Genomes and Genes
molecular probe techniques
Summary: The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.
- Green A, Norris J, Wang J, Xie Z, Zhang H, La Riviere P. In vitro testing of a protease-sensitive contrast agent for optoacoustic imaging. J Biomed Opt. 2010;15:021315 pubmed publisher..However, ultimately, it is detection of the cleaved probe that is of the greatest import, since it reports on the protease activity of interest. ..
- Parri V, Katzaki E, Uliana V, Scionti F, Tita R, Artuso R, et al. High frequency of COH1 intragenic deletions and duplications detected by MLPA in patients with Cohen syndrome. Eur J Hum Genet. 2010;18:1133-40 pubmed publisher..Given the high percentage of identified copy number variations, we suggest that this technique could be used as the initial screening method for molecular diagnosis of Cohen syndrome. ..
- Lin S, Wang W, Palm C, Davis R, Juneau K. A molecular inversion probe assay for detecting alternative splicing. BMC Genomics. 2010;11:712 pubmed publisher..Fully optimized, we estimate that the assay could accommodate a throughput of greater than 20,000 splice junctions in a single reaction. This would represent a significant improvement over existing technologies. ..
- Kopp P. [Molecular tests for (early) recognition of endocrine disorders - towards a sophisticated management of complex endocrine and metabolic diseases]. Ther Umsch. 2010;67:367-73 pubmed publisher..This review provides a short overview about genetic analyses in the field of endocrinology that are relevant for the practicing physician. ..
- Grossman M, Sela Passwell N, Sagi I. Achieving broad molecular insights into dynamic protein interactions by integrated structural-kinetic approaches. Curr Opin Struct Biol. 2011;21:678-85 pubmed publisher..Here we review representative studies utilizing such an integrated real-time structural approach designed to reveal molecular mechanisms underlying protein interactions at atomic resolution. ..
- Jungmann R, Steinhauer C, Scheible M, Kuzyk A, Tinnefeld P, Simmel F. Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett. 2010;10:4756-61 pubmed publisher..The method is demonstrated for flat monomeric DNA structures as well as multimeric, ribbon-like DNA structures. ..
- M ller B, Streicher E, Hoek K, Tait M, Trollip A, Bosman M, et al. inhA promoter mutations: a gateway to extensively drug-resistant tuberculosis in South Africa?. Int J Tuberc Lung Dis. 2011;15:344-51 pubmed
- Schwab C, Jones L, Morrison H, Ryan S, Yigittop H, Schouten J, et al. Evaluation of multiplex ligation-dependent probe amplification as a method for the detection of copy number abnormalities in B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer. 2010;49:1104-13 pubmed publisher
- Jacobson O, Chen X. PET designated flouride-18 production and chemistry. Curr Top Med Chem. 2010;10:1048-59 pubmed..Flouride-18 can be thereafter introduced into small molecules or biomolecules using various chemical synthetic routes, to give the desired imaging agent. ..
- Elson E. Fluorescence correlation spectroscopy: past, present, future. Biophys J. 2011;101:2855-70 pubmed publisher..For example, a new and potentially interesting field for FCS studies could be the study of nonequilibrium steady states, especially in living cells. ..
- Bürki N. [Hereditary breast and ovarian cancer - indications for genetic testing, counseling and options for mutation carriers]. Ther Umsch. 2010;67:359-66 pubmed publisher..Each of the three management options 'intensified cancer screening', 'chemoprevention' and 'prophylactic surgery' is discussed thoroughly. Recommended cancer screening in male mutation carriers are mentioned as well. ..
- Seo K, Chu H, Yoo T, Lee S, Won J. Separation efficiency of free-solution conjugated electrophoresis with drag-tags incorporating a synthetic amino acid. Electrophoresis. 2016;37:818-25 pubmed publisher..In addition, to produce strong and site-specific conjugation, a methionine residue in drag-tags is replaced with homopropargylglycine (Hpg), which can be conjugated specifically to a DNA fragment with an azide site. ..
- Guan L, van der Heijden G, Bortvin A, Greenberg M. Intracellular detection of cytosine incorporation in genomic DNA by using 5-ethynyl-2'-deoxycytidine. Chembiochem. 2011;12:2184-90 pubmed publisher..Subsequent experiments in mouse male germ cells and zygotes demonstrated that EdC is a specific and reliable reporter of DNA replication, in vivo. ..
- Fairfax M, Salimnia H. Diagnostic molecular microbiology: a 2013 snapshot. Clin Lab Med. 2013;33:787-803 pubmed publisher..Tests are grouped together by technique and target. Tests with similar roles for similar analytes are compared with respect to benefits, drawbacks, and possible problems. ..
- Bradford J, Clarke S. Dual-pulse labeling using 5-ethynyl-2'-deoxyuridine (EdU) and 5-bromo-2'-deoxyuridine (BrdU) in flow cytometry. Curr Protoc Cytom. 2011;Chapter 7:Unit 7.38 pubmed publisher..EdU detection using click chemistry does not cross-react with incorporated BrdU. Cells are first pulsed with EdU, and then pulsed with BrdU; sequential pulses of EdU, followed by BrdU, are done without removing or washing out EdU. ..
