Minireview
Reading Polymers: Sequencing of Natural and Synthetic Macromolecules
Dr. Hatice Mutlu,
Dr. Jean-François Lutz,
Dr. Hatice Mutlu
Precision Macromolecular Chemistry, Institut Charles Sadron, UPR22-CNRS, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2 (France)
Search for more papers by this authorCorresponding Author
Dr. Jean-François Lutz
Precision Macromolecular Chemistry, Institut Charles Sadron, UPR22-CNRS, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2 (France)
Precision Macromolecular Chemistry, Institut Charles Sadron, UPR22-CNRS, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2 (France)Search for more papers by this authorDr. Hatice Mutlu,
Dr. Jean-François Lutz,
Dr. Hatice Mutlu
Precision Macromolecular Chemistry, Institut Charles Sadron, UPR22-CNRS, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2 (France)
Search for more papers by this authorCorresponding Author
Dr. Jean-François Lutz
Precision Macromolecular Chemistry, Institut Charles Sadron, UPR22-CNRS, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2 (France)
Precision Macromolecular Chemistry, Institut Charles Sadron, UPR22-CNRS, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2 (France)Search for more papers by this authorGraphical Abstract
Read the small print: Sophisticated sequencing methods have been developed for deciphering the sequences of proteins and nucleic acids. Can these tools be transfered to the characterization of monomer sequences in synthetic polymers? The techniques employed in both fields are compared and critically analyzed.
Abstract
The sequencing of biopolymers such as proteins and DNA is among the most significant scientific achievements of the 20th century. Indeed, modern chemical methods for sequence analysis allow reading and understanding the codes of life. Thus, sequencing methods currently play a major role in applications as diverse as genomics, gene therapy, biotechnology, and data storage. However, in terms of fundamental science, sequencing is not really a question of molecular biology but rather a more general topic in macromolecular chemistry. Broadly speaking, it can be defined as the analysis of comonomer sequences in copolymers. However, relatively different approaches have been used in the past to study monomer sequences in biological and manmade polymers. Yet, these “cultural” differences are slowly fading away with the recent development of synthetic sequence-controlled polymers. In this context, the aim of this Minireview is to present an overview of the tools that are currently available for sequence analysis in macromolecular science.
References
- 1
- 1aInternational Human Genome Sequencing Consortium, Nature 2001, 409, 860–921;
- 1bJ. C. Venter, et al., Science 2001, 291, 1304–1351.
- 2J. R. Ecker, W. A. Bickmore, I. Barroso, J. K. Pritchard, Y. Gilad, E. Segal, Nature 2012, 489, 52–55.
- 3E. S. Lander, Nature 2011, 470, 187–197.
- 4M. Bergmann, C. Niemann, J. Biol. Chem. 1938, 122, 577–596.
- 5M. F. Perutz, Nature 1942, 149, 491–494.
- 6F. Sanger, Nature 1948, 162, 491–492.
- 7F. Sanger, H. Tuppy, Biochem. J. 1951, 49, 481–490.
- 8F. Sanger, S. Nicklen, A. R. Coulson, Proc. Natl. Acad. Sci. USA 1977, 74, 5463–5467.
- 9A. M. Maxam, W. Gilbert, Proc. Natl. Acad. Sci. USA 1977, 74, 560–564.
- 10
- 10aR. N. Zuckermann, J. M. Kerr, S. B. H. Kent, W. H. Moos, J. Am. Chem. Soc. 1992, 114, 10646–10647;
- 10bC. Y. Cho, E. J. Moran, S. R. Cherry, J. C. Stephans, S. P. Fodor, C. L. Adams, A. Sundaram, J. W. Jacobs, P. G. Schultz, Science 1993, 261, 1303–1305;
- 10cL. Hartmann, H. G. Börner, Adv. Mater. 2009, 21, 3425–3431.
- 11
- 11aD. J. Hill, M. J. Mio, R. B. Prince, T. S. Hughes, J. S. Moore, Chem. Rev. 2001, 101, 3893–4012;
- 11bE. Yashima, K. Maeda, H. Iida, Y. Furusho, K. Nagai, Chem. Rev. 2009, 109, 6102–6211;
- 11cG. Guichard, I. Huc, Chem. Commun. 2011, 47, 5933–5941.
