Bøger i Biomethods serien

The understanding of molecular informa tion handling in nature is essential for the molecular optimization in chem istry, molecular biology, molecular pharmacology and therefore - as an ex ample - for the development of specifically acting drugs.

A Safety Considerations Genomie sequencing involves a number oj hazard­ ous steps, such as high eurrent, high voltage, radioaetive and highly toxie chemieals. It is, the- jore, absolutely essential that the instruetions oj equipment manu/aeturers bejollowed and that par­ tieular attention is paid to the loeal and jederal safety regulations. I Introduction 13 B Introduction Hypomethylation ofDNA has been positively correlated with thc activation of many eucaryotic genes. During the transition from inactive to active genes changes in the protein/DNA interaction pattern occur. Tran­ scriptional activation of eucaryotic genes is mediated by specific interac­ tions oftransacting factors with their respective DNA binding sites in Lhe control regions (promoters, enhancers) ofthe genes. This process is ofLen accompanied by changes in local chromatin strucLure, witnessed by the appearance of nuclease hypersensitive sites, as weil as by changes in protein-DNA interactions and, in the case of higher eucaryotes, alterations ofthe cytosine methylation pattern. The sole available experimental tech­ nique that permits the study ofthe latter phenomena at single nucleotide resolution is direct genomic sequencing/footprinting, pioneered by Church and Gilbert (1984). This method combines the chemical DNA­ sequencing procedure of Maxam amI Gilbert (1980) with thc detection 01' DNA sequences by electroblotting and indirect end-Iabeling by hybridiza­ tl0n. An alternative possibility is the novel procedure (Saluz and . lost, 1989), using Taq polymerase. The first steps 01' both meLhods are essen­ tially the same: total genomic DNA is digested wiLh a suilable restriction enzyme and the resulting DNA fragments are chemically sequeneed.

More recently, the widely expressed intuition that discrete sequences within these elements constitute binding sites for sequence-specific binding proteins has been confirmed, especially through the use of "footprinting" assays (for examples, Galas and Schmitz, 1978).

18. 2 Principle of FACE/Gel Retardation Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349 18. 3 Labelling of Oligosaccharides with ANTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350 18. 4 Screening of Carbohydrate Ligands for Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . 352 18. 5 Measurement of Binding Constant for the Interaction Between Protein and ANTS-Labelled Carbohydrate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355 18. 6 Measurement of Binding Constant for the Interaction Between Protein and Native Carbohydrate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 360 ~ The Application of Capillary Affinity Electrophoresis to the Analysis _ of Carbohydrate-Protein Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361 19. 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361 19. 2 Principle of CAE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 363 19. 3 Determination of Association Constants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364 19. 4 Technical Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366 General considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366 19. 5 Limitations of the Technique . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . 370 19. 6 Application of CAE to the Analysis of Carbohydrate-Protein Interactions . . . . . . 371 19. 7 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 375 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 377 20. 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379 Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380 20. 2 Technical Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381 20. 3 Sample Detection and Sample Recovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389 Autoradiography and staining . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389 Sample detection by blotting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389 Semipreparative ACE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 390 20. 4 Analysis of Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391 Measuring sample mobilities - calculating a retardation coefficient . . . . . . . . . . . . 391 Graphical analysis of data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 392 Interpreting ACE patterns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393 Reverse ACE . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 395 20. 5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397 Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398 References . . . .

ceptor-Binding Assay ................................................. 57 3.3 Results and Discussion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . 58 . . . . . . . . . . . . . 3.4 Troubleshooting ....................................................... 61 Impurity in PACAP27-Cys-NH............................................ 61 2 Low specific activity of the PACAP receptor despite a single band ............. 62 Acknowledgments ..................................................... 62 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . 63 . . . . . . . . . . . . . . . . . Photoreactive Biotinylated Peptide Ligands for Affinity Labeling ......... " 65 Summary ............................................................. 65 4.1 Introduction................................................ . . . . . . . .. . 66 . 4.2 Technical Procedures ................................................. " 67 Synthesis of a trifunctional photoactivatable biotinylating reagent ............. 67 Synthesis of photo reactive biotinylated peptide hormones ................... 67 Site-specific incorporation of biotin and photo labels in separate steps ........ 69 Photoaffinity labeling ................................................... 72 4.3 Results and Discussion .................................................. 76 Synthesis of photoactivatable insulins with permanent biotin labels ............ 76 Applications: Insulin .................................................... 78 VI Examples for other applications .......................................... 78 4.4 Troubleshooting....................................................... 79 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 . . . . . . . . . . . . . . . . . . .

This laboratory guide comes at a time when several other method books have already been published in this field. Interest was devoted to standardized procedures and culture conditions, avoiding dogmas such as those giving excessive importance to sophisticated culture media with endless adjustments for local or personal considerations.

A Safety Considerations Genomic sequencing involves a number of hazardous steps, such as high current, high voltage, radioactive and highly toxic chemicals. It is, therefore, absolutelyessen­ tial that the instructions of equipment manufacturers be followed and that particular attention is paid to the local and federal safety regulations. INTRODUCTION 9 B Introduction During the cloning of genomic DNA many of its characteristics are perma­ nently lost. It was therefore necessary to develop a new technique that would give us a closer look at a gene in its normal environment. The powerful technique of genomic sequencing, first described by Church and Gilbert (1984) now makes it possible to have a precise view of a given DNA sequence in a chromosome. This method combines the chemical DNA-sequencing procedure of Maxam and Gilbert (1980) with the detection of DNA sequences by electroblotting and indirect end-labeling by hybridization. Besides studies on the methylation state of single bases in a given gene (Nick et al. , 1986; Saluz and Jost, 1986; Saluz et al. , 1986), genomic sequencing can also be used to study specific DNA-protein interactions in vivo (Church et al. , 1985; Giniger et al. , 1985; Becker et al. , 1986; Ephrussi et al. , 1985; Martin et al. , 1986; Nick et al. , 1986; Zinn and Maniatis, 1986).

The understanding of molecular informa tion handling in nature is essential for the molecular optimization in chem istry, molecular biology, molecular pharmacology and therefore - as an ex ample - for the development of specifically acting drugs.

Biological processes in any living organism are based on selective interactions be tween particular biomolecules. If protein conductivity were introduced, then charges mov ing through the protein backbone might produce electromagnetic irradiation or ab sorption with spectral characteristics corresponding to energy distribution along the protein.

"One should rather go horne and mesh a net than jump into the pond and dive far fishes" (Chinese proverb) Recognizing the precise analytical question and planning the analysis according ly is certainly the first prerequisite for successful trace and ultratrace determina tions.

Twenty five years ago, Bill Stebbins presented the principles of animal psychophysics in an edited volume (Stebbins, 1970) describing an array of modem, creative methodologies for investigating the range of sensory systems in a variety of vertebrate species.