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FLUORESCENT LABELING REAGENTS OPTIMIZED for CAPILLARY ELECTROPHORETIC SEPARATIONS a Dissertation by ROY TONACAO ESTRADA, III Su

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FLUORESCENT LABELING REAGENTS OPTIMIZED for CAPILLARY ELECTROPHORETIC SEPARATIONS a Dissertation by ROY TONACAO ESTRADA, III Su FLUORESCENT LABELING REAGENTS OPTIMIZED FOR CAPILLARY ELECTROPHORETIC SEPARATIONS A Dissertation by ROY TONACAO ESTRADA, III Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2010 Major Subject: Chemistry FLUORESCENT LABELING REAGENTS OPTIMIZED FOR CAPILLARY ELECTROPHORETIC SEPARATIONS A Dissertation by ROY TONACAO ESTRADA, III Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Gyula Vigh Committee Members, Kevin Burgess Paul A. Lindahl Emile A. Schweikert Victor M. Ugaz Head of Department, David H. Russell May 2010 Major Subject: Chemistry iii ABSTRACT Fluorescent Labeling Reagents Optimized for Capillary Electrophoretic Separations. (May 2010) Roy Tonacao Estrada, III, B.S., University of San Carlos Chair of Advisory Committee: Dr. Gyula Vigh Fluorescent labeling can improve the detection sensitivity in capillary electrophoretic (CE) separations down to attomolar concentrations. However, most fluorescent labels are not compatible with CE because their fluorescence properties and charge states are pH-dependent, they are often hydrophobic and they have a tendency to significantly change the properties of the analytes after labeling. A group of fluorescent labeling reagents have been prepared whose fluorophores have properties that are optimized for CE separations. These fluorophores have fluorescence properties and charge states that are independent of pH in the 2 < pH < 11 range. Their excitation maxima are also compatible with the 488 nm line of the Argon ion laser. A mono-cationic acridine-based fluorescent label was prepared and was found to not shift the pI of a labeled model protein in capillary isoelectric focusing separation (cIEF). Lower loading, due to increased sensitivity, led to better resolution of closely spaced isoform peaks having a pI = 0.05. A tri-anionic pyrene-based fluorescent labeling reagent was also synthesized and was used in the sodium dodecyl sulfate – capillary gel electrophoresis (SDS-CGE) separation of proteins. The fluorophore led to an LOQ in iv the nM range, and did not alter the migration behavior of proteins in the sieving matrix. A third fluorescent labeling reagent was developed as a solid phase reagent (SPR) where the fluorophore was immobilized on a solid surface through a cleavable anchor. The fluorophore is di-anionic and is based on pyrene. The SPR was designed to allow the simultaneous capture and labeling of an analyte and the efficient release of the label- analyte conjugate under mild acidic conditions. The use of the SPR allowed the labeling of a diamine whose concentration was in the low nanomolar range. The SPR opens up the possibility for mono-labeling and proportional multiple labeling of proteins. v To my wife, Faye, who is my home and the reason that I am. To my children, Francesca and Benedict, who give the simplest, most beautiful pleasures. To Mommy Suzette and Daddy Dong, who took care of us no matter what and taught us patience, forgiveness and love. To Mama Vering, who is always there for us and taught us so many of life’s values. To Mama Winda, who made so many things possible through her prayers and support. vi ACKNOWLEDGEMENTS I thank Dr. Gyula Vigh for instilling in me a passion for life. He has taught me with tremendous enthusiasm and patience. I thank him for taking care of me as a father would. I express my gratitude to the members of our group, both past and present. Thanks to Brent, Silvia, Kingsley, Omar, Shulan, Ann, Evan, Nellie, Sanjiv, Peniel, Brian, Rob, Edward, Ming-Chien and Mavreen for being such good friends. Thanks to Dr. Kevin Burgess who has provided a lot of useful insights on the organic chemistry part of my research. I also give my thanks to Bill, Stephanie, Brad, Vanessa, Shane and Yohannes for their enormous help in acquiring (and re-acquiring) numerous mass spectra. I acknowledge Beckman Coulter and the Gradipore Chair of Separation Science for making this work possible through their financial support. And most of all, all praise, honor, glory and thanksgiving to God who can never be outdone in His generosity, mercy and love. vii TABLE OF CONTENTS Page ABSTRACT .............................................................................................................. iii DEDICATION .......................................................................................................... v ACKNOWLEDGEMENTS ...................................................................................... vi TABLE OF CONTENTS .......................................................................................... vii LIST OF FIGURES ................................................................................................... xiii LIST OF TABLES .................................................................................................... xxiv 1 INTRODUCTION ................................................................................................ 