- 12
- 12aJ.-F. Lutz, M. Ouchi, D. R. Liu, M. Sawamoto, Science 2013, 341, 1238149;
- 12bN. Badi, J.-F. Lutz, Chem. Soc. Rev. 2009, 38, 3383–3390;
- 12cJ.-F. Lutz, Polym. Chem. 2010, 1, 55–62.
- 13
- 13aS. Pfeifer, J.-F. Lutz, J. Am. Chem. Soc. 2007, 129, 9542–9543;
- 13bS. Ida, T. Terashima, M. Ouchi, M. Sawamoto, J. Am. Chem. Soc. 2009, 131, 10808–10809;
- 13cS. Pfeifer, Z. Zarafshani, N. Badi, J.-F. Lutz, J. Am. Chem. Soc. 2009, 131, 9195–9196;
- 13dK. Satoh, et al., Nat. Commun. 2010, 1, 6;
- 13eY. Hibi, M. Ouchi, M. Sawamoto, Angew. Chem. 2011, 123, 7572–7575;
10.1002/ange.201103007 Google ScholarAngew. Chem. Int. Ed. 2011, 50, 7434–7437;
- 13fM. Zamfir, J.-F. Lutz, Nat. Commun. 2012, 3, 1138;
- 13gP. Espeel, L. L. G. Carrette, K. Bury, S. Capenberghs, J. C. Martins, F. E. Du Prez, A. Madder, Angew. Chem. 2013, 125, 13503–13506;
10.1002/ange.201307439 Google ScholarAngew. Chem. Int. Ed. 2013, 52, 13261–13264;
- 13hB. Lewandowski, G. De Bo, J. W. Ward, M. Papmeyer, S. Kuschel, M. J. Aldegunde, P. M. E. Gramlich, D. Heckmann, S. M. Goldup, D. M. D’Souza, A. E. Fernandes, D. A. Leigh, Science 2013, 339, 189–193;
- 13iJ. Niu, R. Hili, D. R. Liu, Nat Chem. 2013, 5, 282–292;
- 13jT. G. W. Edwardson, K. M. M. Carneiro, C. J. Serpell, H. F. Sleiman, Angew. Chem. 2014, 126, 4655–4659;
10.1002/ange.201310937 Google ScholarAngew. Chem. Int. Ed. 2014, 53, 4567–4571;
- 13kS. C. Solleder, M. A. R. Meier, Angew. Chem. 2014, 126, 729–732;
10.1002/ange.201308960 Google ScholarAngew. Chem. Int. Ed. 2014, 53, 711–714.
- 14
- 14aJ.-F. Lutz, Acc. Chem. Res. 2013, 46, 2696–2705;
- 14bT. T. Trinh, L. Oswald, D. Chan-Seng, J.-F. Lutz, Macromol. Rapid Commun. 2014, 35, 141–145.
- 15
- 15aH. Colquhoun, J.-F. Lutz, Nat. Chem. 2014, 6, 455–456;
- 15bZ. Zhu, C. J. Cardin, Y. Gan, H. M. Colquhoun, Nat Chem. 2010, 2, 653–660;
- 15cZ. Zhu, C. J. Cardin, Y. Gan, C. A. Murray, A. J. White, D. J. Williams, H. M. Colquhoun, J. Am. Chem. Soc. 2011, 133, 19442–19447.
- 16
- 16aJ. C. Randall, Polymer Sequence Determination: Carbon-13 NMR Method, Academic Press, New York, 1977;
- 16bF. A. Bovey, P. A. Mirau, NMR of Polymers, Academic Press, San Diego, 1996.
10.1016/B978-012119765-0/50001-9 Google Scholar
- 17
- 17aD. C. Koboldt, K. M. Steinberg, D. E. Larson, R. K. Wilson, E. R. Mardis, Cell 2013, 155, 27–38;
- 17bC.-S. Ku, D. H. Roukos, Expert Rev. Med. Devices 2013, 10, 1–6;
- 17cY.-L. Ying, J. Zhang, R. Gao, Y. T. Long, Angew. Chem. 2013, 125, 13392–13399; Angew. Chem. Int. Ed. 2013, 52, 13154–13161.
