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Cell biology, chemogenomics and chemoproteomics – application to drug discovery

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Pages 381-401 | Published online: 20 Mar 2007

Bibliography

  • HERBERT A, RICH A: The biology of left-handed Z-DNA. J. Biol. Chem. (1996) 271:11595-11598.
  • GAGNA CE, LAMBERT WC, KUO HR, FARNSWORTH PN: Localization of B-DNA and Z-DNA in terminally differentiating fiber cells in the adult lens. J. Histochem. Cytochem. (1997) 45:1511-1521.
  • BROWN BA, LOWENHAUPT K, WILBERT CM, HANLON EB, RICH A: The Za domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. Proc. Natl. Acad. Sci. USA (2000) 97:13531-13586.
  • SINDEN RR: DNA structure and function. Academic Press, New York (1994).
  • GAGNA CE, LAMBERT WC: The halting arrival of left-handed Z-DNA. Med. Hypotheses (2003) 60:418-423.
  • VENTER JC, ADAMS MD, MYERS EW et al.: The sequence of the human genome. Science (2001) 291:1304-1351.
  • SEHGAL A: Drug discovery and development using chemical genomics. Curr.Opin. Drug Discov. Dev. (2002) 5:526-531.
  • LOCKHART DJ, WINZELER EA: Genomics, gene expression and DNA arrays. Nature (2000) 405:827-836.
  • JEFFERY DA, BOGYO M: Chemical proteomics and its application to drug discovery. Curr. Opin. Biotechnol. (2003) 14:87-95.
  • BEROZA P, VILLAR HO, WICK MM, MARTIN GR: Chemoproteomics as a basis for post-genomic drug discovery. Drug Discov. Today (2002) 7:807-814.
  • SCHREIBER SL: Chemical genetics resulting from a passion for synthetic organic chemistry. Bioorg. Med. Chem. (1998) 6:1127-1152.
  • BLAKE JF: Chemoinformatics-predicting the physicochemical properties of `drug-like' molecules. Curr. Opin. Biotechnol. (2000) 11:104-107.
  • CARON PR, MULLICAN MD, MASHAL RD, WILSON KP, SU MS, MURCKO MA: Chemogenomic approaches to drug discovery. Curr. Opin. Chem. Biol. (2001) 5:464-470.
  • FALB D, JINDAL S: Chemical genomics: bridging the gap between the proteome and therapeutics. Curr. Opin. Drug Discov. Devel. (2002) 5:532-539.
  • ZHENG XF, CHAN TF: Chemical genomics: a systematic approach in biological research and drug discovery. Curr. Issues. Mol. Biol. (2002) 4:33-43.
  • ZHENG XFS, CHAN TF: Chemical genomics in the global study of protein functions. Drug Discov. Today (2002) 7:197-205.
  • BERTSCH M, KASSNER RJ: Selective staining of proteins with hydrophobic surface sites on a native electrophoretic gel. J. Proteome Res. (2003) 2:469-475.
  • GAGNA CE, WINOKUR D, LAMBERT WC: The use of histotechnology, histochemical and immunohistochemical nucleic acid probes to qualify and quantify cell death in single-, double-, and multiple-stranded DNA in diseased and normal tissues. Recent Res. Dev. Biophys. (2004) 3:207-233.
  • GAGNA CE, LAMBERT WC: Chemistry and the genomic revolution. The Chemist (2004) 81:21-26.
  • GAGNA CE, WINOKUR D, LAMBERT WC: Cell biology, chemogenomics and chemoproteomics. Cell Biol. Int. (2004) 28:755-764.
  • GAGNA CE, CHAN N, LAMBERT WC: The effects of DNA and protein structure on cancer gene expression. Protein Sci. (2004)13:152.
  • GAGNA CE, LAMBERT WC: Effects of nucleic acids structure on normal gene expression. J. Histochem. Cytochem. (2004) 52:S50.
  • GAGNA CE, CHAN NJ, LAMBERT WC: Characterizing changes in the structure of normal and diseased genes which regulate gene expression: transitions in helical conformations of single-, double-, triple-, and four-stranded DNA. Mol. Biol. Cell (2004) 15:445a (2466).
  • GAGNA CE, LAW S, JALAJ S, et al.: The effect of mustard gas on gene expression. FASEB J. (2004) 18:A572.
