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DNA-Assisted Multichromophore Assembly

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Modified Nucleic Acids

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 31))

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Abstract

Chromophores in a π-stacked system show unique photophysical properties, such as energy and charge transfer through the strong electronic coupling interaction between the chromophores. A variety of supramolecular structures to realize efficient light-harvesting and charge conduction properties have been designed and prepared. DNA and RNA are a useful building block and a platform to incorporate functional molecules at defined positions through chemical modification of DNA. Therefore, we can construct a one-dimensional or helical array of multichromophores in DNA or along RNA duplexes. This chapter deals with our recent approaches to DNA-assisted multichromophore assembly that involves the synthesis of pyrene π-stack array on RNA, perylene π-stack array in DNA, charge transfer complex formed in DNA, and multi-organic-dyes assembly based on the interaction between Zn(II)-cyclen and thymine base in DNA.

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References

  1. Hoeben FJM, Jonkheijm P, Meijer EW, Schenning APHJ (2005) About supramolecular assemblies of π-conjugated systems. Chem Rev 105(4):1491–1546. doi:10.1021/cr030070z

    Article  CAS  PubMed  Google Scholar 

  2. Malinovskii VL, Wenger D, Häner R (2010) Nucleic acid-guided assembly of aromatic chromophores. Chem Soc Rev 39(2):410–422. doi:10.1039/b910030j

    Article  CAS  PubMed  Google Scholar 

  3. Malinovskii VL, Samain F, Häner R (2007) Helical arrangement of interstrand stacked pyrenes in a DNA framework. Angew Chem Int Ed 46(24):4464–4467

    Article  CAS  Google Scholar 

  4. Mayer-Enthart E, Wagenknecht H-A (2006) Structure-sensitive and self-assembled helical pyrene array based on DNA architecture. Angew Chem Int Ed 45(20):3372–3375. doi:10.1002/anie.200504210

    Article  CAS  Google Scholar 

  5. Häner R, Samain F, Malinovskii VL (2009) DNA-assisted self-assembly of pyrene foldamers. Chem Eur J 15(23):5701–5708. doi:10.1002/chem.200900369

    Article  PubMed  CAS  Google Scholar 

  6. Bittermann H, Siegemund D, Malinovskii VL, Häner R (2008) Dialkynylpyrenes: strongly fluorescent, environment-sensitive DNA building blocks. J Am Chem Soc 130(46):15285–15287. doi:10.1021/ja806747h

    Article  CAS  PubMed  Google Scholar 

  7. Lewis FD, Letsinger RL, Wasielewski MR (2001) Dynamics of photoinduced charge transfer and hole transport in synthetic DNA hairpins. Acc Chem Res 34(2):159–170. doi:10.1021/ar0000197

    Article  CAS  PubMed  Google Scholar 

  8. Genereux JC, Barton JK (2010) Mechanisms for DNA charge transport. Chem Rev 110(3):1642–1662. doi:10.1021/cr900228f

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Giese B (2000) Long-distance charge transport in DNA: the hopping mechanism. Acc Chem Res 33(9):631–636. doi:10.1021/ar990040b

    Article  CAS  PubMed  Google Scholar 

  10. Kawai K, Majima T (2013) Hole transfer kinetics of DNA. Acc Chem Res 46(11):2616–2625. doi:10.1021/ar400079s

    Article  CAS  PubMed  Google Scholar 

  11. Valis L, Wang Q, Raytchev M, Buchvarov I, Wagenknecht H-A, Fiebig T (2006) Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer. Proc Natl Acad Sci USA 103(27):10192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kanvah S, Joseph J, Schuster GB, Barnett RN, Cleveland CL, Landman U (2010) Oxidation of DNA: damage to nucleobases. Acc Chem Res 43(2):280–287. doi:10.1021/ar900175a

    Article  CAS  PubMed  Google Scholar 

  13. Bhosale R, Míšek J, Sakai N, Matile S (2010) Supramolecular n/p-heterojunction photosystems with oriented multicolored antiparallel redox gradients (OMARG-SHJs). Chem Soc Rev 39(1):138–149. doi:10.1039/b906115k

    Article  CAS  PubMed  Google Scholar 

  14. Acuna GP, Moller FM, Holzmeister P, Beater S, Lalkens B, Tinnefeld P (2012) Fluorescence enhancement at docking sites of DNA-directed self-assembled nanoantennas. Science 338(6106):506–510. doi:10.1126/science.1228638

    Article  CAS  PubMed  Google Scholar 

  15. Liu S, Clever GH, Takezawa Y, Kaneko M, Tanaka K, Guo X, Shionoya M (2011) Direct conductance measurement of individual metallo-DNA duplexes within single-molecule break junctions. Angew Chem Int Ed 50(38):8886–8890. doi:10.1002/anie.201102980

    Article  CAS  Google Scholar 

  16. Guo X, Gorodetsky AA, Hone J, Barton JK, Nuckolls C (2008) Conductivity of a single DNA duplex bridging a carbon nanotube gap. Nat Nanotechnol 3(3):163–167. doi:10.1038/nnano.2008.4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Kawai K, Kodera H, Osakada Y, Majima T (2009) Sequence-independent and rapid long-range charge transfer through DNA. Nat Chem 1(2):156–159. doi:10.1038/nchem.171

