dna array method and protocols

METHODS IN MOLECULAR BIOLOGY John M. Walker, Series Editor 178.'Antihody Phage Display: Mrrhods old Pr~~coro/.\. edited hy 177. Two-Hyhrid Systems: Mrrhoh arrdProroco1.i. edited b) Purr1 176. Steroid Receptor Methods: Pf',J/~JCll/S n~rd ASSO~S. edited hy 175. Genomics Protocols. edlted by M~clrcrrl P SfarAry urltl 171. Epstein-Barr Virus Protocols, edited hy JiJ[lJlJrU B. Wilso~l 173. Calcium-Binding Protein Protocols, Volume 2: Mrrhods om/ 172. Calcium-Binding Protein Protocols, Volume 1: Rer,iew cm/ 171. Proteoglycan Protocols, edited by Rewro 1'. 2001 170. DNA Arrays: Mcrhorls rurd Plororols, edited hy Joyy 8. 169. Neurotrophin Protocols, edited by Roberr A. Rlrsh. 2001 IhX. Protein Structure, Stability, and Folding, edited hy Krurlerh 167. DNA Sequencing Protocols. Se'.od Edirml, ediled hy Co1irr 166. lmmunoloxin Methods and Protocols. ed~ted by ll'rrlrrr A. 165. SV40 Protocols. edited by Ldo Rqm, 2lJlll 161. Kinesin Protocols, edited hy 1sdwllP VrrJws, ?001 163. 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RNA-Protein Interaction Protocols, edited by S~rrarr R. 117. Electron Microscopy Methods and Protocols, edited hy M. n. ~~laplflclrl. 2000 20011 edited hy Duvrd Welnrrr. X100 H. How,, ?OW Jrremr A. Roberr,. 20011 Michael Grunr. 2000 A'. C \Vd/.s, rwd Chrrsrm, Powr. Zoo0 Roc!,! S. 7rm und Crrilin IV. Lo. 2000 S. Trrolr on(/ Crcilirr IV. Lo, 2000 S. Tlrun mrl Cecrliu IV. Lo. 2000 P Ke(rr.w. 2000 Misewr urd Sfephcw A. Knuvtr;. 2000 Rtid, 1YYY 2000 dtl/hwl~ P. C~lr/it,/d, 200fJ Hoyrlcs. lYYY A, Nasser Hujihuxlrerr, 1Y9Y DNA Arrays Methods and Protocols Edited by Jang B. Rampal Beckman Coulter, Inc., Fullerton, CA Humana Press Totowa, New Jersey [...]... concentration of RNAs in From: Methods in Molecular Biology, vol 170: DNA Arrays: Methods and Protocols Edited by: J B Rampal 0 Humana Press Inc., Totowa, NJ 1 2 Southern solution These were early forerunners of the current application of DNA microarrays to the analysis of sequence diversity and levels of gene expression In the late 196Os, Pardue and Gall (5) and Jones and Robertson (6) discovered a... interactions between the arrayed macromolecules and the test molecule of interest Classical examples of such recognition reactions are the interactions between the two complementary strands of a double-helical DNA molecule, betweena single-stranded DNA stretch and the messenger RNA copied fromit during transcription, between an antigen and an antibody, and between small ligands and their nucleic acid... Molecular Biology in Moscow and the Biochip Technology Center at Argonne National Laboratory, Argonne, IL ' From: Methods In Molecular Biology vol 170: DNA Arrays: Methods and Protocols Edited by: J 6.Rampal 0Humana Press Inc Totowa, NJ 17 18 Zlatanova and Mirzabekov 2 General Description of the MAGIChip" Technology MAGIChips'rM (Micro Arrays of Gel-Immobilized Compounds on a Chip) are arrays that we have... any position in the array Reprogramming the system to make a different array is simply a matter of changing the sequence file The oxidation and deprotection steps and the washes are common each cycle and are carried out flooding to by the whole surface with an excess of reagent or solvent Thus, the method is flexible and makes economical useof the most expensive reagents DNA Microarrays 7 As would be... complementary DNA microarray Science 270,467-470 (comments) DNA Microarrays 15 5 1 Shalon, D., Smith, S J and Brown, P 0 ( 1 996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization Genntne Res 6, 639-645 52 Lockhart, D J., Dong, H Byme, M C., Follettie, M.T., Gallo, M V., Chee, M S., Mittmann, M., Wang, C.,Kobayashi, M., Horton, H., and Brown, E...Contributors xi 1 DNA Microarrays History and Overview Edwin M Southern 1 Introduction 1.1 From Double Helix to Dot Blots It may seem premature to be writing a history DNA microarrays because of this technology is relatively new and clearly has more of a future than a past However readers could benefit from learning something about the technical basis of DNA microarrays, and younger readers be... following the introduction of fluorescent probes) The method used to fix chromosomes and nuclei to microscope slides in a way that allowed the DNA to take part in duplex formation with the probe is now used to fix DNA spotted on to slides in one microarray method And the multicolor fluorescent labeling techniques introduced by Ried et al (7) and Balding and Ward(8),for the analysis of multiple probes FISH,... J., Hood, L., and Landegren, U ( 1 990) Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay Proc Nutl Acad Sci USA 87,8923-8927 49 Pastinen, T., Kurg, A., Metspalu, A., Peltonen, L., and Syvanen, A C (1997) Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays Genome Res 7,606-614 P 0 50 Schena, M., Shalon, D., Davis, R.W., and Brown, (1995)... accurately the positions of the spots and to know in advance their precise shape and size, and an additional, major advantage of glass or plastic supports is their dimensional stability and rigidity Permeable membranes swell in solvent and tendto shrink and distort when dried; their fragility and flexibility make it difficult to register their position during spotting and reading Thus, it is not possible... hybridization to high-density oligonucleotide arrays Nut Biotechnol 14, 1675- 1680 (comments) 2 Gel-Immobilized Microarrays of Nucleic Acids and Proteins Production and Application for Macromolecular Research Jordanka Zlatanova and Andrei Mirzabekov 1 Introduction Biochips are small platforms with spatially arrayed macromolecules (or pieces thereof) that allow the collection and analysisof large amounts of biological . use for advanced research. The purpose of DNA Arrcrys: Methods and Protocols is to provide instruction in designing and constructing DNA arrays, as well as hybridizing them with biological. genes using labeled rRNA as probe and to measure the concentration of RNAs in From: Methods in Molecular Biology, vol. 170: DNA Arrays: Methods and Protocols Edited by: J. B. Rampal. Targeting Protocols, edited by E~IC 8. KrrIrn 2001) 132. Bioinformatics Methods and Protocols, edited hy Srcph 131. Flavoprotein Protocols, edited by S. K. C~~IIIUII and G. A.