1 1.1 Capillary Electrophoretic Separation of Proteins ................................. 1 1.2 Fluorescence Detection of Proteins ...................................................... 1 1.3 Fluorescent Labeling of Proteins .......................................................... 2 1.4 Limitations of Existing Fluorescent Labeling Reagents ...................... 3 1.4.1 Hydrophobicity ...................................................................... 3 1.4.2 pH-dependent Fluorescence .................................................. 5 1.4.3 pH-dependent Charge States ................................................. 6 1.4.4 Changes in the Properties of Proteins after Labeling ............ 7 2 DEVELOPMENT OF A pH-INDEPENDENT ACRIDINE-BASED FLUORESCENT LABELING REAGENT ......................................................... 9 2.1 Design and Synthesis ........................................................................... 9 2.1.1 Background and Objectives .................................................. 9 2.1.1.1 Charge State ...................................................... 9 2.1.1.2 pH-independent Fluorescence Properties .......... 14 2.1.1.3 Tether and Reactive Arm .................................. 17 2.1.2 Materials and Methods .......................................................... 18 2.1.2.1 Synthesis of Sulfopropylated Acridine Orange 6 ............................................................ 19 2.1.2.2 Recrystallization of Sulfopropylated Acridine Orange 6 ............................................. 20 2.1.2.3 Synthesis of Sulfonyl Chloride 7 ....................... 20 2.1.2.4 Synthesis of Sulfonamide 8 ............................... 21 viii Page 2.1.2.5 Synthesis of Acridine Orange Carboxylic Acid 9 ............................................. 21 2.1.2.6 Synthesis of Acridine Orange N- Hydroxysuccinimidyl Ester 10 .......................... 21 2.1.3 Results and Discussion .......................................................... 22 2.1.3.1 Quaternarization of Acridine Orange ................ 22 2.1.3.2 Extension of the Tether .................................... 27 2.1.3.3 Activation of the Carboxylate to the Amine-reactive Group ....................................... 31 2.1.3.4 Water Solubility and Hydrophilicity ................. 32 2.2 Spectral Properties ................................................................................ 33 2.2.1 Background and Objectives .................................................. 33 2.2.2 Materials and Methods .......................................................... 34 2.2.3 Results and Discussion .......................................................... 34 2.3 Labeling Reactions Using the Acridine Orange-based Fluorescent Label ................................................................................. 39 2.3.1 Background and Objectives .................................................. 39 2.3.2 Materials and Methods .......................................................... 40 2.3.2.1 Labeling of Small Amines and Their Analysis by CE-LIF ........................................... 40 2.3.2.2 Protein Labeling and Their Analysis by SDS-CGE-LIF ................................................... 41 2.3.2.3 Synthesis of the Fluorescent pI Markers ........... 42 2.3.2.4 Labeling of Chicken Ovalbumin and Its Analysis by SDS-CGE-LIF ............................... 43 2.3.3 Results and Discussion .......................................................... 44 2.3.3.1 Labeling of Small Amines ................................. 44 2.3.3.2 Synthesis of Fluorescent pI Markers for cIEF-LIF ............................................................ 47 2.3.3.3 cIEF Analysis of Labeled Chicken Ovalbumin ......................................................... 55 2.4 Concluding Remarks ............................................................................ 60 3 DEVELOPMENT OF A pH-INDEPENDENT PYRENE-BASED FLUORESCENT LABELING REAGENT ......................................................... 61 3.1 Introduction .......................................................................................... 61 3.2 Optimization of the Sulfonamidation Step ........................................... 64 3.2.1 Background and Objectives .................................................. 64 3.2.2 Materials and Methods .......................................................... 65 3.2.2.1
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