Aptamers Selected by Cell-SELEX for Theranostics PDF
Preview Aptamers Selected by Cell-SELEX for Theranostics
Weihong Tan · Xiaohong Fang E ditors Aptamers Selected by Cell-SELEX for Theranostics Aptamers Selected by Cell-SELEX for Theranostics Weihong Tan Xiaohong Fang (cid:129) Editors Aptamers Selected by Cell-SELEX for Theranostics 123 Editors WeihongTan Xiaohong Fang Molecular Science andBiomedicine Instituteof Chemistry Laboratory,StateKey Laboratoryfor ChineseAcademy ofSciences Chemo/Bio-Sensingand Chemometrics Beijing Collegeof Chemistryand Chemical China Engineering HunanUniversity Changsha China and Department of Chemistry Universityof Florida Gainesville, FL USA ISBN 978-3-662-46225-6 ISBN 978-3-662-46226-3 (eBook) DOI 10.1007/978-3-662-46226-3 LibraryofCongressControlNumber:2015931245 SpringerHeidelbergNewYorkDordrechtLondon ©Springer-VerlagBerlinHeidelberg2015 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilarmethodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthis book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained hereinorforanyerrorsoromissionsthatmayhavebeenmade. Printedonacid-freepaper Springer-VerlagGmbHBerlinHeidelbergispartofSpringerScience+BusinessMedia (www.springer.com) Foreword One of the great disappointments in chemistry over the past half-century has been thefailureoftheorytoallowchemiststodesignmoleculesthatbindspecificallyin aqueous solution to other molecules. This is, of course, the “medicinal chemistry problem”; a classical pharmaceutical is simply a molecule that binds to a protein target with a therapeutically interesting affinity, say a dissociation constant of less than one nanomolar. While heuristic processes are available to sort through hun- dreds of lead molecules to get dozens of hits that might generate single drug candidates ready for clinical trials, these rely on only broad theoretical concepts and, more frequently, chemical intuition, rarely on constructively detailed design. Even the three-dimensional molecular models for protein target that are now often routinethankstomoderncrystallographyhavenotdeliveredadefinitivesolutionto this problem. The complexities of molecular interactions as well as the challenges of modeling the solvent in which they must occur continue to defeat the largest computers and the best theory. The inability of theory to support explicit molecular design stands in stark contrast to the ability of natural biology to deliver molecules that bind other mol- ecules,oftenwithexquisitespecificityandenormousaffinity.Naturalbiologydoes not, of course, exploit explicit design. Rather, the binding molecules that nature delivers come from random variation followed by natural selection, where specif- ically tight binding enhances the fitness of the host organism. The binding mole- cules are often proteins and, in the case of antibodies, a protein scaffold that has evolvedtosupportrandomvariationinabindingpocket.Here,naturalselectionfor tightly binding antibodies occurs within a single organism. However, a primary antibodylibraryofperhaps100millionspeciesissufficient,followingmutation,to generatebinderswithsub-nanomolaraffinities,morethanenoughtosupportfitness. Itwasagainstthisbackdropoftheoreticaldisappointmentthatinthelate1980s, syntheticbiologistsdecidedtotrytodolaboratoryinvitroevolution(LIVE).Here, nucleic acids, not proteins, were to provide the framework from which selective binding molecules were to be delivered “on demand”. As Jack Szostak, one of the developers of this technology was later to write, it was “an idea whose time had come”. Not long before, Thomas Cech, Sidney v vi Foreword Altman, and others had found specific examples where natural biology used RNA molecules to catalyze reactions under physiological conditions. A number of these wereinvolvedintheprocessingofRNAmoleculesthatwereusedbytheribosome tobiosynthesizeproteins.Theribosomeitselfwassuspectedtobe,andlatershown to be, a catalytic RNA molecule. Further, an analysis of the commonalities of organisms all cross Earth suggested that we had all descended from an “RNA world”, a biosphere where the only genetically encoded biological catalysts were themselvesRNAmolecules.Indeed,somehadsuggestedthattheRNAworldhada