- 18P. Edman, Acta Chem. Scand. 1950, 4, 283–293.
- 19A. S. Inglis, Anal. Biochem. 1991, 195, 183–196.
- 20
- 20aH. M. Fales, Y. Nagai, G. W. Milne, H. B. Brewer, Jr., T. J. Bronzert, J. J. Pisano, Anal. Biochem. 1971, 43, 288–299;
- 20bH. R. Schulten, B. Wittmann-Liebold, Anal. Biochem. 1976, 76, 300–310.
- 21
- 21aK. Biemann, Int. J. Mass Spectrom. 2007, 259, 1–7;
- 21bC. K. Barlow, R. A. J. O’Hair, J. Mass Spectrom. 2008, 43, 1301–1319.
- 22
- 22aK. Biemann, S. A. Martin, Mass Spectrom. Rev. 1987, 6, 1–75;
- 22bD. F. Hunt, W. M. Bone, J. Shabanowitz, J. Rhodes, J. M. Ballard, Anal. Chem. 1981, 53, 1704–1706;
- 22cD. F. Hunt, J. R. Yates III, J. Shabanowitz, S. Winston, C. R. Hauer, Proc. Natl. Acad. Sci. USA 1986, 83, 6233–6237.
- 23
- 23aB. Chait, R. Wang, R. C. Beavis, S. B. Kent, Science 1993, 262, 89–92;
- 23bR. Kaufmann, B. Spengler, F. Lutzenkirchen, Rapid Commun. Mass Spectrom. 1993, 7, 902–910.
- 24H. Kumar, Y. Lansac, M. A. Glaser, P. K. Maiti, Soft Matter. 2011, 7, 5898–5907.
- 25
- 25aJ. J. Coon, Anal. Chem. 2009, 81, 3208–3215;
- 25bH. Steen, M. Mann, Nat. Rev. Mol. Cell Biol. 2004, 5, 699–711.
- 26J. A. Shendure, et al., in Curr. Protoc. Mol. Bio, 2011, 96:7.1:7.1.1–7.1.23.
- 27F. Sanger, J. E. Donelson, A. R. Coulson, H. Kössel, D. Fischer, Proc. Natl. Acad. Sci. USA 1973, 70, 1209–1213.
- 28F. Sanger, A. R. Coulson, J. Mol. Biol. 1975, 94, 441–448.
- 29L. M. Smith, et al., Nature 1986, 321, 674–679.
- 30M. Margulies, et al., Nature 2005, 437, 376–380.
- 31J. J. Kasianowicz, E. Brandin, D. Branton, D. W. Deamer, Proc. Natl. Acad. Sci. USA 1996, 93, 13770–13773.
- 32A. Meller, L. Nivon, E. Brandin, J. Golovchenko, D. Branton, Proc. Natl. Acad. Sci. USA 2000, 97, 1079–1084.
- 33
- 33aJ. Li, D. Stein, C. McMullan, D. Branton, M. J. Aziz, J. A. Golovchenko, Nature 2001, 412, 166–169;
- 33bA. J. Storm, C. Storm, J. Chen, H. Zandbergen, J.-F. Joanny, C. Dekker, Nano Lett. 2005, 5, 1193–1197.
- 34
- 34aM. Wanunu, J. Sutin, B. McNally, A. Chow, A. Meller, Biophys. J. 2008, 95, 4716–4725;
- 34bM. Wanunu, A. Meller, Nano Lett. 2007, 7, 1580–1585.
- 35
- 35aH. Liu, J. He, J. Tang, H. Liu, P. Pang, D. Cao, P. Krstic, S. Joseph, S. Lindsay, C. Nuckolls, Science 2010, 327, 64–67;
- 35bC. Y. Lee, W. Choi, J. H. Han, M. S. Strano, Science 2010, 329, 1320–1324.
- 36B. McNally, A. Singer, Z. Yu, Y. Sun, Z. Weng, A. Meller, Nano Lett. 2010, 10, 2237–2244.