    Article  CAS  PubMed  Google Scholar 

  18. Willner I, Patolsky F, Wasserman J (2001) Photoelectrochemistry with controlled DNA-cross-linked CdS nanoparticle arrays this research is supported by the U.S.-Israel Binational Science Foundation. The Max Planck Research Award for International Cooperation (I.W.) is gratefully acknowledged. Angew Chem Int Ed 40(10):1861–1864

    Article  CAS  Google Scholar 

  19. Okamoto A, Kamei T, Saito I (2006) DNA hole transport on an electrode: application to effective photoelectrochemical SNP typing. J Am Chem Soc 128(2):658–662. doi:10.1021/ja057040t

    Article  CAS  PubMed  Google Scholar 

  20. Zhang H, Baker BA, Cha T-G, Sauffer MD, Wu Y, Hinkson N, Bork MA, McShane CM, Choi K-S, McMillin DR, Choi JH (2012) DNA oligonucleotide templated nanohybrids using electronic type sorted carbon nanotubes for light harvesting. Adv Mater 24(40):5447–5451. doi:10.1002/adma.201201628

    Article  CAS  PubMed  Google Scholar 

  21. Schenning APHJ, von Herrikhuyzen J, Jonkheijm P, Chen Z, Würthner F, Meijer EW (2002) Photoinduced electron transfer in hydrogen-bonded oligo(p-phenylene vinylene)—perylene bisimide chiral assemblies. J Am Chem Soc 124(35):10252–10253. doi:10.1021/ja020378s

    Article  CAS  PubMed  Google Scholar 

  22. Garo F, Häner R (2012) A DNA-based light-harvesting antenna. Angew Chem Int Ed 51(4):916–919. doi:10.1002/anie.201103295

    Article  CAS  Google Scholar 

  23. Sakai N, Bhosale R, Emery D, Mareda J, Matile S (2010) Supramolecular n/p-heterojunction photosystems with antiparallel redox gradients in electron- and hole-transporting pathways. J Am Chem Soc 132(20):6923–6925. doi:10.1021/ja101944r

    Article  CAS  PubMed  Google Scholar 

  24. Teo YN, Kool ET (2012) DNA-multichromophore systems. Chem Rev 112(7):4221–4245. doi:10.1021/cr100351g

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kashida H, Takatsu T, Sekiguchi K, Asanuma H (2010) An efficient fluorescence resonance energy transfer (FRET) between pyrene and perylene assembled in a DNA duplex and its potential for discriminating single-base changes. Chem Eur J 16(8):2479–2486. doi:10.1002/chem.200902078

    Article  CAS  PubMed  Google Scholar 

  26. Ono T, Wang S, Koo C-K, Engstrom L, David SS, Kool ET (2012) Direct fluorescence monitoring of DNA base excision repair. Angew Chem Int Ed 51(7):1689–1692. doi:10.1002/anie.201108135

    Article  CAS  Google Scholar 

  27. Teo YN, Wilson JN, Kool ET (2009) Polyfluorophores on a DNA backbone: a multicolor set of labels excited at one wavelength. J Am Chem Soc 131(11):3923–3933. doi:10.1021/ja805502k

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Khakshoor O, Kool ET (2011) Chemistry of nucleic acids: impacts in multiple fields. Chem Commun 47(25):7018–7024. doi:10.1039/C1CC11021G

    Article  CAS  Google Scholar 

  29. Sargsyan G, Schatz AA, Kubelka J, Balaz M (2013) Formation and helicity control of ssDNA templated porphyrin nanoassemblies. Chem Commun 49(10):1020–1022. doi:10.1039/c2cc38150h

    Article  CAS  Google Scholar 

  30. Sezi S, Wagenknecht H-A (2013) DNA-templated formation of fluorescent self-assembly of ethynyl pyrenes. Chem Commun 49(81):9257–9259. doi:10.1039/c3cc44733b

    Article  CAS  Google Scholar 

  31. Narayanaswamy N, Suresh G, Priyakumar UD, Govindaraju T (2014) Double zipper helical assembly of deoxyoligonucleotides: mutual templating and chiral imprinting to form hybrid DNA ensembles. Chem Commun. doi:10.1039/c4cc06759b

    Google Scholar 

  32. Sargsyan G, Leonard BM, Kubelka J, Balaz M (2014) Supramolecular ssDNA templated porphyrin and metalloporphyrin nanoassemblies with tunable helicity. Chem Eur J 20(7):1878–1892. doi:10.1002/chem.201304153

    Article  CAS  PubMed  Google Scholar 

  33. Janssen PGA, Ruiz-Carretero A, González-Rodríguez D, Meijer EW, Schenning APHJ (2009) pH-Switchable helicity of DNA-templated assemblies. Angew Chem Int Ed 48(43):8103–8106. doi:10.1002/anie.200903507

    Article  CAS  Google Scholar 

  34. Benvin AL, Creeger Y, Fisher GW, Ballou B, Waggoner AS, Armitage BA (2007) Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates. J Am Chem Soc 129(7):2025–2034. doi:10.1021/ja066354t

