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https://www.readbyqxmd.com/read/28535205/a-transcriptional-serenaid-the-role-of-noncoding-rnas-in-class-switch-recombination
#1
William T Yewdell, Jayanta Chaudhuri
During an immune response, activated B cells may undergo class switch recombination (CSR), a molecular rearrangement that allows B cells to switch from expressing IgM and IgD to a secondary antibody heavy chain isotype such as IgG, IgA, or IgE. Secondary antibody isotypes provide the adaptive immune system with distinct effector functions to optimally combat various pathogens. CSR occurs between repetitive DNA elements within the immunoglobulin heavy chain (Igh) locus, termed switch (S) regions, and requires the DNA modifying enzyme activation-induced cytidine deaminase (AID)...
May 23, 2017: International Immunology
https://www.readbyqxmd.com/read/28524648/instantaneous-ph-boosted-functionalization-of-stellate-gold-nanoparticles-for-intracellular-imaging-of-mirna
#2
Jisun Ki, Eunji Jang, Seungmin Han, Moo-Kwang Shin, Byunghoon Kang, Yong-Min Huh, Seungjoo Haam
Various types of nanoprobes have recently been utilized to monitor living organisms by detecting and imaging intracellular biomarkers, such as microRNAs (miRs). We here present a simple one-pot method to prepare stellate gold nanoparticles functionalized with miR-detecting molecular beacons (SGNP-MBs); low pH conditions permitted the rapid-high loading of MBs on the surface of SGNPs. Compared to the conventional gold nanoparticle-based MBs, SGNPs carried a 4.5-fold higher load of MBs and exhibited a 6.4-fold higher cellular uptake...
May 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28485713/super-resolution-imaging-of-a-2-5-kb-non-repetitive-dna-in-situ-in-the-nuclear-genome-using-molecular-beacon-probes
#3
Yanxiang Ni, Bo Cao, Tszshan Ma, Gang Niu, Yingdong Huo, Jiandong Huang, Danni Chen, Yi Liu, Bin Yu, Michael Q Zhang, Hanben Niu
High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence...
May 9, 2017: ELife
https://www.readbyqxmd.com/read/28484218/a-molecular-beacon-based-approach-for-live-cell-imaging-of-rna-transcripts-with-minimal-target-engineering-at-the-single-molecule-level
#4
Mingming Chen, Zhao Ma, Xiaotian Wu, Shiqi Mao, Yantao Yang, Jie Tan, Christopher J Krueger, Antony K Chen
Analysis of RNA dynamics and localization at the single-molecule level in living cells has been predominantly achieved by engineering target RNAs with large insertions of tandem repeat sequences that are bound by protein-based or oligonucleotide-based fluorescent probes. Thus, individual RNAs are tagged by multiple fluorescent probes, making them detectable by fluorescence microscopy. Since large insertions may affect RNA processes including trafficking and localization, here we present a strategy to visualize single RNA transcripts in living cells using molecular beacons (MBs) - fluorogenic oligonucleotide probes - with minimal target engineering...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28475957/double-loop-hairpin-probe-and-doxorubicin-loaded-gold-nanoparticles-for-the-ultrasensitive-electrochemical-sensing-of-microrna
#5
Yiyi Tao, Dan Yin, Mingchao Jin, Jie Fang, Tao Dai, Yi Li, Yuxia Li, Qinli Pu, Guoming Xie
An electrochemical microRNA (miRNA) analysis platform by combining double-loop hairpin probe (DHP) and doxorubicin-loaded gold nanoparticles (AuNPs@Dox) for ultrasensitive miRNA detection is proposed. Firstly, we here report a DHP that is simultaneously engineered to incorporate a miRNA recognition sequence, an output segment and output's complementary fragment. The important aspect of this hairpin probe is that it would not be degraded by duplex specific nuclease (DSN) and circumvents elaborately chemical modification disadvantages encountered by classic molecular beacon...