- 37
- 37aF. A. Bovey, J. Polym. Sci. 1962, 62, 197–209;
- 37bR. E. Cais, J. H. O′Donnell, F. A. Bovey, Macromolecules 1977, 10, 254–260;
- 37cS. A. Heffner, F. A. Bovey, L. A. Verge, P. A. Mirau, A. E. Tonelli, Macromolecules 1986, 19, 1628–1634;
- 37dF. A. Bovey, Makromol. Chem. Macromol. Symp. 1988, 20–21, 105–126.
- 38
- 38aJ. C. Randall, Macromolecules 1978, 11, 592–597;
- 38bD. B. Bailey, P. M. Henrichs, J. Polym. Sci. Polym. Chem. Ed. 1978, 16, 3185–3199;
- 38cE. T. Hsieh, J. C. Randall, Macromolecules 1982, 15, 1402–1406;
- 38dT. L. Bluhm, et al., Macromolecules 1986, 19, 2871–2876.
- 39
- 39aB. Kirci, J. F. Lutz, K. Matyjaszewski, Macromolecules 2002, 35, 2448–2451;
- 39bJ.-F. Lutz, B. Kirci, K. Matyjaszewski, Macromolecules 2003, 36, 3136–3145.
- 40D. Benoit, C. J. Hawker, E. E. Huang, Z. Lin, T. P. Russell, Macromolecules 2000, 33, 1505–1507.
- 41K. Matyjaszewski, M. J. Ziegler, S. V. Arehart, D. Greszta, T. Pakula, J. Phys. Org. Chem. 2000, 13, 775–786.
- 42D. Chan-Seng, M. Zamfir, J.-F. Lutz, Angew. Chem. 2012, 124, 12420–12423;
10.1002/ange.201206371 Google ScholarAngew. Chem. Int. Ed. 2012, 51, 12254–12257.
- 43A. Alkan, A. Natalello, M. Wagner, H. Frey, F. R. Wurm, Macromolecules 2014, 47, 2242–2249.
- 44
- 44aH. M. Colquhoun, Z. Zhu, Angew. Chem. 2004, 116, 5150–5155;
10.1002/ange.200460382 Google ScholarAngew. Chem. Int. Ed. 2004, 43, 5040–5045;
- 44bH. M. Colquhoun, Z. X. Zhu, C. J. Cardin, Y. Gan, Chem. Commun. 2004, 2650–2652;
- 44cH. M. Colquhoun, Z. Zhu, C. J. Cardin, Y. Gan, M. G. B. Drew, J. Am. Chem. Soc. 2007, 129, 16163–16174;
- 44dH. M. Colquhoun, Z. Zhu, C. J. Cardin, M. G. B. Drew, Y. Gan, Faraday Discuss. 2009, 143, 205–220;
- 44eB. W. Greenland, M. B. Bird, S. Burattini, R. Cramer, R. K. O′Reilly, J. P. Patterson, W. Hayes, C. J. Cardin, H. M. Colquhoun, Chem. Commun. 2013, 49, 454–456.
- 45S. G. Ramkumar, S. Ramakrishnan, Macromolecules 2010, 43, 2307–2312.
- 46A. E. Tonelli, Macromolecules 2009, 42, 3830–3840.
- 47S. N. Hardrict, R. Gurarslan, C. J. Galvin, H. Gracz, D. Roy, B. S. Sumerlin, J. Genzer, A. E. Tonelli, J. Polym. Sci. Part A 2013, 51, 735–741.
- 48
- 48aA. E. Tonelli, Macromolecules 1977, 10, 153–157;
- 48bG. Khanarian, R. E. Cais, J. Kometani, A. E. Tonelli, Macromolecules 1982, 15, 866–869;
- 48cJ. J. Semler, Y. K. Jhon, A. Tonelli, M. Beevers, R. Krishnamoorti, J. Genzer, Adv. Mater. 2007, 19, 2877–2883.
- 49G. Montaudo, F. Samperi, M. S. Montaudo, Prog. Polym. Sci. 2006, 31, 277–357.
- 50
- 50aM. S. Montaudo, Mass Spectrom. Rev. 2002, 21, 108–144;
- 50bM. W. F. Nielen, Mass Spectrom. Rev. 1999, 18, 309–344.