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Duhamel J (2012) New insights in the study of pyrene excimer fluorescence to characterize macromolecules and their supramolecular assemblies in solution. Langmuir 28(16):6527–6538

    Article  CAS  PubMed  Google Scholar 

  36. Winnik FM (1993) Photophysics of preassociated pyrenes in aqueous polymer solutions and in other organized media. Chem Rev 93(2):587–614

    Article  CAS  Google Scholar 

  37. Choi J, Konno T, Takai M, Ishihara K (2009) Controlled drug release from multilayered phospholipid polymer hydrogel on titanium alloy surface. Biomaterials 30(28):5201–5208

    Article  CAS  PubMed  Google Scholar 

  38. Garai K, Baban B, Frieden C (2011) Dissociation of apolipoprotein E oligomers to monomer is required for high-affinity binding to phospholipid vesicles. Biochemistry 50(13):2550–2558

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. You L, Gokel GW (2008) Fluorescent, synthetic amphiphilic heptapeptide anion transporters: evidence for self-assembly and membrane localization in liposomes. Chem Eur J 14(19):5861–5870

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Hong H, Blois TM, Cao Z, Bowie JU (2010) Method to measure strong protein-protein interactions in lipid bilayers using a steric trap. Proc Natl Acad Sci USA 107(46):19802–19807. doi:10.1073/pnas.1010348107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Okada K, Bartolini F, Deaconescu AM, Moseley JB, Dogic Z, Grigorieff N, Gundersen GG, Goode BL (2010) Adenomatous polyposis coli protein nucleates actin assembly and synergizes with the formin mDia1. J Cell Biol 189(7):1087–1096. doi:10.1083/jcb.201001016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Oh KJ, Cash KJ, Plaxco KW (2006) Excimer-based peptide beacons: a convenient experimental approach for monitoring polypeptide-protein and polypeptide-oligonucleotide interactions. J Am Chem Soc 128(43):14018–14019

    Article  CAS  PubMed  Google Scholar 

  43. Bains G, Patel AB, Narayanaswami V (2011) Pyrene: a probe to study protein conformation and conformational changes. Molecules 16(9):7909–7935

    Article  CAS  PubMed  Google Scholar 

  44. Ono T, Wang S, Koo C-K, Engstrom L, David SS, Kool ET (2012) Direct fluorescence monitoring of DNA base excision repair. Angew Chem Int Ed 51(7):1689–1692

    Article  CAS  Google Scholar 

  45. Sezi S, Varghese R, Vilaivan T, Wagenknecht H-A (2012) Conformational control of dual emission by pyrrolidinyl PNA–DNA hybrids. ChemistryOpen 1(4):173–176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Zhu H, Lewis FD (2007) Pyrene excimer fluorescence as a probe for parallel G-quadruplex formation. Bioconjug Chem 18(4):1213–1217

    Article  CAS  PubMed  Google Scholar 

  47. Nagatoishi S, Nojima T, Juskowiak B, Takenaka S (2005) A pyrene-labeled G-quadruplex oligonucleotide as a fluorescent probe for potassium ion detection in biological applications. Angew Chem Int Ed 44(32):5067–5070. doi:10.1002/anie.200501506

    Article  CAS  Google Scholar 

  48. Okamoto A, Ichiba T, Saito I (2004) Pyrene-labeled oligodeoxynucleotide probe for detecting base insertion by excimer fluorescence emission. J Am Chem Soc 126(27):8364–8365. doi:10.1021/ja049061d

    Article  CAS  PubMed  Google Scholar 

  49. Figueira-Duarte TM, Müllen K (2011) Pyrene-based materials for organic electronics. Chem Rev 111(11):7260–7314. doi:10.1021/cr100428a

    Article  CAS  PubMed  Google Scholar 

  50. Xu X, Yuan H, Chang J, He B, Gu Z (2012) Cooperative hierarchical self-assembly of peptide dendrimers and linear polypeptides into nanoarchitectures mimicking viral capsids. Angew Chem Int Ed 51(13):3130–3133

    Article  CAS  Google Scholar 

  51. Lim Y-B, Moon K-S, Lee M (2009) Recent advances in functional supramolecular nanostructures assembled from bioactive building blocks. Chem Soc Rev 38(4):925–934

    Article  CAS  PubMed  Google Scholar 

  52. Wei B, Dai M, Yin P (2012) Complex shapes self-assembled from single-stranded DNA tiles. Nature 485(7400):623–626. doi:10.1038/nature11075

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Wang T, Sha R, Dreyfus R, Leunissen ME, Maass C, Pine DJ, Chaikin PM, Seeman NC (2012) Self-replication of information-bearing nanoscale patterns. Nature 478(7368):225–228

    Article  CAS  Google Scholar 

  54. Gu H, Chao J, Xiao S-J, Seeman NC (2010) A proximity-based programmable DNA nanoscale assembly line. Nature 465(7295):202–205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Ackermann D, Jester S-S, Famulok M (2012) Design strategy for DNA rotaxanes with a mechanically reinforced PX100 axle. Angew Chem Int Ed 51(27):6771–6775

