自動化プロトコール

Automated protocols

• Meng Q. et al. (2001). Automated multiplex assay system for simultaneous detection of hepatitis B virus DNA, hepatitis C virus RNA and human immunodeficiency virus type 1 RNA. J.Clin.Microbiol. 39(8):2937-2945.
• Pollock GS. et al. (2001). Effects of early visual experience and diurnal rhythms on BDNF mRNA and protein levels in the visual system, hippocampus and cerebellum. J. Neurosci.21(11):3923-3931.
• Miyashiro I. et al. (2001). Molecular strategy for detecting metastatic cancers with use of multiple tumor-specific MAGE-A genes. Clin.Chem. 47(3):505-512.
• Stevens SJC. et al. (1999). Monitoring of Epstein-Barr virus DNA load in peripheral blood by quantitative competitive PCR. J.Clin.Microbiol. 37:2852-2857.

核酸アプリケーション

Genome analysis

• Fletcher TM. et al. (2002). Structure and dynamic properties of a glucocorticoid receptor-induced chromatin transition. Mol. Cel. Biol. 20(17): 6466-6475.
• Hansen-Hagge TE. et al. (2001). Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation mediated subtraction (Limes). Nucl. Acids Res. 29(4):e20.
• Pradel N. et al. (2002). Genomic subtraction to identify and characterize sequences of Shiga toxin-producing Escherichia coli O91:H21. Appl. Env. Microbiol. 68(5):2316-2325.
• Heald R. et al. (1996) Self-organization of microtubules into bipolar spindles around artificial chromosomes in Xenopus egg extracts. Nature 382:420-425.
• Beulieu M. et al. (2001). PCR candidate region mismatch scanning:adaption to quantitative, high-throughput genotyping. Nucleic Acids Res. 29(5): 114-1124.

Single-stranded DNA templates

• von Wintzingerode F. et al. (2002). Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass-spectrometry: A tool for rapid bacterial identification. PNAS.99(10):7039-7044.
• Pourmand N. et al. (2002). Multiplex pyrosequencing. Nucleic Acids Res. 30(7):e31. Lindblad-Toh K. et al. (2000). Large-scale discovery and genotyping of single nucleotide polymorphisms in the mouse. Nature Genetics. 24:381-386.
• Dziembowski A. et al. (2001). Analysis of 3’ and 5’ ends of RNA by solid-phase S1 nuclease mapping. Anal. Biochem. 294:87-89.
• Fletcher TM et al. (2002) Structure and dynamic properties of a glucocorticoid receptor-induced chromatin transition. Mol Cell Biol 20(17):6466–6475.
• Hansen-Hagge TE et al. (2001) Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes). Nucleic Acids Res 29(4):e20.
• Beulieu M et al. (2001) PCR candidate region mismatch scanning: adaptation to quantitative, high-throughput genotyping. Nucleic Acids Res 29(5):1114–1124.
• Leunissen ME et al. (2009) Switchable self-protected attractions in DNA-functionalized colloids. Nature Mater 8:590-595.
• Persson H et al. (2009) The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs. Nature Cell Biol 11(10):1268-1271.

Sequence clean-up

• Fangan BM. et al. (1999) Automated system for purification of dye terminator sequencing products eliminates up-stream purification of templates. Biotechniques 26:980-983.
• Bhalerao R. et al. (2003) Gene expression in autumn leaves. Plant Physiol. 131:1-13.

Sequence-specific capture

• Dong SM. et al. (2001). Detection of colorectal cancer in stool with the use of multiple genetic targets. J Natl Cancer Inst. 93(11): 858-865.
• Shuber AP. et al. (2002). Accurate, non-invasive detection of Helicobacter pylori DNA from stool samples: Potential usefulness for monitoring treatment. J. Clin. Microbiol. 40(1):262-264.
• Kornmann B et al. (2001) Analysis of circadian liver gene expression by ADDER, a highly sensitive method for the display of differentially expressed mRNAs. Nucleic Acids Res 29(11):e51.
• Schramm G et al. (2000) A simple and reliable 5’-RACE approach. Nucleic Acids Res 28(22):e96.
• Mangiapan G. et al. (1996). Sequence capture-PCR improves detection of mycobacterial DNA in clinical specimens. J. Clin. Microbiol. 34(5):1209-1215.
• Sutcliffe JG et al. (2000) TOGA: An automated parsing technology for analyzing expression of nearly all genes. Proc Natl Acad Sci U S A 97(5):1976–1981.
• Refseth UH. et al. (1997). Hybridization capture of microsatellites directly from genomic DNA. Electrophoresis. 18(9):1519-1523.
• Gnirke A et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnol 27(2):182–189.