May 2, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28451274/a-metal-mediated-base-pair-that-discriminates-between-the-canonical-pyrimidine-nucleobases
#6
Biswarup Jash, Philipp Scharf, Nikolas Sandmann, Célia Fonseca Guerra, Dominik A Megger, Jens Müller
A nucleoside analogue comprising the ligand 1H-imidazo[4,5-f][1,10]phenanthroline (P) was applied to develop a molecular beacon capable of discriminating the canonical nucleobases cytosine and thymine. The beacon is based on the formation of a stable Ag(+)-mediated base pair between P and cytosine, whereas the presence of Ag(+) strongly destabilizes nucleic acids comprising an artificial base pair between P and thymine. Metal-mediated base pair formation was investigated by temperature-dependent UV spectroscopy and CD spectroscopy and complemented by extensive DFT calculations...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28451240/ultra-specific-discrimination-of-single-nucleotide-mutations-using-sequestration-assisted-molecular-beacons
#7
Shichao Hu, Wei Tang, Yan Zhao, Na Li, Feng Liu
Reliably distinguishing single-nucleotide mutations (SNMs) at low abundance is of great significance in clinical diagnosis. However, the specificity of most current SNM discrimination methods based on the Watson-Crick hybridization is seriously limited by the cross-reactivity of the probe with closely related unintended sequences. Herein, we propose a sequestration-assisted molecular beacon (MB) strategy for highly specific SNM discrimination. The new SNM discrimination system consists of a target-specific MB and a series of hairpin sequestering agents (SEQs)...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28445812/portable-aptamer-biosensor-of-platelet-derived-growth-factor-bb-using-a-personal-glucose-meter-with-triply-amplified
#8
Lu Hong, Fu Zhou, Dongmin Shi, Xiaojun Zhang, Guangfeng Wang
Sensitive and rapid detection of platelet-derived growth factor BB (PDGF-BB), a cancer-related protein, could help early diagnosis, treatment, and prognosis of cancers. Although some methods have been developed to detect PDGF-BB, few can provide quantitative results using an affordable and portable device that is suitable for home use or field application. In this work, we report the first use of a portable kind of personal glucose meter (PGM) combining a catalytic and molecular beacon (CAMB) system with a cation exchange reaction (CX reaction) for ultrasensitive PDGF-BB assay...
September 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28441712/virus-based-devices-prospects-for-allopoiesis
#9
Bogdan Dragnea
The assembly line is a commonly invoked example of allopoiesis, the process whereby a system produces a different system than itself. In this sense, virus production in plants is an instance of bio-enabled bottom-up allopoiesis because the plant host can be regarded as a programmable assembly line for the virus. Reprogramming this assembly line and integrating it into a larger lineup of chemical manipulations has seen a flurry of activity recently, with more sophisticated systems emerging every year. The field of virus nanomaterials now has several subdisciplines that focus on virus shells as assemblers, scaffolds for molecular circuitry, chemical reactors, magnetic and photonic beacons, and therapeutic carriers...
April 25, 2017: ACS Nano
https://www.readbyqxmd.com/read/28424856/homogenous-assay-for-protein-detection-based-on-proximity-dna-hybridization-and-isothermal-circular-strand-displacement-amplification-reaction
#10
Manjun Zhang, Ruimin Li, Liansheng Ling
This work proposed a homogenous fluorescence assay for proteins, based on the target-triggered proximity DNA hybridization in combination with strand displacement amplification (SDA). It benefited from target-triggered proximity DNA hybridization to specifically recognize the target and SDA making recycling signal amplification. The system included a molecular beacon (MB), an extended probe (EP), and an assistant probe (AP), which were not self-assembly in the absence of target proteins, due to the short length of the designed complementary sequence among MB, EP, and AP...