    Article  CAS  Google Scholar 

  56. Verbiest T, Samyn C, Boutton C, Houbrechts S, Kauranen M, Persoons A (1996) Second-order nonlinear optical properties of a chromophore-functionalized polypeptide. Adv Mater 8(9):756–759

    Article  CAS  Google Scholar 

  57. Parkash J, Robblee JH, Agnew J, Gibbs E, Collings P, Pasternack RF, de Paula JC (1998) Depolarized resonance light scattering by porphyrin and chlorophyll a aggregates. Biophys J 74(4):2089–2099

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Pieroni O, Fissi A, Angelini N, Lenci F (2001) Photoresponsive polypeptides. Acc Chem Res 34(1):9–17

    Article  CAS  PubMed  Google Scholar 

  59. Jones G, Vullev VI (2002) Photoinduced electron transfer between non-native donor-acceptor moieties incorporated in synthetic polypeptide aggregates. Org Lett 4(23):4001–4004

    Article  CAS  PubMed  Google Scholar 

  60. Channon KJ, Devlin GL, MacPhee CE (2009) Efficient energy transfer within self-assembling peptide fibers: a route to light-harvesting nanomaterials. J Am Chem Soc 131(35):12520–12521

    Article  CAS  PubMed  Google Scholar 

  61. Rao KV, Datta KKR, Eswaramoorthy M, George SJ (2012) Light-harvesting hybrid assemblies. Chem Eur J 18(8):2184–2194

    Article  CAS  PubMed  Google Scholar 

  62. Hainke S, Seitz O (2009) Binaphthyl-DNA: stacking and fluorescence of a nonplanar aromatic base surrogate in DNA. Angew Chem Int Ed 48(44):8250–8253. doi:10.1002/anie.200903194

    Article  CAS  Google Scholar 

  63. Brotschi C, Leumann CJ (2003) DNA with hydrophobic base substitutes: a stable, zipperlike recognition motif based on interstrand-stacking interactions. Angew Chem Int Ed 42(14):1655–1658

    Article  CAS  Google Scholar 

  64. Kashida H, Asanuma H, Komiyama M (2004) Alternating hetero H aggregation of different dyes by interstrand stacking from two DNA–dye conjugates. Angew Chem Int Ed 43(47):6522–6525

    Article  CAS  Google Scholar 

  65. Asanuma H, Shirasuka K, Takarada T, Kashida H, Komiyama M (2003) DNA-dye conjugates for controllable H* aggregation. J Am Chem Soc 125(8):2217–2223

    Article  CAS  PubMed  Google Scholar 

  66. Baumstark D, Wagenknecht H-A (2008) Fluorescent hydrophobic zippers inside duplex DNA: interstrand stacking of perylene-3,4:9,10-tetracarboxylic acid bisimides as artificial DNA base dyes. Chem Eur J 14(22):6640–6645

    Article  CAS  PubMed  Google Scholar 

  67. Wilson TM, Zeidan TA, Hariharan M, Lewis FD, Wasielewski MR (2010) Electron hopping among cofacially stacked perylenediimides assembled by using DNA hairpins. Angew Chem Int Ed 49(13):2385–2388

    Article  CAS  Google Scholar 

  68. Sharma N, Top A, Kiick KL, Pochan DJ (2009) One-dimensional gold nanoparticle arrays by electrostatically directed organization using polypeptide self-assembly. Angew Chem Int Ed 48(38):7078–7082

    Article  CAS  Google Scholar 

  69. Kuzyk A, Schreiber R, Fan Z, Pardatscher G, Roller E-M, Hogele A, Simmel FC, Govorov AO, Liedl T (2012) DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483(7389):311–314

    Article  CAS  PubMed  Google Scholar 

  70. Sharma J, Chhabra R, Cheng A, Brownell J, Liu Y, Yan H (2009) Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science 323(5910):112–116. doi:10.1126/science.1165831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Rajendran A, Endo M, Sugiyama H (2012) Single-molecule analysis using DNA origami. Angew Chem Int Ed 51(4):874–890

    Article  CAS  Google Scholar 

  72. Nakata E, Liew FF, Uwatoko C, Kiyonaka S, Mori Y, Katsuda Y, Endo M, Sugiyama H, Morii T (2012) Zinc-finger proteins for site-specific protein positioning on DNA-origami structures. Angew Chem Int Ed 51(10):2421–2424

    Article  CAS  Google Scholar 

  73. Tanaka K, Clever GH, Takezawa Y, Yamada Y, Kaul C, Shionoya M, Carell T (2006) Programmable self-assembly of metal ions inside artificial DNA duplexes. Nat Nanotechnol 1(3):190–194

    Article  CAS  PubMed  Google Scholar 

  74. Egusa S, Sisido M, Imanishi Y (1985) One-dimensional aromatic crystals in solution. 4. Ground- and excited-state interactions of poly(L-1-pyrenylalanine) studied by chiroptical spectroscopy including circularly polarized fluorescence and fluorescence-detected circular dichroism. Macromolecules 18(5):882–889

    Article  CAS  Google Scholar 

  75. Sisido M, Imanishi Y (1985) One-dimensional aromatic crystals in solution. 5. Empirical energy and theoretical circular dichroism calculations on helical poly(L-1-pyrenylalanine). Macromolecules 18(5):890–894