Gene expression analysis

• Kornmann B. et al. (2001). Analysis of circadian liver gene expression by ADDER, a highly sensitive method for the display of differentially expressed mRNAs. Nucleic Acids Res. 29(11). e51
• Laveder P. et al. (2002). A two-step strategy for constructing specifically self-subtracted cDNA libraries. Nucleic Acids Res. 30(9): e38
• Schramm G. et al. (2000).A simple and reliable 5’-RACE approach. Nucl. Acids Res. 28(22):e96
• Velculescu VE. et al. (1995). Serial analysis of gene expression. Science. 270(5235): 484-487.
• Brenner S. et al. (2000). In vitro cloning of complex mixtures of DNA on microbeads:
• Physical separation of differentially expressed cDNAs. PNAS. 97(4): 1665-1670.
• Sutcliffe JG. et al. (2000). TOGA: An automated parsing technology for analyzing expression of nearly all genes. PNAS. 97(5): 1976-1981.
• Wang A. et al. (1999). Rapid analysis of gene expression (RAGE) facilitates universal expression profiling. Nucleic Acids Res. 27(23): 4609-4618.

Nucleic acid binding proteins

• Noguchi E et al. (2009) A Crohn’s disease–associated NOD2 mutation suppresses transcription of human IL10 by inhibiting activity of the nuclear ribonucleoprotein hnRNP-A1. Nature Immunol 10(5):471–479.
• Brodsky AS. and Silver A. (2002). A microbead based system for identifying and characterizing RNA-protein interactions by flow cytometry. Mol. Cel. Proteomics 1(12):922-929.
• Nordhoff E. et al. (1999). Rapid identification of DNA-binding proteins by mass spectrometry. Nat. Biotechnol. 17: 884-888.
• Mehta A et al. (1998). A sequence-specific RNA binding protein complements Apobec-1 to edit apolipo protein B mRNA. Mol. Cel. Biol. 18(8):4426-4432.
• Li D et al. (2009) Down-Regulation of MHC Class II Expression through Inhibition of CIITA Transcription by Lytic Transactivator Zta during Epstein-Barr Virus Reactivation. J Immunol 182(4):1799–1809.

細胞分離

Specific cell isolation

• Konishi Y. et al. (2002). Isolation of living neurons from human elderly brains using immunomagnetic sorting DNA-liker system. Am. J. Pathol. 161(5):1567-1576.
• Fahrer AM. et al. (2001). Attributes of gd intrepithelial lymphocytes as suggested by their transcription profile. PNAS 98(18):10261-10266.
• Johansen M. et al. (2002). An investigation of methods for enriching trophoblasts from maternal blood. Prenatal Diagnosis 15:921-931.
• Sun W. et al. (2001). Food-borne pathogens. Use of bioluminescent Salmonella for assessing the efficiency of constructed phagebased biosorbent. J Ind. Microbiol. Biotech. 27:126-128.

タンパク質精製

Protein purification

• Lehrbach NJ et al. (2009) LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans. Nat Struct Mol Biol 16(10):1016–1020.
• O’Reilly FM. et al. (2002). FKBP12 modulation of the binding of the skeletal ryanodine receptor onto the II-III loop of the dihydropyridine receptor. Biophys. J 82:145-155.
• Chao S-H. and Price DH. (2001). Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo. J. Biol. Chem. 276(34):31793-31799.
• deBaar MP. et al. (1999). Detection of human immunodeficiency virus type I nucleocapsid protein p7 in vitro and in vivo. J Clin. Microbiol. 37(1):63-67.
• Girault S. et al. (1996). Coupling of MALDI-TOF mass analysis to the separation of biotinylated peptides by magnetic streptavidin beads. Anal. Chem. 68:2122-2126.
• Cook PJ et al. (2009) Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions. Nature 16(458):591–596.

バイオパニング

Biopanning

• Nord K. et al. (2001). Recombinant human factor VIII-specific affinity ligands selected from phage-displayed combinatorial libraries of protein A. Eur. J. Biochem. 268:4269-4277.
• Biroccio A. et al. (2002). Selection of RNA aptamers that are specific and high-affinity ligands of the hepatitis C virus RNA-dependent RNA polymerase. J. Virol. 76(8):3688-3696.
• Legendre D. et al. (1999). Engineering a regulatable enzyme for homogenous immunoassays. Nature Biotech. 17:67-72.
• Lev A. et al. (2002). Isolation and characterization of human recombinant antibodies endowed with the antigen-specific, major histocompatibility complex-restricted specificity of T-cells directed toward the widely expressed tumor T-cell epitopes of the telomerase catalytic subunit. Cancer Res. 62(11):3184-3194.
• Cumbers SJ. et al. (2002). Generation and iterative affinity maturation of antibodies in vitro using hypermutating B-cell lines. Nat. Biotech. 20(11):1129-1134.
• Demartis S. et al. (1999). A strategy for the isolation of catalytic activities from repertoires of enzymes displayed on phage. J. Mol. Biol. 286:617-633.
• Pini A. et al. (1998). Design and use of a phage display library. J. Biol. Chem. 273(34):21769-21776.
• Cox JC. et al. (2002). Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res. 30(20):e108.

近接依存性標識法

Proximity-labeling

• Andrea M. et al. Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID. Tools and Resources Sep 19, 2019

DNA-タンパク質相互作用

DNA-Protein intruction

• Yasuhiro Fujiwara, Yuji Tanno, Hiroki Sugishita, Yusuke Kishi, Yoshinori Makino and Yuki Okada : Preparation of “stress-free” concanavalin A-conjugated magnetic beads for CUT&TAG

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