April 19, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28418641/classics-in-chemical-neuroscience-ketamine
#11
Marshall W Tyler, Harmony B Yourish, Dawn F Ionescu, Stephen J Haggarty
Ketamine, a molecule of many faces, has contributed immeasurably to numerous realms of clinical practice and scientific inquiry. From anesthesia and analgesia to depression and schizophrenia, it continues to shed light on the molecular underpinnings of pain, consciousness, and the pathophysiology of neuropsychiatric disorders. In particular, research on ketamine's mechanism of action is providing new hope in the search for therapies for treatment-resistant depression and affords insights into disorders of glutamatergic dysfunction...
April 21, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28379274/a-sensitive-ratiometric-electrochemical-biosensor-based-on-dna-four-way-junction-formation-and-enzyme-assisted-recycling-amplification
#12
Lin Cui, Mengfei Lu, Xiao-Yun Yang, Bo Tang, Chun-Yang Zhang
A simple ratiometric electrochemical biosensor is developed for sensitive detection of target DNA based on DNA four-way junction (DNA-4WJ) formation and enzyme-assisted recycling amplification. This biosensor can be easily fabricated by a one-step assembly of ratiometric probes and simply performed by a one-step incubation procedure. In the presence of target DNA, two unmodified DNA oligonucleotides may cooperatively hybridize with a hairpin probe in the triple-helix molecular beacon (THMB) to form a DNA-4WJ, which may cause conformational transduction and induce the change in the distance between two redox labeling probes and the electrode surface...
May 2, 2017: Analyst
https://www.readbyqxmd.com/read/28370207/micrornas-based-imaging-techniques-in-cancer-diagnosis-and-therapy
#13
Maryam Keshavarzi, Mohammad Jafar Rezaie, Saba Sorayayi, Mohsen Mohammadi, Amir Ghaderi, Ayoob Rostamzadeh, Aria Masoudifar, Hamed Mirzaei
Cancer is one of the most serious global health concerns in different populations. Several studies indicated that there are many potentially promising cellular and molecular targets for cancer therapy within cancer cells and their microenvironment. Among different cellular and molecular targets involved in cancer pathogenesis, microRNAs (miRNAs) are well known as key targets for cancer therapy. miRNAs are one of main classes of non-coding RNAs. These molecules play important roles in different critical processes of cancer pathogenesis...
March 29, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28343104/localized-surface-plasmon-resonance-mediated-fluorescence-signals-in-plasmonic-nanoparticle-quantum-dot-hybrids-for-ultrasensitive-zika-virus-rna-detection-via-hairpin-hybridization-assays
#14
Oluwasesan Adegoke, Masahiro Morita, Tatsuya Kato, Masahito Ito, Tetsuro Suzuki, Enoch Y Park
The current epidemic caused by the Zika virus (ZIKV) and the devastating effects of this virus on fetal development, which result in an increased incidence of congenital microcephaly symptoms, have prompted the World Health Organization (WHO) to declare the ZIKV a public health issue of global concern. Efficient probes that offer high detection sensitivity and specificity are urgently required to aid in the point-of-care treatment of the virus. In this study, we show that localized surface plasmon resonance (LSPR) signals from plasmonic nanoparticles (NPs) can be used to mediate the fluorescence signal from semiconductor quantum dot (Qdot) nanocrystals in a molecular beacon (MB) biosensor probe for ZIKV RNA detection...
March 22, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28340773/label-free-molecular-beacons-based-cascade-amplification-dna-machine-for-sensitive-detection-of-telomerase-activity
#15
Kan Li, Lei Wang, Xiaowen Xu, Wei Jiang
Sensitive detection of telomerase activity is critical to cancer diagnosis, screening of anticancer drugs and evaluation of cancer therapy. Herein, a label-free molecular beacons-based DNA machine was developed for sensitive detection of telomerase activity. The DNA machine consisted of T7 exonuclease (T7 Exo), label-free recognition molecular beacon (RMB) and signal molecular beacon (SMB) with projecting 5'-terminuses, which can protect RMB and SMB from being digested by T7 Exo. Firstly, telomerase elongated telomerase substrate (TS) primer, generating a telomerase elongation production (TEP) with tandem repeats (TTAGGG)n...