- Palanisamy R, Connolly A, Trau M. Accurate detection of methylated cytosine in complex methylation landscapes. Anal Chem. 2013;85:6575-9 pubmed publisher..This enabled the methylation status of a specific cytosine to be accurately measured with a high level of specificity, irrespective of adjacent epigenetic modifications. ..
- Cheng G, Shen B, Zhang F, Wu J, Xu Y, He P, et al. A new electrochemically active-inactive switching aptamer molecular beacon to detect thrombin directly in solution. Biosens Bioelectron. 2010;25:2265-9 pubmed publisher..Besides, CAs-MB/MNB can be easily regenerated by using 2M NaCl solution to cleave the thrombin from the aptasensor. ..
- Loskutov V, Sevriugin V. A novel approach to interpretation of the time-dependent self-diffusion coefficient as a probe of porous media geometry. J Magn Reson. 2013;230:1-9 pubmed publisher..Applicability of the solution obtained to the analysis of experimental data is shown. The possibility of passing to short-time and long-time regimes is discussed. ..
- Stocks B, Konermann L. Time-dependent changes in side-chain solvent accessibility during cytochrome c folding probed by pulsed oxidative labeling and mass spectrometry. J Mol Biol. 2010;398:362-73 pubmed publisher..Hence, the two approaches yield complementary information. Considering the very short time scale of pulsed oxidative labeling, an extension of the approach used here to sub-millisecond folding studies should be feasible. ..
- Pernites R, Ponnapati R, Felipe M, Advincula R. Electropolymerization molecularly imprinted polymer (E-MIP) SPR sensing of drug molecules: pre-polymerization complexed terthiophene and carbazole electroactive monomers. Biosens Bioelectron. 2011;26:2766-71 pubmed publisher..Various surface characterizations (contact angle, ellipsometry, XPS, AFM) of the E-MIP film verified the templating and release of the drug from the cross-linked conducting polymer film. ..
- Kashiwayama Y, Tomohiro T, Narita K, Suzumura M, Glumoff T, Hiltunen J, et al. Identification of a substrate-binding site in a peroxisomal beta-oxidation enzyme by photoaffinity labeling with a novel palmitoyl derivative. J Biol Chem. 2010;285:26315-25 pubmed publisher..These data suggest that MFE2 anchors its substrate around the region from Trp(249) to Arg(251) and positions the substrate along the hydrophobic cavity in the proper direction toward the catalytic center...
- Fabris D, Yu E. Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D. J Mass Spectrom. 2010;45:841-60 pubmed publisher..Examples are provided to illustrate how the concerted application of very diverse probing techniques can lead to the solution of actual biological systems. ..
- Dittami S, Riisberg I, Edvardsen B. Molecular probes for the detection and identification of ichthyotoxic marine microalgae of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta). Environ Sci Pollut Res Int. 2013;20:6824-37 pubmed publisher..The molecular probes designed in this study will be a valuable asset to microscopical detection methods in the monitoring of harmful algae and for biogeographical and ecological studies of this genus. ..
- Cox F, Momot K, Kuchel P. Magnetic-resonance evaluation of the suitability of microstructured polymer optical fibers as sensors for ionic aqueous solutions. ACS Appl Mater Interfaces. 2009;1:197-203 pubmed publisher..The findings suggest that microstructured PMMA fibers are compatible with ionic aqueous solutions and could provide a robust and durable platform for chemical-sensing applications. ..
- Ghafoory S, Breitkopf Heinlein K, Li Q, Dzieran J, Scholl C, Dooley S, et al. A fast and efficient polymerase chain reaction-based method for the preparation of in situ hybridization probes. Histopathology. 2012;61:306-13 pubmed publisher..Purified PCR fragment-based in vitro transcription enables preparation of in situ hybridization probes which allow the rapid detection of gene expression distribution in tissue slices from any gene of interest. ..
- Noda N, Awais R, Sutton R, Awais M, Ozawa T. Dynamic monitoring of p53 translocation to mitochondria for the analysis of specific inhibitors using luciferase-fragment complementation. Biotechnol Bioeng. 2017;114:2818-2827 pubmed publisher..This p53 mitochondrial translocation assay is a new tool for high-throughput screening to identify novel p53 inhibitors, which could be developed as drugs to treat diseases in which necrotic cell death is a major contributor. ..
- Coyne C, Rashmir Raven A, Jones T, Mochal C, Linford R, Brashier M, et al. Delineation of pulmonary airway fluid protein fractions with HRPO binding-avidity by far-Western ligand blot and mass spectrometry analyses: a model methodology for detecting mannose-binding protein expression profiles. Acta Biomed. 2009;80:243-61 pubmed..Based on its known molecular composition and structure, HRPO provides an opportunity for the development of diagnostics methodologies relevant to disease biomarkers that possess mannose-binding avidity. ..