sufficient number of RNA catalysts to support a complex metabolism. IflibrariesofRNAcouldleadtocatalyticRNAmoleculesondemand,surely(it was thought) that they could solve a simpler problem: creating binding RNA molecules on demand. Accordingly, Larry Gold, Andrew Ellington, and Jack Szostak himself undertook to develop the technology that would create binding moleculesstartingwithRNAlibraries.GeraldJoyceandothersthenfollowedwith efforts to do the same thing where DNA was the matrix. In either case, perhaps 100 trillion different DNA or RNA (collectively xNA) species were synthesized in a library. The library was then presented to a target receptor, in an experimental architecture that allowed the receptor to extract from these libraries specific binding xNA species. Then, the special ability of nucleic acids to direct their own replication would allow amplification to follow. A few binding molecules would have descendants by the polymerase chain reaction. Perhaps with some mutation, laboratory selection and evolution would produce higher affinity binding molecules by a process analogous to the maturation of antibody affinity. Perhaps xNA “aptamers” (as they came to be called) could have an affinity that would rival the affinity of antibodies. Of course, this was easier said than done, and a rich literature emerged in the followingquartercenturyattemptingtoachievethisgoal.Muchofthisliteratureis represented by the chapters in this book. However, these chapters take the next steps in many dimensions. For example, rather than aptamers that bind to simple protein or small molecule targets, the practitioners who contribute to this volume haveincludedcellsasthemajortargetsforbindingmoleculesondemand.Thefield of “Cell SELEX” is today exploding. Thisbookisfocusedoncell-targetedselection,andiseditedbythepeoplewho firstmadeitworkconvincingly.Inthisrespect,ithasthecharacterofamonograph, withtheeditorsbeingtheco-authorsofmanychapters,andwithstillotherchapters being written by those who were trained in the editor’s laboratories. Some of the unique features of this book include its description of the cell- SELEX process itself, with potential applications in molecular medicine being linked in a logical and coherent way. This reflects the design of the book chapters by the editors to allow individual authors to make contributions that blend coher- ently with the other contributions. Thus, the product contrasts with many edited books where each set of authors has written a self-standing chapter that need not blend with the other chapters. In the chapters on medical applications, the visionary question is addressed: How should we use cell-targeted aptamers? Binding is often insufficient to meet a Foreword vii particular biomedical goal. One often also wants to capture, signal, or create downstream action. This book has numerous chapters that meet this challenge, including labeling, immobilization, and signaling that actually use the binding molecules created “on demand”. The book contains individual chapters on each. My own contributions to this field have been minimal. In December 1985, just before I moved my laboratory to Switzerland to pursue these goals, I had dinner with Jack Szostak, who told me of his plans to do directed evolution offunctional RNAlibraries.MycommenttoJackwasbasedonachemist’sperception.Ipointed out to Jack that unlike proteins, which have a rich collection offunctional groups, nucleic acids have very few of the moieties that are needed to do catalysis or binding. Further, with only four nucleotides, xNA as delivered to us by prebiotic chemistry and subsequent evolution, has too few folding motifs, too much con- formational ambiguity, and too little structural diversity to have any hope of rivaling antibodies as a matrix to support binding molecules on demand. However,IexplainedthateveningtoJack,therewasasolutiontothisproblem, recorded in a witnessed notebook on November 14. All one needed to do was rearrange the hydrogen bonding moieties on the nucleobases to give different hydrogenbondingpatterns. Ifonedidso,onecouldcreate12different nucleotides that should be able to form six independently replicable nucleobase pairs. Some of these could carry functional groups similar to those found on proteins. In short, this was the invention of a single biopolymer that had the replicability of nucleic acids and the functional group diversity of proteins. Jack’sresponsewasprescient.