    Article  CAS  Google Scholar 

  76. Endo M, Wang H, Fujitsuka M, Majima T (2006) Pyrene-stacked nanostructures constructed in the recombinant tobacco mosaic virus rod scaffold. Chem Eur J 12(14):3735–3740

    Article  CAS  PubMed  Google Scholar 

  77. Wilson JN, Teo YN, Kool ET (2007) Efficient quenching of oligomeric fluorophores on a DNA backbone. J Am Chem Soc 129(50):15426–15427

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Kashida H, Sekiguchi K, Liang X, Asanuma H (2010) Accumulation of fluorophores into DNA duplexes to mimic the properties of quantum dots. J Am Chem Soc 132(17):6223–6230. doi:10.1021/ja101007d

    Article  CAS  PubMed  Google Scholar 

  79. Seo YJ, Rhee H, Joo T, Kim BH (2007) Self-duplex formation of an APy-substituted oligodeoxyadenylate and its unique fluorescence. J Am Chem Soc 129(16):5244–5247

    Article  CAS  PubMed  Google Scholar 

  80. Nakamura M, Fukunaga Y, Sasa K, Ohtoshi Y, Kanaori K, Hayashi H, Nakano H, Yamana K (2005) Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference. Nucleic Acids Res 33(18):5887–5895. doi:10.1093/nar/gki889

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Maie K, Miyagi K, Takada T, Nakamura M, Yamana K (2009) RNA-mediated electron transfer: double exponential distance dependence. J Am Chem Soc 131(37):13188–13189. doi:10.1021/ja902647j

    Article  CAS  PubMed  Google Scholar 

  82. Fukuda M, Nakamura M, Takada T, Yamana K (2010) Syntheses and fluorescence of RNA conjugates having pyrene-modified adenosine and nitrobenzene-modified uridine base pairs. Tetrahedron Lett 51(13):1732–1735. doi:10.1016/j.tetlet.2010.01.081

    Article  CAS  Google Scholar 

  83. Yamana K, Zako H, Asazuma K, Iwase R, Nakano H, Murakami A (2001) Fluorescence detection of specific RNA sequences using 2′-pyrene-modified oligoribonucleotides. Angew Chem Int Ed 40(6):1104–1106. doi:10.1002/1521-3773(20010316)40:6<1104::AID-ANIE11040>3.0.CO;2-2

    Article  CAS  Google Scholar 

  84. Mahara A, Iwase R, Sakamoto T, Yamana K, Yamaoka T, Murakami A (2002) Bispyrene-conjugated 2′-O-methyloligonucleotide as a highly specific RNA-recognition probe. Angew Chem Int Ed 41(19):3648–3650. doi:10.1002/1521-3773(20021004)41:19<3648::AID-ANIE3648>3.0.CO;2-Y

    Article  CAS  Google Scholar 

  85. Nakamura M, Ohtoshi Y, Yamana K (2005) Helical pyrene-array along the outside of duplex RNA. Chem Commun 41:5163. doi:10.1039/b507808c

    Article  CAS  Google Scholar 

  86. Nakamura M, Shimomura Y, Ohtoshi Y, Sasa K, Hayashi H, Nakano H, Yamana K (2007) Pyrene aromatic arrays on RNA duplexes as helical templates. Org Biomol Chem 5(12):1945–1951. doi:10.1039/B705933G

    Article  CAS  PubMed  Google Scholar 

  87. Maie K, Nakamura M, Takada T, Yamana K (2009) Fluorescence quenching properties of multiple pyrene-modified RNAs. Bioorg Med Chem 17(14):4996–5000. doi:10.1016/j.bmc.2009.05.074

    Article  CAS  PubMed  Google Scholar 

  88. Nakamura M, Murakami Y, Sasa K, Hayashi H, Yamana K (2008) Pyrene-zipper array assembled via RNA duplex formation. J Am Chem Soc 130(22):6904–6905. doi:10.1021/ja801054t

    Article  CAS  PubMed  Google Scholar 

  89. Nakamura M, Fukuda M, Takada T, Yamana K (2012) Highly ordered pyrene [small pi]-stacks on an RNA duplex display static excimer fluorescence. Org Biomol Chem 10(48):9620–9626. doi:10.1039/C2OB26773J

    Article  CAS  PubMed  Google Scholar 

  90. Görl D, Zhang X, Würthner F (2012) Molecular assemblies of perylene bisimide dyes in water. Angew Chem Int Ed 51(26):6328–6348. doi:10.1002/anie.201108690

    Article  CAS  Google Scholar 

  91. Xie Z, Stepanenko V, Radacki K, Würthner F (2012) Chiral J-aggregates of atropo-enantiomeric perylene bisimides and their self-sorting behavior. Chem Eur J 18(23):7060–7070. doi:10.1002/chem.201200089

    Article  CAS  PubMed  Google Scholar 

  92. Shao C, Stolte M, Würthner F (2013) Quadruple π stack of two perylene bisimide tweezers: a bimolecular complex with kinetic stability. Angew Chem Int Ed 52(29):7482–7486. doi:10.1002/anie.201302479