  • GAGNA CE, CHAN N, LAMBERT WC: Structural transitional chemogenomics and structural transitional chemoproteomics: two novel drug discovery approaches. FASEB J. (2005) 19:521.4.
  • GAGNA CE, CHAN NJ, SPINELLI D, LAMBERT WC: Regulation of gene expression by novel antisense technology, based on structures of DNA and RNA: structural transitional genomics (and proteomics). Biophys. J. (2005) 88:2804.
  • GARAVELLI JS, HOU Z, PATTABIRAMAN N, STEPHENS RM: The RESID database of protein structure modifications and the NRL-3D sequence–structure database. Nucleic Acids Res. (2001) 29:199-201.
  • MERRICK BA: The human proteome organization (HUPO) and environmental health. EHP Toxicogenomics (2003) 111:1-5.
  • BURGER G, PLOEM JS, GOERTTLER K: Clinical cytometry and histometry. Academic Press, New York (1987).
  • SHOTTON D: Electronic light microscopy: techniques in modern biomedical microscopy. Wiley-Liss, New York (1993).
  • MURPHY DB: Fundamentals of light microscopy and electronic imaging. Wiley-Liss, New York (2001).
  • REKHTER MD, CHEN J: Molecular analysis of complex tissues is facilitated by laser capture microdissection: critical role of upstream tissue processing. Cell Biochem. Biophys. (2001) 35:103-113.
  • MCDONALD WH, YATES JR: Proteomic tools for cell biology. Traffic (2000) 1:747-754.
  • ALBERTS B, JOHNSON A, LEWIS J, RAFF M, ROBERTS K, WALTER P: Molecular biology of the cell. Garland Science, New York (2002).
  • MOCELLIN S, PROVENZANO M, ROSSI CR, PILATI P, NITTI D, LISE M: DNA array-based gene profiling from surgical specimen to the molecular portrait of cancer. Ann Surg (2005) 241:16-26.
  • HOPKINS AL, GROOM CR: The druggable genome. Nat. Rev. Drug Discov. (2002) 1:727-730.
  • ASHTON GH, MCGRATH JA, SOUTH AP: Strategies to identify disease genes. Drugs Today (2002) 38:235-244.
  • BREDEL M, JACOBY E: Chemogenomics: an emerging strategy for rapid target and drug discovery. Nat. Rev. Genet. (2004) 5:262-275.
  • AUSTIN CP: The completed human genome: implications for chemical biology. Curr. Opin. Chem. Biol. (2003) 7:511-515.
  • CREWS CM, SPLITTGERBER U: Chemical genetics: exploring and controlling cellular processes with chemical probes. Trends Biochem. Sci. (1999) 24:317-320.
  • RUSSELL RB, EGGLESTON DS: New roles for structure in biology and drug discovery. Nat. Struct. Biol. Suppl. (2000) 7:928-930.
  • GAGNA CE: Structural nucleic acids microarray. Biochemistry. (2001) 40:8648.
  • HAUGLAND RP: Handbook of Fluorescent Probes. Ninth Edition. Molecular Probes, Eugene, OR (2004).
  • GILBERT DE, FEIGON J: Structural analysis of drug–DNA interactions. Curr. Opin. Struct. Biol. (1991) 1:439-445.
  • BLASZAK RT, POTAMAN V, SINDEN RR. BISSLER JJ: DNA structural transitions within the PKD1 gene. Nucleic Acids Res. (1999) 27:2610-2617.
  • PUFALL MA, LEE GM, NELSON ML et al.: Variable control of Ets-1 DNA binding by multiple phosphates in an unstructured region. Science (2005) 309:142-145.
  • RAO PV, GONZALEZ P, PERSSON B, JORNVALL H, GARLAND D, ZIGLER S: Guinea pig and bovine ζ-crystallins have distinct functional characteristics highlighting replacements in otherwise similar structures. Biochem. (1997) 36:5353-5362.
  • CHEN JH, KANG LY: The pleiotropic role of RF-36 gene product. homeotic switch during lens growth and differentiation. In: Cellular and Molecular Aspects of Eye Research. Sino-American Technology, New York (1986) 107-113.
  • LAVERS GC, TANG JC, CHEN JH: Effect of lens protein (RF-36) isolated from cortical fiber cells on mRNA translation. In: Lavers GC, and Chen JH, editors. Cellular and Molecular Aspects of Eye Research. Sino-American Technology, New York (1988) 92-100.
