Embracing proteins: structural themes in aptamer–protein complexes

Ellington, 1990, In vitro selection of RNA molecules that bind specific ligands, Nature, 346, 818, 10.1038/346818a0 Tuerk, 1990, Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase, Science, 249, 505, 10.1126/science.2200121 Hermann, 2000, Adaptive recognition by nucleic acid aptamers, Science, 287, 820, 10.1126/science.287.5454.820 Kim, 1974, The general structure of transfer RNA molecules, Proc Natl Acad Sci U S A, 71, 4970, 10.1073/pnas.71.12.4970 Robertus, 1974, Structure of yeast phenylalanine tRNA at 3Å resolution, Nature, 250, 546, 10.1038/250546a0 Uhlenbeck, 1997, RNA structure comes of age, Cell, 90, 833, 10.1016/S0092-8674(00)80348-7 Hendrix, 2005, RNA structural motifs: building blocks of a modular biomolecule, Q Rev Biophys, 38, 221, 10.1017/S0033583506004215 Holbrook, 2005, RNA structure: the long and the short of it, Curr Opin Struct Biol, 15, 302, 10.1016/j.sbi.2005.04.005 Leontis, 2006, The building blocks and motifs of RNA architecture, Curr Opin Struct Biol, 16, 279, 10.1016/j.sbi.2006.05.009 Klosterman, 2002, SCOR: a structural classification of RNA database, Nucleic Acids Res, 30, 392, 10.1093/nar/30.1.392 Nagaswamy, 2002, NCIR: a database of non-canonical interactions in known RNA structures, Nucleic Acids Res, 30, 395, 10.1093/nar/30.1.395 Tamura, 2004, SCOR. Structural classification of RNA, version 2.0, Nucleic Acids Res, 32, D182, 10.1093/nar/gkh080 McKeague, 2015, Analysis of in vitro aptamer selection parameters, J Mol Evol, 10.1007/s00239-015-9708-6 Ozer, 2014, New technologies provide quantum changes in the scale, speed, and success of SELEX methods and aptamer characterization, Mol Ther Nucleic Acids, 3, e183, 10.1038/mtna.2014.34 Mirmira, 1996, NMR structure of a bacteriophage T4 RNA hairpin involved in translational repression, Biochemistry, 35, 7664, 10.1021/bi960414y Bullock, 2000, Tertiary core rearrangements in a tight binding transfer RNA aptamer, Nat Struct Biol, 7, 497, 10.1038/75910 Convery, 1998, Crystal structure of an RNA aptamer-protein complex at 2.8Å resolution, Nat Struct Biol, 5, 133, 10.1038/nsb0298-133 Rowsell, 1998, Crystal structures of a series of RNA aptamers complexed to the same protein target, Nat Struct Biol, 5, 970, 10.1038/2946 Davlieva, 2014, Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis, Nucleic Acids Res, 42, 10795, 10.1093/nar/gku743 Huang, 2003, Crystal structure of NF-kappaB (p50)2 complexed to a high-affinity RNA aptamer, Proc Natl Acad Sci U S A, 100, 9268, 10.1073/pnas.1632011100 Padlan, 2014, An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates, RNA, 20, 447, 10.1261/rna.043034.113 Tesmer, 2012, Molecular mechanism for inhibition of g protein-coupled receptor kinase 2 by a selective RNA aptamer, Structure, 20, 1300, 10.1016/j.str.2012.05.002 Long, 2008, Crystal structure of an RNA aptamer bound to thrombin, RNA, 14, 2504, 10.1261/rna.1239308 Nomura, 2010, Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex, Nucleic Acids Res, 38, 7822, 10.1093/nar/gkq615 Oberthur, 2015, Crystal structure of a mirror-image L-RNA aptamer (Spiegelmer) in complex with the natural L-protein target CCL2, Nat Commun, 6, 6923, 10.1038/ncomms7923 Yatime, 2015, Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer, Nat Commun, 6, 6481, 10.1038/ncomms7481 Cheung, 2013, Structural basis for discriminatory recognition of Plasmodium lactate dehydrogenase by a DNA aptamer, Proc Natl Acad Sci U S A, 110, 15967, 10.1073/pnas.1309538110 