    Article  CAS  Google Scholar 

  93. Marty R, Nigon R, Leite D, Frauenrath H (2014) Two-fold odd-even effect in self-assembled nanowires from oligopeptide-polymer-substituted perylene bisimides. J Am Chem Soc 136(10):3919–3927. doi:10.1021/ja412384p

    Article  CAS  PubMed  Google Scholar 

  94. Würthner F (2004) Perylene bisimide dyes as versatile building blocks for functional supramolecular architectures. Chem Commun 14:1564. doi:10.1039/b401630k

    Article  Google Scholar 

  95. Bevers S, Schutte S, McLaughlin LW (2000) Naphthalene- and perylene-based linkers for the stabilization of hairpin triplexes. J Am Chem Soc 122(25):5905–5915. doi:10.1021/ja0001714

    Article  CAS  Google Scholar 

  96. Rahe N, Rinn C, Carell T (2003) Development of donor? Acceptor modified DNA hairpins for the investigation of charge hopping kinetics in DNA. Chem Commun 17:2120. doi:10.1039/b307395e

    Article  Google Scholar 

  97. Neelakandan PP, Pan Z, Hariharan M, Zheng Y, Weissman H, Rybtchinski B, Lewis FD (2010) Hydrophobic self-assembly of a perylenediimide-linked DNA dumbbell into supramolecular polymers. J Am Chem Soc 132(44):15808–15813. doi:10.1021/ja1076525

    Article  CAS  PubMed  Google Scholar 

  98. Menacher F, Stepanenko V, Würthner F, Wagenknecht H-A (2011) Assembly of DNA triangles mediated by perylene bisimide caps. Chem Eur J 17(24):6683–6688. doi:10.1002/chem.201100141

    Article  CAS  PubMed  Google Scholar 

  99. Baumstark D, Wagenknecht H-A (2008) Perylene bisimide dimers as fluorescent “glue” for DNA and for base-mismatch detection. Angew Chem Int Ed 47(14):2612–2614. doi:10.1002/anie.200705237

    Article  CAS  Google Scholar 

  100. Wagner C, Wagenknecht H-A (2006) Perylene-3,4:9,10-tetracarboxylic acid bisimide dye as an artificial DNA base surrogate. Org Lett 8(19):4191–4194. doi:10.1021/ol061246x

    Article  CAS  PubMed  Google Scholar 

  101. Abdalla MA, Bayer J, Rädler JO, Müllen K (2004) Synthesis and self-assembly of perylenediimide–oligonucleotide conjugates. Angew Chem Int Ed 43(30):3967–3970. doi:10.1002/anie.200353621

    Article  CAS  Google Scholar 

  102. Liu ZR, Rill RL (1996) N,N′-bis[3,3′-(dimethylamino)propylamine]-3,4,9,10-perylenetetracarboxylic diimide, a dicationic perylene dye for rapid precipitation and quantitation of trace amounts of DNA. Anal Biochem 236(1):139–145. doi:10.1006/abio.1996.0142

    Article  CAS  PubMed  Google Scholar 

  103. Takada T, Yamaguchi K, Tsukamoto S, Nakamura M, Yamana K (2014) Light-up fluorescent probes utilizing binding behavior of perylenediimide derivatives to a hydrophobic pocket within DNA. Analyst 139(16):4016–4021. doi:10.1039/c4an00493k

    Article  CAS  PubMed  Google Scholar 

  104. Tuntiwechapikul W, Lee JT, Salazar M (2001) Design and synthesis of the G-quadruplex-specific cleaving reagent perylene-EDTA· iron(II). J Am Chem Soc 123(23):5606–5607. doi:10.1021/ja0156439

    Article  CAS  PubMed  Google Scholar 

  105. Szelke H, Schübel S, Harenberg J, Krämer R (2010) Interaction of heparin with cationic molecular probes: probe charge is a major determinant of binding stoichiometry and affinity. Bioorg Med Chem Lett 20(4):1445–1447. doi:10.1016/j.bmcl.2009.12.105

    Article  CAS  PubMed  Google Scholar 

  106. Samudrala R, Zhang X, Wadkins RM, Mattern DL (2007) Synthesis of a non-cationic, water-soluble perylenetetracarboxylic diimide and its interactions with G-quadruplex-forming DNA. Bioorg Med Chem 15(1):186–193. doi:10.1016/j.bmc.2006.09.075

    Article  CAS  PubMed  Google Scholar 

  107. Kern JT, Thomas PW, Kerwin SM (2002) The relationship between ligand aggregation and G-quadruplex DNA selectivity in a series of 3,4,9,10-perylenetetracarboxylic acid diimides †. Biochemistry 41(38):11379–11389. doi:10.1021/bi0263107

    Article  CAS  PubMed  Google Scholar 

  108. Furst A, Landefeld S, Hill MG, Barton JK (2013) Electrochemical patterning and detection of DNA arrays on a two-electrode platform. J Am Chem Soc 135(51):19099–19102. doi:10.1021/ja410902j

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Genereux JC, Barton JK (2009) Molecular electronics: DNA charges ahead. Nat Chem 1(2):106–107. doi:10.1038/nchem.188

