Fluorescence in Bio-inspired Nanotechnology: First as Probe, Then as Function

[1]  A. Turing.  On Computable Numbers, with an Application to the Entscheidungsproblem. , 1937 .

[2]  F. Crick,et al.  Genetical Implications of the Structure of Deoxyribonucleic Acid , 1953, Nature.

[3]  Hao Wang,et al.  Proving theorems by pattern recognition I , 1960, Commun. ACM.

[4]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1974, Nature.

[5]  N. Seeman.  Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.

[6]  N. Seeman,et al.  An immobile nucleic acid junction constructed from oligonucleotides , 1983, Nature.

[7]  Y. Imanishi,et al.  Investigation on the interactions of peptides in the assembly of liposome and peptide by fluorescence. , 1983, Biochimica et biophysica acta.

[8]  T. Moore,et al.  Photodriven charge separation in a carotenoporphyrin–quinone triad , 1984, Nature.

[9]  N. Seeman,et al.  DNA double-crossover molecules. , 1993, Biochemistry.

[10]  M. Guéron,et al.  A tetrameric DNA structure with protonated cytosine-cytosine base pairs , 1993, Nature.

[11]  Thomas A. Moore,et al.  Molecular mimicry of photosynthetic energy and electron transfer , 1993 .

[12]  N. Seeman,et al.  Construction of a DNA-Truncated Octahedron , 1994 .

[13]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[14]  Jonathan S. Lindsey,et al.  A molecular photonic wire , 1994 .

[15]  K. Schulten,et al.  The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum. , 1996, Structure.

[16]  R. Wagner,et al.  Molecular Optoelectronic Gates , 1996 .

[17]  B. Valeur,et al.  Multichromophoric Cyclodextrins. 4. Light Conversion by Antenna Effect , 1996 .

[18]  Thomas A. Moore,et al.  Conversion of light energy to proton potential in liposomes by artificial photosynthetic reaction centres , 1997, Nature.

[19]  Klaus Schulten,et al.  How Nature Harvests Sunlight , 1997 .

[20]  K Schulten,et al.  Architecture and mechanism of the light-harvesting apparatus of purple bacteria. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[21]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[22]  T. Moore,et al.  An Artificial Photosynthetic Antenna-Reaction Center Complex , 1999 .

[23]  S. Murata,et al.  Sequential multistep energy transfer: enhancement of efficiency of long-range fluorescence resonance energy transfer , 1999 .

[24]  N. Seeman,et al.  A nanomechanical device based on the B–Z transition of DNA , 1999, Nature.

[25]  R. Wagner,et al.  Structural Control of Photoinduced Energy Transfer between Adjacent and Distant Sites in Multiporphyrin Arrays , 2000 .

[26]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[27]  J. Reif,et al.  Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes , 2000 .

[28]  T. Moore,et al.  Mimicking photosynthetic solar energy transduction. , 2001, Accounts of chemical research.

[29]  S. Jockusch,et al.  Triple fluorescence energy transfer in covalently trichromophore-labeled DNA. , 2001, Journal of the American Chemical Society.

[30]  N. Seeman,et al.  A robust DNA mechanical device controlled by hybridization topology , 2002, Nature.

[31]  S. Boxer,et al.  Micropattern formation in supported lipid membranes. , 2002, Accounts of chemical research.

[32]  R. Wagner,et al.  Weakly coupled molecular photonic wires: synthesis and excited-state energy-transfer dynamics. , 2002, The Journal of organic chemistry.

[33]  I. Yamazaki,et al.  Dendritic multiporphyrin arrays as light-harvesting antennae: effects of generation number and morphology on intramolecular energy transfer. , 2002, Chemistry.

[34]  Masafumi Hashimoto,et al.  Multistep fluorescence resonance energy transfer in sequential chromophore array constructed on oligo-DNA assemblies. , 2003, Bioconjugate chemistry.

[35]  S. Boxer,et al.  Arrays of mobile tethered vesicles on supported lipid bilayers. , 2003, Journal of the American Chemical Society.

[36]  N. Seeman.  DNA in a material world , 2003, Nature.

[37]  F. Würthner,et al.  Energy transfer in multichromophoric self-assembled molecular squares. , 2003, Organic & biomolecular chemistry.

[38]  D. Reinhoudt,et al.  Single molecule photobleaching probes the exciton wave function in a multichromophoric system. , 2004, Physical Review Letters.

[39]  William M. Shih,et al.  A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron , 2004, Nature.

[40]  N. Seeman,et al.  A precisely controlled DNA biped walking device , 2004 .

[41]  Mike Heilemann,et al.  Multistep energy transfer in single molecular photonic wires. , 2004, Journal of the American Chemical Society.

[42]  J. Reif,et al.  A unidirectional DNA walker that moves autonomously along a track. , 2004, Angewandte Chemie.

[43]  Andrew J Turberfield,et al.  The single-step synthesis of a DNA tetrahedron. , 2004, Chemical communications.

[44]  David R. Liu,et al.  DNA-templated organic synthesis: nature's strategy for controlling chemical reactivity applied to synthetic molecules. , 2004, Angewandte Chemie.