- 51G. Adamus, W. Sikorska, M. Kowalczuk, M. Montaudo, M. Scandola, Macromolecules 2000, 33, 5797–5802.
- 52F. Samperi, M. S. Montaudo, C. Puglisi, S. Di Giorgi, G. Montaudo, Macromolecules 2004, 37, 6449–6459.
- 53P. Rizzarelli, C. Puglisi, G. Montaudo, Rapid Commun. Mass Spec. 2005, 19, 2407–2418.
- 54M. G. Paulick, K. M. Hart, K. M. Brinner, M. Tjandra, D. H. Charych, R. N. Zuckermann, J. Comb. Chem. 2006, 8, 417–426.
- 55
- 55aT. Gruendling, S. Weidner, J. Falkenhagen, C. Barner-Kowollik, Polym. Chem. 2010, 1, 599–617;
- 55bG. Hart-Smith, C. Barner-Kowollik, Macromol. Chem. Phys. 2010, 211, 1507–1529;
- 55cA. H. Soeriyadi, M. R. Whittaker, C. Boyer, T. P. Davis, J. Polym. Sci. Part A 2013, 51, 1475–1505.
- 56
- 56aW. Heerma, C. Versluis, C. G. de Koster, J. A. W. Kruijtzer, I. Zigrovic, R. M. J. Liskamp, Rapid Commun. Mass Spec. 1996, 10, 459–464;
10.1002/(SICI)1097-0231(19960315)10:4<459::AID-RCM501>3.0.CO;2-J CAS PubMed Web of Science® Google Scholar
- 56bR. Ruijtenbeek, C. Versluis, A. J. Heck, F. A. Redegeld, F. P. Nijkamp, R. M. Liskamp, J. Mass Spec. 2002, 37, 47–55.
- 57G. De Bo, S. Kuschel, D. A. Leigh, B. Lewandowski, M. Papmeyer, J. W. Ward, J. Am. Chem. Soc. 2014, 136, 5811–5814.
- 58V. Mass, W. Schrepp, B. von Vacona, H. Pasch, Macromol. Chem. Phys. 2009, 210, 1957–1965.
- 59I. C. Wienhöfer, H. Luftmann, A. Studer, Macromolecules 2011, 44, 2510–2523.
- 60E. Altuntaş, U. S. Schubert, Anal. Chim. Acta 2014, 808, 56–69.
- 61
- 61aR. Hill, et al., Trans. Faraday Soc. 1939, 35, 1073–1079;
- 61bK. Tada, et al., Makromol. Chem. 1964, 71, 71–85;
- 61cS. Tsuge, et al., Macromolecules 1975, 8, 721–725.
- 62H. J. Harwood, Angew. Chem. 1965, 77, 1124–1134;
10.1002/ange.19650772404 Google ScholarAngew. Chem. Int. Ed. Engl. 1965, 4, 1051–1060.
- 63
- 63aC. H. Bamford, C. F. H. Tipper, Degradation of Polymers, Elsevier, Amsterdam, 1975;
- 63bR. Lenz in Biopolymers I, Bd. 107 (Eds.: ), Springer, Berlin/Heidelberg, 1993, pp. 1–40.
10.1007/BFb0027550 Google Scholar
- 64E. Zagar, A. Kržan, G. Adamus, M. Kowalczuk, Biomacromolecules 2006, 7, 2210–2216.
- 65C. M. Thomas, J.-F. Lutz, Angew. Chem. 2011, 123, 9412–9414; Angew. Chem. Int. Ed. 2011, 50, 9244–9246.
- 66
- 66aR. M. Stayshich, T. Y. Meyer, J. Am. Chem. Soc. 2010, 132, 10920–10934;
- 66bJ. Li, R. M. Stayshich, T. Y. Meyer, J. Am. Chem. Soc 2011, 133, 6910–6913;
- 66cJ. Li, S. N. Rothstein, S. R. Little, H. M. Edenborn, T. Y. Meyer, J. Am. Chem. Soc. 2012, 134, 16352–16359.