- Kimura M, Aviv A. Measurement of telomere DNA content by dot blot analysis. Nucleic Acids Res. 2011;39:e84 pubmed publisher..The method might help researchers and clinicians alike in understanding risks for and extent of human diseases. ..
- Yaghmai V, Miller F, Rezai P, Benson A, Salem R. Response to treatment series: part 2, tumor response assessment--using new and conventional criteria. AJR Am J Roentgenol. 2011;197:18-27 pubmed publisher..Because of the new methods of treatment, assessment of necrosis and volumetric information will need to be incorporated into size-based criteria. ..
- Gupta G, Bhaskar A, Tripathi B, Pandey P, Boopathi M, Rao P, et al. Supersensitive detection of T-2 toxin by the in situ synthesized ?-conjugated molecularly imprinted nanopatterns. An in situ investigation by surface plasmon resonance combined with electrochemistry. Biosens Bioelectron. 2011;26:2534-40 pubmed publisher
- Galban S, Brisset J, Rehemtulla A, Chenevert T, Ross B, Galban C. Diffusion-weighted MRI for assessment of early cancer treatment response. Curr Pharm Biotechnol. 2010;11:701-8 pubmed..The utility of DW-MRI for assessing therapeutic-induced response is further evaluated on tumors residing in the brain, head and neck and bone. ..
- Park K, Choi B, Kim Y, Shin S, Hah S, Jung W, et al. Detection of single-base mutation in RNA using T4 RNA ligase-based nick-joining or DNAzyme-based nick-generation. Anal Biochem. 2011;414:303-5 pubmed publisher..T4 RNA ligase successfully discriminated a one-base mismatch in the ligation junction, and the designed DNAzyme cleaved RNA by discerning a single-base mismatch in the cleaving site. ..
- Hsieh K, Xiao Y, Tom Soh H. Electrochemical DNA detection via exonuclease and target-catalyzed transformation of surface-bound probes. Langmuir. 2010;26:10392-6 pubmed publisher..Combined with the advantages of electrochemical detection and its ready integration with microelectronics, our approach may represent a promising path toward direct DNA detection at the point of care. ..
- Karim M, Kohale S, Indei T, Schieber J, Khare R. Determination of viscoelastic properties by analysis of probe-particle motion in molecular simulations. Phys Rev E Stat Nonlin Soft Matter Phys. 2012;86:051501 pubmed
- Petris G, Vecchi L, Bestagno M, Burrone O. Efficient detection of proteins retro-translocated from the ER to the cytosol by in vivo biotinylation. PLoS ONE. 2011;6:e23712 pubmed publisher..We observed specific mono-biotinylation of cytosolically dislocated molecules, resulting in a novel, reliable way of determining the extent of retro-translocation. ..
- Lohmüller T, Iversen L, Schmidt M, Rhodes C, Tu H, Lin W, et al. Single molecule tracking on supported membranes with arrays of optical nanoantennas. Nano Lett. 2012;12:1717-21 pubmed publisher..The nanoantenna array thus enables enhanced observation of a fluid membrane system without static entrapment of the molecules. ..
- Mieda S, Amemiya Y, Kihara T, Okada T, Sato T, Fukazawa K, et al. Mechanical force-based probing of intracellular proteins from living cells using antibody-immobilized nanoneedles. Biosens Bioelectron. 2012;31:323-9 pubmed publisher..This method was shown to affect neither the doubling time of cells nor does it leave extrinsic antibodies within the examined cells, allowing to be used in subsequent analyses in their native state. ..
- Zeng C, Vangveravong S, Jones L, Hyrc K, Chang K, Xu J, et al. Characterization and evaluation of two novel fluorescent sigma-2 receptor ligands as proliferation probes. Mol Imaging. 2011;10:420-33 pubmed
- Tan S, Ouyang Y, Li X, Wen M, Li S. [Connection of magnetic antisense probe with SK-Br-3 oncocyte mRNA nucleotide detected by high resolution atomic force microscope]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2011;28:442-5 pubmed..05). These experiments demonstrated that the high resolution AFM could be used to show the binding of magnetic antisense probe and SK-Br-3 mRNA of tumor cell nuclear...
- Zhang Y, Hong H, Cai W. Imaging with Raman spectroscopy. Curr Pharm Biotechnol. 2010;11:654-61 pubmed..It is expected that imaging with Raman Spectroscopy will continue to be a dynamic research field over the next decade. ..
- Fond B, Abram C, Heyes A, Kempf A, Beyrau F. Simultaneous temperature, mixture fraction and velocity imaging in turbulent flows using thermographic phosphor tracer particles. Opt Express. 2012;20:22118-33 pubmed publisher..Correlated single shots are presented with a precision of 2 to 5% and an accuracy of 2%. ..
- Aughey G, Southall T. Dam it's good! DamID profiling of protein-DNA interactions. Wiley Interdiscip Rev Dev Biol. 2016;5:25-37 pubmed publisher..WIREs Dev Biol 2016, 5:25-37. doi: 10.1002/wdev.205 For further resources related to this article, please visit the WIREs website. ..