    Article  CAS  PubMed  Google Scholar 

  110. Gill R, Patolsky F, Katz E, Willner I (2005) Electrochemical control of the photocurrent direction in intercalated DNA/CdS nanoparticle systems. Angew Chem Int Ed 44(29):4554–4557. doi:10.1002/anie.200500830

    Article  CAS  Google Scholar 

  111. Lu C-H, Willner B, Willner I (2013) DNA nanotechnology: from sensing and DNA machines to drug-delivery systems. ACS Nano 7(10):8320–8332. doi:10.1021/nn404613v

    Article  CAS  PubMed  Google Scholar 

  112. Woller JG, Hannestad JK, Albinsson B (2013) Self-assembled nanoscale DNA-porphyrin complex for artificial light harvesting. J Am Chem Soc 135(7):2759–2768. doi:10.1021/ja311828v

    Article  CAS  PubMed  Google Scholar 

  113. Stein IH, Steinhauer C, Tinnefeld P (2011) Single-molecule four-color FRET visualizes energy-transfer paths on DNA origami. J Am Chem Soc 133(12):4193–4195. doi:10.1021/ja1105464

    Article  CAS  PubMed  Google Scholar 

  114. Ruiz-Carretero A, Janssen PGA, Kaeser A, Schenning APHJ (2011) DNA-templated assembly of dyes and extended π-conjugated systems. Chem Commun 47(15):4340. doi:10.1039/c0cc05155a

    Article  CAS  Google Scholar 

  115. Takada T, Otsuka Y, Nakamura M, Yamana K (2012) Molecular arrangement and assembly guided by hydrophobic cavities inside DNA. Chem Eur J 18(30):9300–9304. doi:10.1002/chem.201201469

    Article  CAS  PubMed  Google Scholar 

  116. Takada T, Ashida A, Nakamura M, Fujitsuka M, Majima T, Yamana K (2014) Photocurrent generation enhanced by charge delocalization over stacked perylenediimide chromophores assembled within DNA. J Am Chem Soc 136(19):6814–6817. doi:10.1021/ja501535z

    Article  CAS  PubMed  Google Scholar 

  117. Takada T, Ashida A, Nakamura M, Yamana K (2013) Cationic perylenediimide as a specific fluorescent binder to mismatch containing DNA. Bioorg Med Chem 21(19):6011–6014. doi:10.1016/j.bmc.2013.07.040

    Article  CAS  PubMed  Google Scholar 

  118. Zheng Y, Long H, Schatz GC, Lewis FD (2005) Duplex and hairpin dimer structures for perylene diimide-oligonucleotide conjugates. Chem Commun 38:4795–4797. doi:10.1039/b509754a

    Article  CAS  Google Scholar 

  119. Zeidan TA, Carmieli R, Kelley RF, Wilson TM, Lewis FD, Wasielewski MR (2008) Charge-transfer and spin dynamics in DNA hairpin conjugates with perylenediimide as a base-pair surrogate. J Am Chem Soc 130(42):13945–13955. doi:10.1021/ja803765r

    Article  CAS  PubMed  Google Scholar 

  120. Krausharp S, Lysetska M, Würthner F (2005) DNA-binding fourfold spermine functionalized perylene bisimide dye. Lett Org Chem 2(4):349–353

    Article  Google Scholar 

  121. Menacher F, Wagenknecht H-A (2011) Synthesis of DNA with green perylene bisimides as DNA base substitutions. Eur J Org Chem 2011(24):4564–4570. doi:10.1002/ejoc.201100519

    Article  CAS  Google Scholar 

  122. Das A, Molla MR, Maity B, Koley D, Ghosh S (2012) Hydrogen-bonding induced alternate stacking of donor (D) and acceptor (A) chromophores and their supramolecular switching to segregated states. Chem Eur J 18(32):9849–9859. doi:10.1002/chem.201201140

    Article  CAS  PubMed  Google Scholar 

  123. Au-Yeung HY, Dan Pantoş G, Sanders JKM (2009) Amplifying different [2]catenanes in an aqueous donor−acceptor dynamic combinatorial library. J Am Chem Soc 131(44):16030–16032. doi:10.1021/ja906634h

    Article  CAS  PubMed  Google Scholar 

  124. Ghosh S, Ramakrishnan S (2005) Small-molecule-induced folding of a synthetic polymer. Angew Chem Int Ed 44(34):5441–5447. doi:10.1002/anie.200501448

    Article  CAS  Google Scholar 

  125. Gabriel GJ, Iverson BL (2002) Aromatic oligomers that form hetero duplexes in aqueous solution. J Am Chem Soc 124(51):15174–15175. doi:10.1021/ja0275358

    Article  CAS  PubMed  Google Scholar 

  126. Peebles C, Piland R, Iverson BL (2013) More than meets the eye: conformational switching of a stacked dialkoxynaphthalene-naphthalenetetracarboxylic diimide (DAN-NDI) foldamer to an NDI-NDI fibril aggregate. Chem Eur J 19(35):11598–11602. doi:10.1002/chem.201302009