[45]  C. Mao,et al.  Tensegrity: construction of rigid DNA triangles with flexible four-arm DNA junctions. , 2004, Journal of the American Chemical Society.

[46]  A. Granéli,et al.  DNA-based formation of a supported, three-dimensional lipid vesicle matrix probed by QCM-D and SPR. , 2004, Chemphyschem : a European journal of chemical physics and physical chemistry.

[47]  P. Prasad,et al.  Fluorescence resonance energy transfer in novel multiphoton absorbing dendritic structures , 2004 .

[48]  N. Seeman,et al.  Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology. , 2004, Journal of the American Chemical Society.

[49]  A. Turberfield,et al.  Self-assembly of chiral DNA nanotubes. , 2004, Journal of the American Chemical Society.

[50]  J. Reif,et al.  DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[51]  I. Yamazaki,et al.  Bioinspired molecular design of light-harvesting multiporphyrin arrays. , 2004, Angewandte Chemie.

[52]  S. Quake,et al.  Nanometer-scale Fluorescence Resonance Optical Waveguides , 2004 .

[53]  E. Winfree,et al.  Design and characterization of programmable DNA nanotubes. , 2004, Journal of the American Chemical Society.

[54]  Jeffery T. Davis.  G-Quartets 40 Years Later: From 5′-GMP to Molecular Biology and Supramolecular Chemistry , 2004 .

[55]  F. Simmel,et al.  Switching the conformation of a DNA molecule with a chemical oscillator. , 2005, Nano letters.

[56]  Mike Heilemann,et al.  Design of molecular photonic wires based on multistep electronic excitation transfer. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[57]  J. Joanny,et al.  Single-file electrophoretic transport and counting of individual DNA molecules in surfactant nanotubes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Russell P. Goodman,et al.  Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication , 2005, Science.

[59]  I. V. van Stokkum,et al.  Ultrafast energy-electron transfer cascade in a multichromophoric light-harvesting molecular square. , 2005, Journal of the American Chemical Society.

[60]  N. Seeman,et al.  Six-helix bundles designed from DNA. , 2005, Nano letters.

[61]  Chengde Mao,et al.  Self-assembly of hexagonal DNA two-dimensional (2D) arrays. , 2005, Journal of the American Chemical Society.

[62]  Tim Liedl,et al.  A surface-bound DNA switch driven by a chemical oscillator. , 2006, Angewandte Chemie.

[63]  R. Erdmann,et al.  DNA-based molecular wires: multiple emission pathways of individual constructs. , 2006, The journal of physical chemistry. B.

[64]  Darko Stefanovic,et al.  Behavior of polycatalytic assemblies in a substrate-displaying matrix. , 2006, Journal of the American Chemical Society.

[65]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[66]  O. Orwar,et al.  Controlling enzymatic reactions by geometry in a biomimetic nanoscale network. , 2006, Nano letters.

[67]  N. Seeman,et al.  Operation of a DNA Robot Arm Inserted into a 2D DNA Crystalline Substrate , 2006, Science.

[68]  G. Seelig,et al.  Enzyme-Free Nucleic Acid Logic Circuits , 2022 .

[69]  Mike Heilemann,et al.  Dissecting and reducing the heterogeneity of excited-state energy transport in DNA-based photonic wires. , 2006, Journal of the American Chemical Society.

[70]  Raphael Zahn,et al.  DNA-induced programmable fusion of phospholipid vesicles. , 2007, Journal of the American Chemical Society.

[71]  A. Waggoner,et al.  Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates. , 2007, Journal of the American Chemical Society.

[72]  Russell P. Goodman,et al.  A self-assembled DNA bipyramid. , 2007, Journal of the American Chemical Society.

[73]  R. Holliday.  A mechanism for gene conversion in fungi. , 1964, Genetical research.

[74]  B. Nordén,et al.  Triplex addressability as a basis for functional DNA nanostructures. , 2007, Nano letters.

[75]  N. Aratani,et al.  Cyclic Porphyrin Arrays as Artificial Photosynthetic Antenna: Synthesis and Excitation Energy Transfer , 2007 .

[76]  M. Francis,et al.  Self-assembling light-harvesting systems from synthetically modified tobacco mosaic virus coat proteins. , 2007, Journal of the American Chemical Society.

[77]  O. Orwar,et al.  Direct immobilization of cholesteryl-TEG-modified oligonucleotides onto hydrophobic SU-8 surfaces. , 2007, Langmuir.

[78]  S. Boxer,et al.  Kinetics of DNA-mediated docking reactions between vesicles tethered to supported lipid bilayers , 2007, Proceedings of the National Academy of Sciences.

[79]  D. Y. Zhang,et al.  Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.

[80]  Piero Baglioni,et al.  Addressable high-information-density DNA nanostructures , 2007 .

[81]  C. Mao,et al.  Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra , 2008, Nature.

[82]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[83]  O Orwar,et al.  Controlling the rates of biochemical reactions and signaling networks by shape and volume changes , 2008, Proceedings of the National Academy of Sciences.