  • CHEN JH, SHEN DF, TONG TC, ZHANG L, LIU HL: The pleiotropic roles of RF-36 nucleic acid binding protein: DNA topology and receptor response in crystallin gene expression. In: Papas TS, editor. Gene Regulation and AIDS: Transcriptional Activation, Retroviruses and Pathogenesis. Advances In Applied Biotechnology Series. Vol. 7. Gulf Publishers, Houston (1987) 107-121.
  • GAGNA CE, LAMBERT WC: Binding properties of bovine ocular lens ζ-crystallin to right-handed B-DNA, single-stranded DNA and left-handed Z-DNA. Cell Biol. Int. (1998) 22:217-225.
  • CHEN JH, TONG TC, ZHANG L: Rapid enhancement of ‘MIP’ 26Da protein phosphorylation by RF-36 nucleic acid binding protein in lens cells. Lens Eye Toxic Res. (1991) 8:469-487.
  • GAGNA CE, KUO HR, AGOSTINO N et al.: Novel use of bovine ζ-crystallin as a conformational DNA probe to characterize a phase transition zone and terminally differentiating fiber cells in the adult canine ocular lens. Arch. Histol. Cytol. (2001) 64:379-391.
  • KIM CK, HAIDER KH, LIM SJ: Gene medicine: a new field of molecular medicine. Arch. Pharm. Res. (2001) 24:1-15.
  • ZARLING DA, CALHOUN CJ, HARDIN CC, ZARLING AH: Cytoplasmic Z-RNA. Proc. Natl. Acad. Sci. USA (1987) 84:6117-6121.
  • HOOS A, CORDON-CARDO C: Tissue microarray profiling of cancer specimens and cell lines: opportunities and limitations. Lab Invest. (2001) 81:1331-1338.
  • WILDSMITH SE, ELCOCK FJ. Microarrays under the microscope. Mol. Pathol. (2001) 54:8-16.
  • MOCH H, KONONEN J, KALLIONIEMI OP, SAUTER G: Tissue microarrays: what will they bring to molecular and anatomic pathology. Anat. Pathol. (2001) 8:14-20.
  • SKACEL M, SKILTON B, PETTAY JD, TUBBS RR: Tissue microarrays: a powerful tool for high-throughput analysis of clinical specimens: a review of the method with validation data. Appl. Immunohistochem. (2002) 10:1-6.
  • DAS PM, RAMACHANDRAN K, VANWERT J, SINGAL R: Chromatin immunoprecipitation assay. Biotechniques. (2004) 37:961-969.
  • ORLANDO V: Mapping chromosomal proteins in vivo by formaldehyde-cross-linked-chromatin immunoprecipitation. Trends Biochem Sci. (2000) 25:99-104.
  • JOHNSON KD, BRESNICK EH: Dissecting long-range transcriptional mechanisms by chromatin immunoprecipitation. Methods. (2002) 26:27-36.
  • NEWMAN-GAGE: Fetal tissue banking: standards and regulatory issues. J. Hematother. (1996) 5:189-193.
  • HAIMOWITZ MD: Practical issues in tissue banking. Am. J. Clin. Pathol. (1997) 107:S75-81.
  • OOSTERHUIS JW, COEBERGH JW, VAN VEEN EB: Tumor banks: well-guarded treasures in the interest of patients. Nature (2003) 3:73-77.
  • LO KC, CHUANG WW, LAMB DJ: Stem cell research: the facts, the myths and the promises. J. Urol. (2003) 170:2453-2458.
  • COGLE CR, GUTHRIE SM, SANDERS RC, ALLEN WL, SCOTT EW, PETERSEN BE: An overview of stem cell research and regulatory issues. Mayo. Clin. Proc. (2003) 78:993-1003.
  • REYA T, MORRISON SJ, CLARKE MF, WEISSMAN IL: Stem cells, cancer, and cancer stem cells. Nature (2001) 414:105-111.
  • GAGNA CE, KUO HR, LAMBERT WC: Terminal differentiation and left-handed Z-DNA: a review. Cell Biol. Int. (1999) 23:1-5.