May 15, 2017: Talanta
https://www.readbyqxmd.com/read/28302966/highly-sensitive-fluorescence-quantitative-detection-of-mercury-in-soil-based-on-non-labeled-molecular-beacon-and-fluorescent-dye-hoechst-33258
#16
Dongshan Xiang, Kun Zhai, Qiuzhang Sang, Boan Shi, Xiaohong Yang
A highly sensitive and selective fluorescence method of quantitative detection for mercury in soil was developed using non-labeled molecular beacon (MB), single-stranded nucleic acid (ssDNA) and fluorescent dye Hoechst 33258. In this analytical method, the loop of MB was designed to be a sequence that was complementary to the ssDNA with multiple T-T mismatches, the stem of MB was completely designed as C-G base pairs, and both ends of the MB are not modified by any fluorophore and quencher. In the absence of Hg(2+), the interaction between Hoechst 33258 and the MB was very weak, and the fluorescence signal of Hoechst 33258 was very low...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/28255356/microrna-detection-using-a-double-molecular-beacon-approach-distinguishing-between-mirna-and-pre-mirna
#17
Amanda Marie James, Meredith B Baker, Gang Bao, Charles D Searles
MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally regulate gene expression and are recognized for their roles both as modulators of disease progression and as biomarkers of disease activity, including neurological diseases, cancer, and cardiovascular disease (CVD). Commonly, miRNA abundance is assessed using quantitative real-time PCR (qRT-PCR), however, qRT-PCR for miRNA can be labor intensive, time consuming, and may lack specificity for detection of mature versus precursor forms of miRNA...
2017: Theranostics
https://www.readbyqxmd.com/read/28220155/specificity-of-snp-detection-with-molecular-beacons-is-improved-by-stem-and-loop-separation-with-spacers
#18
Valentina M Farzan, Mikhail L Markelov, Alexander Yu Skoblov, German A Shipulin, Timofei S Zatsepin
Molecular beacons (MBs) are valuable tools in molecular biology, clinical diagnostics and analytical chemistry. Here we describe a novel approach for the design of MBs with nucleotide or non-nucleotide linkers between the stem and loop regions. Such modified MBs have significantly improved specificity and performance for single nucleotide polymorphism (SNP) detection. These advantages are especially distinct, when compared to the classic MBs, in the case of possible interactions between the stem and loop regions...
March 13, 2017: Analyst
https://www.readbyqxmd.com/read/28217801/nucleic-acid-detection-using-bret-beacons-based-on-bioluminescent-protein-dna-hybrids
#19
Wouter Engelen, Kayleigh M van de Wiel, Lenny H H Meijer, Bedabrata Saha, Maarten Merkx
Bioluminescent molecular beacons have been developed using a modular design approach that relies on BRET between the bright luciferase NanoLuc and a Cy3 acceptor. While classical molecular beacons are hampered by background fluorescence and scattering, these BRET-beacons allow detection of low pM concentrations of nucleic acids directly in complex media.
March 2, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28213328/an-integrated-dual-functional-recognition-amplification-bio-label-for-the-one-step-impedimetric-detection-of-micro-rna-21
#20
Sawsen Azzouzi, Wing Cheung Mak, Kamalodin Kor, Anthony P F Turner, Mounir Ben Ali, Valerio Beni
Alteration in expression of miRNAs has been correlated with different cancer types, tumour stage and response to treatments. In this context, a structurally responsive oligonucleotide-based electrochemical impedimetric biosensor has been developed for the simple and sensitive detection of miRNA-21. A highly specific biotinylated DNA/LNA molecular beacon (MB) probe was conjugated with gold nanoparticles (AuNPs) to create an integrated, dual function bio-label (biotin-MB-AuNPs) for both biorecognition and signal generation...
June 15, 2017: Biosensors & Bioelectronics
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