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Synthesis of Oligodeoxynucleotides Containing Sensitive Electrophiles

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Synthesis of Oligodeoxynucleotides Containing Sensitive Electrophiles Michigan Technological University Digital Commons @ Michigan Tech Dissertations, Master's Theses and Master's Reports 2019 Synthesis of Oligodeoxynucleotides Containing Sensitive Electrophiles Shahien Shahsavari Michigan Technological University, [email protected] Copyright 2019 Shahien Shahsavari Recommended Citation Shahsavari, Shahien, "Synthesis of Oligodeoxynucleotides Containing Sensitive Electrophiles", Open Access Dissertation, Michigan Technological University, 2019. https://doi.org/10.37099/mtu.dc.etdr/911 Follow this and additional works at: https://digitalcommons.mtu.edu/etdr Part of the Medicinal-Pharmaceutical Chemistry Commons, and the Organic Chemistry Commons SYNTHESIS OF OLIGODEOXYNUCLEOTIDES CONTAINING SENSITIVE ELECTROPHILES By Shahien Shahsavari A DISSERTATION Submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY In Chemistry MICHIGAN TECHNOLOGICAL UNIVERSITY 2019 © 2019 Shahien Shahsavari This dissertation has been approved in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY in Chemistry. Department of Chemistry Dissertation Advisor: Dr. Shiyue Fang Committee Member: Dr. Marina Tansova Committee Member: Dr. Tarun Dam Committee Member: Dr Feng Zhao Department Chair: Dr. John Jaszczak Table of Contents Preface..................................................................................................................................v Acknowledgements ............................................................................................................ vi Abstract ............................................................................................................................ viii Chapter 1 Introduction .........................................................................................................1 1.1 Oligodeoxynucleotides (ODNs) .......................................................................1 1.2 Applications of ODNs ......................................................................................1 1.3 Solid Phase ODN Synthesis .............................................................................1 1.4 Limitations of Solid Phase ODN Synthesis .....................................................3 1.5 The Need for Modified ODNs ..........................................................................4 1.6 Current Methods to Modify ODNs and Their Drawbacks ...............................4 1.7 Our Non-Nucleophilic Technology to Incorporate Electrophiles on ODN .....5 1.7.1 Dmoc Technology ...............................................................................6 1.7.2 Dmoc Dim Technology.......................................................................7 1.7.3 dM-Dmoc Technology ........................................................................9 References .................................................................................................................11 Chapter 2 Synthesis of Oligonucleotides Containing Electrophilic Groups ......................13 2.1 Introduction ....................................................................................................15 2.2 Results and Discussion ...................................................................................17 2.3 Conclusion ......................................................................................................25 2.4 Experimental Section .....................................................................................26 References .................................................................................................................40 Chapter 3 Sensitive ODN Synthesis Using Dim for Phosphate Protection .......................43 3.1 Introduction ....................................................................................................45 3.2 Results and Discussion ...................................................................................49 3.3 Conclusion ......................................................................................................59 3.4 Experimental Section .....................................................................................60 References .................................................................................................................72 Chapter 4 Electrophilic ODN Synthesis Using dM-Dmoc ................................................77 4.1 Introduction ....................................................................................................79 iii 4.2 Results and Discussion ...................................................................................84 4.3 Conclusion ......................................................................................................97 4.4 Experimental Section .....................................................................................98 References .......................................................................................110 4.5 References ....................................................................................................111 Appendix A. Supporting Information for Chapter 2 ........................................................114 Appendix B. Supporting Information for Chapter 3 ........................................................154 Appendix C. Supporting Information for Chapter 4 ........................................................214 iv Preface The initial ideas of all research projects in this dissertation were directed under the supervision of Dr. Shiyue Fang. All of the writing of this dissertation (Chapter 1 – 4) was carried out by Mr. Shahien Shahsavari and revised by Dr. Shiyue Fang. In chapter 2, Dr. Xi Lin and Dr. Jinsen Chen equally contributed to the experiments. The content was published in The American Chemical Society Organic Letters 2016, 18, 3870–3873. In chapter 3, all the experiments, purification, and data analysis were conducted by Mr. Shahien Shahsavari. The content has been submitted to The American Chemical Society Journal of Organic Chemistry. In chapter 4, all the experiments, purification, and data analysis were conducted by Mr. Shahien Shahsavari. The content has been accepted in Beilstein Journal of Organic Chemistry. v Acknowledgements I am deeply grateful for the patience, guidance, and support of my advisor Dr. Shiyue Fang. Words cannot describe how thankful and appreciative I am to his open- mindedness and his eager willingness to contribute to the success of everyone’s journey in his laboratory. I am grateful for the support of my former and present laboratory members Dr. Suntara Fueangfung, Dr. Durga Pokharel, Dr. Ashok Khanal, Dr. Jinsen Chen, Mr. Bhaskar Halami, Ms. Adikari Mudiyanselage Dhananjani Nisansala Eriyagama (DJ), Ms. Komal Chillar, Mr. Criss Yin, Mr. Chase McNamara, Mr. James Gooding, Mr. Travis Wigstrom, Ms. Emily Bromely, and Ms. Savannah Joslin. All contributed to an extremely friendly and productive laboratory environment. I greatly thank my committee members Dr. Feng Zhao, Dr. Tarun Dam, and Dr. Marina Tanasova for their time, support, and input regarding my dissertation and defense. I would like to thank the Department of Chemistry for providing financial assistance throughout this journey. Other financial support sources are also appreciated such as the Portage Health Foundation Graduate Fellowship, Life Science and Technology (LSTI), Graduate Student Government (GSG), as well as the funding agencies NIH and NSF. The assistance from the all staff of the Department of Chemistry such as Charlene Page, Denise Laux, Jerry Lutz, Dean Seppala, Kimberly McMullan, and Joel Smith is greatly appreciated. vi I would like to express special thanks to my family whose unconditional love and support pushed me through this journey. My parents (Ray and Sarah) and my brother (Ashkan) have been a true blessing for which I thank God Almighty daily. I leave this last section for my dearest friend Vagarshak Begoyan whose love and support has been unimaginable. Thank you all for making this possible. vii Abstract Oligodeoxynucleotides (ODNs) containing electrophilic groups are useful in many studies including antisense drug development and DNA/protein interaction. Due to the use of strong nucleophiles for cleavage and deprotection, traditional ODN synthesis methods are not suitable for their preparation. To solve this problem, a new ODN synthesis technology using the 1,3-dithiane-2-yl-methoxycarbonyl (Dmoc) function as protecting groups and linker has been developed. Furthermore, Dmoc-derivatives were developed to demonstrate the feasibility of the technology. The Dmoc and Dmoc derivative functions are stable under all ODN synthesis conditions using the phosphoramidite chemistry. Upon oxidation of the sulfides in them, because of the drastically increased acidity of H-2, the groups and linker are readily cleaved under nearly non-nucleophilic conditions. Many sensitive electrophiles were able to be incorporated on DNA strands successfully using these technologies. These include but are not limited to sensitive thioester, ethyl ester, alkyl chloride, and α-chloroacetamide moieties. viii Chapter 1 Introduction 1.1 Oligodeoxynucleotides (ODNs) Oligodeoxynucleotides (ODNs) are single-stranded deoxyribonucleic acids, also known as DNA, which consist of four nucleotides – deoxythymidine (dT), deoxycytidine (dC), deoxyadenosine (dA), and deoxyguanosine (dG). All four nucleotides contain their respective nucleobase, a 2’-deoxribose sugar moiety, and are linked
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