    Article  CAS  PubMed  Google Scholar 

  127. Bradford VJ, Iverson BL (2008) Amyloid-like behavior in abiotic, amphiphilic foldamers. J Am Chem Soc 130(4):1517–1524. doi:10.1021/ja0780840

    Article  CAS  PubMed  Google Scholar 

  128. Takada T, Otsuka Y, Nakamura M, Yamana K (2014) Formation of a charge transfer complex within a hydrophobic cavity in DNA. RSC Adv 4(103):59440–59443. doi:10.1039/C4RA11761A

    Article  CAS  Google Scholar 

  129. Bhosale R, Misek J, Sakai N, Matile S (2010) Supramolecular n/p-heterojunction photosystems with oriented multicolored antiparallel redox gradients (OMARG-SHJs). Chem Soc Rev 39(1):138–149

    Article  CAS  PubMed  Google Scholar 

  130. Chen C-H, Liu K-Y, Sudhakar S, Lim T-S, Fann W, Hsu C-P, Luh T-Y (2005) Efficient light harvesting and energy transfer in organic-inorganic hybrid multichromophoric materials. J Phys Chem B 109(38):17887–17891

    Article  CAS  PubMed  Google Scholar 

  131. Peng K-Y, Chen S-A, Fann W-S (2001) Efficient light harvesting by sequential energy transfer across aggregates in polymers of finite conjugational segments with short aliphatic linkages. J Am Chem Soc 123(46):11388–11397

    Article  CAS  PubMed  Google Scholar 

  132. Fleming CN, Maxwell KA, DeSimone JM, Meyer TJ, Papanikolas JM (2001) Ultrafast excited-state energy migration dynamics in an efficient light-harvesting antenna polymer based on Ru(II) and Os(II) polypyridyl complexes. J Am Chem Soc 123(42):10336–10347

    Article  CAS  PubMed  Google Scholar 

  133. Zang L, Che Y, Moore JS (2008) One-dimensional self-assembly of planar pi-conjugated molecules: adaptable building blocks for organic nanodevices. Acc Chem Res 41(12):1596–1608

    Article  CAS  PubMed  Google Scholar 

  134. Hide F, Díaz-García MA, Schwartz BJ, Heeger AJ (1997) New developments in the photonic applications of conjugated polymers. Acc Chem Res 30(10):430–436

    Article  CAS  Google Scholar 

  135. Greyson EC, Stepp BR, Chen X, Schwerin AF, Paci I, Smith MB, Akdag A, Johnson JC, Nozik AJ, Michl J, Ratner MA (2010) Singlet exciton fission for solar cell applications: energy aspects of interchromophore coupling. J Phys Chem B 114(45):14223–14232

    Article  CAS  PubMed  Google Scholar 

  136. Hardin BE, Hoke ET, Armstrong PB, Yum J-H, Comte P, Torres T, Frechet JMJ, Nazeeruddin MK, Gratzel M, McGehee MD (2009) Increased light harvesting in dye-sensitized solar cells with energy relay dyes. Nat Photon 3(7):406–411

    Article  CAS  Google Scholar 

  137. Coakley KM, McGehee MD (2004) Conjugated polymer photovoltaic cells. Chem Mater 16(23):4533–4542

    Article  CAS  Google Scholar 

  138. Shionoya M, Kimura E, Shiro M (1993) A new ternary zinc(II) complex with [12]aneN4 (=1,4,7,10-tetraazacyclododecane) and AZT (=3′-azido-3′-deoxythymidine). Highly selective recognition of thymidine and its related nucleosides by a zinc(II) macrocyclic tetraamine complex with novel complementary associations. J Am Chem Soc 115(15):6730–6737

    Article  CAS  Google Scholar 

  139. Kikuta E, Murata M, Katsube N, Koike T, Kimura E (1999) Novel recognition of thymine base in double-stranded DNA by zinc(II)-macrocyclic tetraamine complexes appended with aromatic groups. J Am Chem Soc 121(23):5426–5436

    Article  CAS  Google Scholar 

  140. Nakamura M, Okaue T, Takada T, Yamana K (2012) DNA-templated assembly of naphthalenediimide arrays. Chem Eur J 18(1):196–201

    Article  CAS  PubMed  Google Scholar 

  141. Tsuto K, Nakamura M, Takada T, Yamana K (2014) Diketopyrrolopyrrole J-aggregates formed by self-organization with DNA. Chem Asian J 9:1618–1622. doi:10.1002/asia.201402063

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan

    Tadao Takada, Mitsunobu Nakamura & Kazushige Yamana

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  1. Tadao Takada
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  2. Mitsunobu Nakamura
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  3. Kazushige Yamana
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Correspondence to Kazushige Yamana .

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  1. The Institute of Scientific and Industri, Osaka University, Ibaraki, Osaka, Japan

    Kazuhiko Nakatani

  2. University of California, San Diego, La Jolla, California, USA

    Yitzhak Tor

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Takada, T., Nakamura, M., Yamana, K. (2016). DNA-Assisted Multichromophore Assembly. In: Nakatani, K., Tor, Y. (eds) Modified Nucleic Acids. Nucleic Acids and Molecular Biology, vol 31. Springer, Cham. https://doi.org/10.1007/978-3-319-27111-8_5

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