  • GAGNA CE, KUO HR, HORNAN C, HAMMOND I, LAMBERT WC: Use of anti-single-stranded DNA antibodies to localize and quantify denatured DNA during cell death. Cell Biol. Int. (2000) 24:657-659.
  • GAGNA CE, KUO HR, FLOREA E et al.: Comparison of apoptosis and terminal differentiation: the mammalian aging process. J. Histochem. Crytochem. (2001) 49:929-930.
  • AROSARENA O: Tissue engineering. Curr. Opin. Otolaryngol. Head Neck Surg. (2005) 13:233-241.
  • DREGER M: Proteome analysis at the level of subcellular structures. Eur. J. Biochem. (2003) 270:589-599.
  • HUBER LA, PFALLER K, VICTOR I: Organelle proteomics: implications for subcellular fractionation in proteomics. Circ. Res. (2003) 92:962-968.
  • MCKAY CS, MCLEOD JA, MURRAY GI: Laser capture microscopy. Br. Med. J. (2000) 53:64-68.
  • ELTOUM IA, SIEGAL GP, FROST AR: Microdissection of histologic sections: past, present, and future. Adv. Anat. Pathol. (2002) 9:316-322.
  • HSU FD, NIELSEN TO, ALKUSHI A et al.: Tissue microarrays are an effective quality assurance tool for diagnostic immunohistochemistry. Mod. Pathol. (2002) 15:1374-1380.
  • BOWTELL D, SAMBROOK J: DNA microarrays: a molecular cloning manual. Cold Spring Harbor Laboratory Press, Cold Spring, NY (2003).
  • HELL SW: Toward fluorescent nanoscopy. Nat. Biotechnol. (2003) 21:1347-1355.
  • DOMBECK DA, BLANCHARD-DESCE M, WEBB WW: Optical recording of action potentials with second-harmonic generation microscopy. J. Neurosci. (2004) 24:999-1003.
  • GEORGE N: TIRF microscopy: the evanescent wave of the future. Am. Lab (2004) 36:26-28.
  • MEEK GA, ELDER HY: Analytical and quantitative methods in microscopy. Cambridge University Press, Cambridge, UK (1977).
  • STRAUB M, LODEMANN P, HOLROYD P, JAHN R, HELL SW: Live cell imaging by multifocal multiphoton microscopy. Eur. J. Cell Biol. (2000) 79:726-734.
  • BAHLMANN K, JAKOBS S, HELL SW: 4Pi-confocal microscopy of live cells. Ultramicroscopy (2001) 87:155-164.
  • MANN SA, HAPPEL P, HOFFMANN G, DIETZEL ID: Imaging living cells with scanning ion-conductance microscopy. GIT Imaging Microsc. (2004) 6:40-42.
  • NISHIGAKI T, WOOD CD, SHIBA K, BABA SA, DARSZON A: Stroboscopic illumination using light-emitting diodes reduces phototoxicity in fluorescence cell imaging. Biotechniques. (2006) 41:191-197.
  • HIRAOKA Y, MINDEN JS, SWEDLOW JR, SEDAT JW, AGARD DA: Focal points for chromosome condensation and decondensation revealed by three-dimensional in vivo time-lapse microscopy. Nature (1989) 342:293-296.
  • LUNTE CE, SCOTT DO: Sampling living systems using microdialysis probes. Anal. Chem. (1991) 63:773-780.
  • NICASTRO D, SCHWARTZ C, PIERSON J, GAUDETTE R, PORTER ME, MCINTOSH JR: The molecular architecture of axonemes revealed by cryoelectron tomography. Science. (2006) 313:944-948.
  • SCHIFFMANN DA, DIKOVSKAYA D, APPLETON PL et al.: Open microscopy environment and findspots: integrating image informatics with quantitative multidimensional image analysis. Biotechniques. (2006) 41:199-208.
  • BAILEY DS, BONDAR A, FURNESS LM: Pharmacogenomics: it's not just pharmacogenetics. Curr. Opin. Biotech. (1998) 9:595-601.
  • RUDERT F: Genomics and proteomics tools for the clinic. Curr. Opin. Mol. Ther. (2000) 2:633-642.
  • PORUBLEVA L, CHITNIS PR: Proteomics: a powerful tool in the post-genomic era. Indian J. Biochem. Biophys. (2000) 37:360-368.
  • KIM JH: Bioinformatics and genomic medicine. Genet. Med. (2002) 4:625-655.

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