- 67Y. Ishido, A. Kanazawa, S. Kanaoka, S. Aoshima, Macromolecules 2012, 45, 4060–4068.
- 68
- 68aJ. K. Haken, T. R. McKay, Anal. Chem. 1973, 45, 1251–1257;
- 68bT. Shimono, J. Anal. Appl. Pyrolysis 1979, 1, 77–84;
- 68cM. S. Choudhary, K. Lederer, Eur. Polym. J. 1982, 18, 1021–1027.
- 69
- 69aN. Grassie, D. R. Bain, J. Polym. Sci. Part A 1970, 8, 2653–2664;
- 69bD. A. Smith, J. W. Youren, Br. Polym. J. 1976, 8, 101–117;
- 69cG. Pan, H. Li, Y. Cao, J. Appl. Polym. Sci. 2004, 93, 577–583.
- 70H. McCormick, J. Chrom. A 1969, 40, 1–15.
- 71G. Schliecker, C. Schmidt, S. Fuchs, T. Kissel, Biomaterials 2003, 24, 3835–3844.
- 72
- 72aA. Sagi, R. Weinstain, N. Karton, D. Shabat, J. Am. Chem. Soc. 2008, 130, 5434–5435;
- 72bG. I. Peterson, M. B. Larsen, A. J. Boydston, Macromolecules 2012, 45, 7317–7328;
- 72cS. T. Phillips, A. M. DiLauro, ACS Macro Lett. 2014, 3, 298–304.
- 73L.-J. Zhang, X.-X. Deng, F.-S. Du, Z.-C. Li, Macromolecules 2013, 46, 9554–9562.
- 74
- 74aS. M. Bezrukov, I. Vodyanoy, R. A. Brutyan, J. J. Kasianowicz, Macromolecules 1996, 29, 8517–8522;
- 74bJ. E. Reiner, J. J. Kasianowicz, B. J. Nablo, J. W. F. Robertson, Proc. Natl. Acad. Sci. USA 2010, 107, 12080–12085;
- 74cL. Movileanu, H. Bayley, Proc. Natl. Acad. Sci. USA 2001, 98, 10137–10141.
- 75
- 75aG. Baaken, M. Sondermann, C. Schlemmer, J. Rühe, J. C. Behrends, Lab Chip 2008, 8, 938–944;
- 75bA. G. Oukhaled, A.-L. Biance, J. Pelta, L. Auvray, L. Bacri, Phys. Rev. Lett. 2012, 108, 088104;
- 75cA. Balijepalli, J. W. F. Robertson, J. E. Reiner, J. J. Kasianowicz, R. W. Pastor, J. Am. Chem. Soc. 2013, 135, 7064–7072;
- 75dM. F. Breton, F. Discala, L. Bacri, D. Foster, J. Pelta, A. Oukhaled, J. Phys. Chem. Lett. 2013, 4, 2202–2208.
- 76
- 76aG. Baaken, N. Ankri, A.-K. Schuler, J. Rühe, J. C. Behrends, ACS Nano 2011, 5, 8080–8088;
- 76bG. Baaken, et al., Biophys. J. 2012, 102, 28A–28A.
- 77
- 77aL. Brun, M. Pastoriza-Gallego, G. Oukhaled, J. Mathé, L. Bacri, L. Auvray, J. Pelta, Phys. Rev. Lett. 2008, 100, 158302;
- 77bG. Gibrat, M. Pastoriza-Gallego, B. Thiebot, M.-F. Breton, L. Auvray, J. Pelta, J. Phys. Chem. B 2008, 112, 14687–14691;
- 77cG. Oukhaled, L. Bacri, J. Mathe, J. Pelta, L. Auvray, Europhys. Lett. 2008, 82, 48003.
- 78R. J. Murphy, M. Muthukumar, J. Chem. Phys. 2007, 126, 051101.
- 79T. Sakaue, F. Brochard-Wyart, ACS Macro Lett. 2014, 3, 194–197.
- 80S. Mirigian, Y. Wang, M. Muthukumar, J. Chem. Phys. 2012, 137, 064904.
- 81J.-F. Lutz, Nat. Chem. 2010, 2, 84–85.
