, effectively quenched while it stays alone or it hybridizes to a single base mismatched complementary target.

968: Gelsolin Gene Silencing Involving Unusual Chromatin Structures and a Novel Stem Loop Structure of the Promoter Region in Human Bladder Cancer

2004 ◽  
Vol 171 (4S) ◽  
pp. 256-257
Author(s):  
Kazunori Haga ◽  
Ataru Sazawa ◽  
Toru Harabayashi ◽  
Nobuo Shinohara ◽  
Minoru Nomoto ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Gene Silencing ◽  
Promoter Region ◽  
Loop Structure ◽  
Human Bladder Cancer ◽  
Human Bladder ◽  
Stem Loop ◽  
Stem Loop Structure
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