[84]  P. Dedecker,et al.  Excitation energy migration processes in cyclic porphyrin arrays probed by single molecule spectroscopy. , 2008, Journal of the American Chemical Society.

[85]  Mingdong Dong,et al.  DNA origami design of dolphin-shaped structures with flexible tails. , 2008, ACS nano.

[86]  Russell P. Goodman,et al.  Reconfigurable, braced, three-dimensional DNA nanostructures. , 2008, Nature nanotechnology.

[87]  C. Mao,et al.  Conformational flexibility facilitates self-assembly of complex DNA nanostructures , 2008, Proceedings of the National Academy of Sciences.

[88]  B. Albinsson,et al.  Enhanced pi conjugation around a porphyrin[6] nanoring. , 2008, Angewandte Chemie.

[89]  Ryan J. Kershner,et al.  Placement and orientation of individual DNA shapes on lithographically patterned surfaces. , 2009, Nature nanotechnology.

[90]  B. Armitage,et al.  Fluorescent DNA nanotags based on a self-assembled DNA tetrahedron. , 2009, ACS nano.

[91]  J. Kjems,et al.  Self-assembly of a nanoscale DNA box with a controllable lid , 2009, Nature.

[92]  N. Seeman,et al.  Prototyping nanorod control: A DNA double helix sheathed within a DNA six-helix bundle. , 2009, Chemistry & biology.

[93]  Erik Winfree,et al.  An information-bearing seed for nucleating algorithmic self-assembly , 2009, Proceedings of the National Academy of Sciences.

[94]  A. Paul Alivisatos,et al.  Pyramidal and chiral groupings of gold nanocrystals assembled using DNA scaffolds. , 2009, Journal of the American Chemical Society.

[95]  Shawn M. Douglas,et al.  Self-assembly of DNA into nanoscale three-dimensional shapes , 2009, Nature.

[96]  Ruojie Sha,et al.  A Bipedal DNA Brownian Motor with Coordinated Legs , 2009, Science.

[97]  Yan Liu,et al.  DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires , 2003, Science.

[98]  Pamela E. Constantinou,et al.  From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal , 2009, Nature.

[99]  Dongho Kim,et al.  Discrete cyclic porphyrin arrays as artificial light-harvesting antenna. , 2009, Accounts of chemical research.

[100]  F. Höök,et al.  Liposome-based chemical barcodes for single molecule DNA detection using imaging mass spectrometry. , 2010, Nano letters.

[101]  Erik Winfree,et al.  Molecular robots guided by prescriptive landscapes , 2010, Nature.

[102]  F. Simmel,et al.  Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. , 2010, Nano letters.

[103]  N. Seeman,et al.  A Proximity-Based Programmable DNA Nanoscale Assembly Line , 2010, Nature.

[104]  Wael Mamdouh,et al.  Single-molecule chemical reactions on DNA origami. , 2010, Nature nanotechnology.

[105]  Nadrian C Seeman,et al.  Structural DNA nanotechnology: growing along with Nano Letters. , 2010, Nano letters.

[106]  F. Höök,et al.  Site-specific DNA-controlled fusion of single lipid vesicles to supported lipid bilayers. , 2010, Chemphyschem : a European journal of chemical physics and physical chemistry.

[107]  A new fixation strategy for addressable nano-network building blocks. , 2010, Chemical communications.

[108]  Amy L. Stevens,et al.  Directing energy transfer in discrete one-dimensional oligonucleotide-templated assemblies. , 2011, Chemical communications.

[109]  Jehoshua Bruck,et al.  Neural network computation with DNA strand displacement cascades , 2011, Nature.

[110]  T. Brown,et al.  Self-assembled DNA-based fluorescence waveguide with selectable output. , 2011, Small.

[111]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[112]  S. Boxer,et al.  Vesicle fusion observed by content transfer across a tethered lipid bilayer. , 2011, Biophysical journal.

[113]  B. Nordén,et al.  Nanofabrication yields. Hybridization and click-fixation of polycyclic DNA nanoassemblies. , 2011, ACS nano.

[114]  Hao Yan,et al.  DNA-directed artificial light-harvesting antenna. , 2011, Journal of the American Chemical Society.

[115]  Hao Yan,et al.  Challenges and opportunities for structural DNA nanotechnology. , 2011, Nature nanotechnology.

[116]  Philip Tinnefeld,et al.  Single-molecule four-color FRET visualizes energy-transfer paths on DNA origami. , 2011, Journal of the American Chemical Society.

[117]  Florian Garo,et al.  A DNA-based light-harvesting antenna. , 2012, Angewandte Chemie.

[118]  F. Simmel,et al.  DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response , 2011, Nature.

[119]  Shawn M. Douglas,et al.  A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads , 2012, Science.

[120]  Jonathan Bath,et al.  A DNA-based molecular motor that can navigate a network of tracks. , 2012, Nature nanotechnology.

[121]  G. Church,et al.  Next-Generation Digital Information Storage in DNA , 2012, Science.