Huang, 2009, A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1, Structure, 17, 1476, 10.1016/j.str.2009.09.011 Russo Krauss, 2011, Thrombin-aptamer recognition: a revealed ambiguity, Nucleic Acids Res, 39, 7858, 10.1093/nar/gkr522 Davies, 2012, Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets, Proc Natl Acad Sci U S A, 109, 19971, 10.1073/pnas.1213933109 Gelinas, 2014, Crystal structure of interleukin-6 in complex with a modified nucleic acid ligand, J Biol Chem, 289, 8720, 10.1074/jbc.M113.532697 Jarvis, 2015, Non-helical DNA triplex forms a unique aptamer scaffold for high affinity recognition of nerve growth factor, Structure, 23, 1293, 10.1016/j.str.2015.03.027 Leontis, 2003, Analysis of RNA motifs, Curr Opin Struct Biol, 13, 300, 10.1016/S0959-440X(03)00076-9 Phan, 2005, An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase, Proc Natl Acad Sci U S A, 102, 634, 10.1073/pnas.0406278102 Gold, 2010, Aptamer-based multiplexed proteomic technology for biomarker discovery, PLoS One, 5, e15004, 10.1371/journal.pone.0015004 Rohloff, 2014, Nucleic acid ligands with protein-like side chains: modified aptamers and their use as diagnostic and therapeutic agents, Mol Ther Nucleic Acids, 3, e201, 10.1038/mtna.2014.49 Vaught, 2010, Expanding the chemistry of DNA for in vitro selection, J Am Chem Soc, 132, 4141, 10.1021/ja908035g Mian, 1991, Structure, function and properties of antibody binding sites, J Mol Biol, 217, 133, 10.1016/0022-2836(91)90617-F Ramaraj, 1824, Antigen–antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures, Biochim Biophys Acta, 2012, 520 Sokoloski, 2011, Prevalence of syn nucleobases in the active sites of functional RNAs, RNA, 17, 1775, 10.1261/rna.2759911 Kligun, 2015, The role of RNA conformation in RNA–protein recognition, RNA Biol, 12, 720, 10.1080/15476286.2015.1040977 Duarte, 1998, Stepping through an RNA structure: a novel approach to conformational analysis, J Mol Biol, 284, 1465, 10.1006/jmbi.1998.2233 Wadley, 2004, The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery, Nucleic Acids Res, 32, 6650, 10.1093/nar/gkh1002 Ochsner, 2014, Systematic selection of modified aptamer pairs for diagnostic sandwich assays, Biotechniques, 56, 125, 10.2144/000114134 Lawrence, 1993, Shape complementarity at protein/protein interfaces, J Mol Biol, 234, 946, 10.1006/jmbi.1993.1648 Reiter, 2008, DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer, Nucleic Acids Res, 1227, 10.1093/nar/gkm1141 Lee, 2008, Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF165-targeting aptamer, Macugen, FEBS Lett, 582, 1835, 10.1016/j.febslet.2008.05.003 Williamson, 2000, Induced fit in RNA–protein recognition, Nat Struct Biol, 7, 834, 10.1038/79575 DeLano, 2002 Baker, 2001, Electrostatics of nanosystems: application to microtubules and the ribosome, Proc Natl Acad Sci U S A, 98, 10037, 10.1073/pnas.181342398 Collaborative Computational Project N, 1994, The CCP4 suite: programs for protein crystallography, Acta Crystallogr D: Biol Crystallogr, 50, 760, 10.1107/S0907444994003112 Ban, 2000, The complete atomic structure of the large ribosomal subunit at 2.4 A resolution, Science, 289, 905, 10.1126/science.289.5481.905 Padavattan, 2015, Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming, Biochem Biophys Res Commun, 464, 929, 10.1016/j.bbrc.2015.07.070 Qin, 2014, Cocrystal structures of glycyl-tRNA synthetase in complex with tRNA suggest multiple conformational states in glycylation, J Biol Chem, 289, 20359, 10.1074/jbc.M114.557249