“Steve,”Irememberhimsaying,“itwilltakeyou 10years tomake thesemoleculesandanother10yearstogetpolymerasestoeven acceptthem”inaPCRreaction.Hewasapproximatelycorrect.Onlylastyearwere we finally able to do LIVE with an AEGIS alphabet. Nevertheless, I am delighted to see a chapter by Liqin Zhang in this volume, showing the first examples where an artificially expanded genetic system has been usedtocreate bindingmoleculesondemand.Catalysts arenowfollowing,andthe deficienciesoftheDarwiniansystempresentedtousbynaturemightnowbesolved bymoleculardesign,notexplicitlyforeveryspecifictarget-receptorinteraction,but ratherbythedesignofasystemthatismoreevolvableandthusbetterabletocreate functional species. Steven A. Benner Foundation for Applied Molecular Evolution and The Westheimer Institute for Science and Technology Gainesville, FL Contents 1 Introduction to Aptamer and Cell-SELEX. . . . . . . . . . . . . . . . . . 1 Libo Zhao, Weihong Tan and Xiaohong Fang 2 Cell-SELEX: Aptamer Selection Against Whole Cells. . . . . . . . . . 13 Dihua Shangguan, Tao Bing and Nan Zhang 3 Unnatural Nucleic Acids for Aptamer Selection . . . . . . . . . . . . . . 35 Liqin Zhang 4 Cell-Specific Aptamer Characterization . . . . . . . . . . . . . . . . . . . . 67 Tao Chen, Cuichen Wu and Weihong Tan 5 Molecular Engineering to Enhance Aptamer Functionality. . . . . . 89 Da Han, Cuichen Wu and Weihong Tan 6 Aptamers-GuidedDNANanomedicineforCancerTheranostics.... 111 Guizhi Zhu, Liping Qiu, Hongmin Meng, Lei Mei and Weihong Tan 7 Properties of Nucleic Acid Amphiphiles and Their Biomedical Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139 Haipeng Liu 8 Aptamer-Based Hydrogels and Their Applications. . . . . . . . . . . . 163 Chun-Hua Lu, Xiu-Juan Qi, Juan Li and Huang-Hao Yang 9 Cell-Specific Aptamers for Disease Profiling and Cell Sorting. . . . 197 Kwame Sefah, Joseph Phillips and Cuichen Wu ix x Contents 10 Using Cell-Specific Aptamer-Nanomaterial Conjugates for Cancer Cell Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 Zhi Zhu 11 Cell-Specific Aptamers for Molecular Imaging. . . . . . . . . . . . . . . 239 Jing Zheng, Chunmei Li and Ronghua Yang 12 Discovery of Biomarkers Using Aptamers Evolved in Cell-SELEX Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265 Prabodhika Mallikaratchy, Hasan Zumrut and Naznin Ara 13 Cell-Specific Aptamers for Targeted Therapy. . . . . . . . . . . . . . . . 301 Yue He, Andrea del Valle and Yu-Fen Huang 14 The Clinical Application of Aptamers: Future Challenges and Prospects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339 Yanling Song, Huimin Zhang, Zhi Zhu and Chaoyong Yang Contributors Naznin Ara Department of Chemistry, Lehman College-City University of New York, Bronx, NY, USA TaoBing BeijingNationalLaboratoryforMolecularSciences,KeyLaboratoryof Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, People’s Republic of China Tao Chen Genentech Inc., South San Francisco, CA, USA Xiaohong Fang Beijing National Laboratory for Molecular Sciences, Key Labo- ratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China Da Han Intel Corporation, Hillsboro, OR, USA; Departments of Chemistry Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter- face, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, USA Yue He Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan, ROC Yu-Fen Huang Department of Biomedical Engineering and Environmental Sci- ences, National Tsing Hua University, Hsinchu, Taiwan, ROC ChunmeiLi KeyLaboratoryofLuminescentandReal-TimeAnalyticalChemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing,China;BeijingNationalLaboratoryforMolecularSciences,Instituteof Chemistry, Chinese Academy of Sciences, Beijing,China Juan Li The Key Lab of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry, Fuzhou University, Fuzhou, China HaipengLiu DepartmentofChemicalEngineeringandMaterialsScience,Wayne State University, Detroit, MI, USA xi
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