Metal–base pairing in DNA

Abstract The use of DNA as a molecular wire in nanoscale electronic architectures would greatly benefit from its capability of sequence-specific self-assembly. Although single electrons and positive charges have been shown to be transmitted by natural DNA over a distance of several base pairs, the high ohmic resistance of unmodified oligonucleotides imposes a serious obstacle. Exchanging some or all of the Watson–Crick base pairs in DNA by metal complexes may solve this problem and evolve DNA-like materials with superior conductivity for future nano-electronic applications. The so-called metal–base pairs are formed from suitable transition metal ions and ligand-like nucleosides which are introduced into both of the two pairing strands by automated DNA synthesis. This review illustrates the basic concepts of metal–base pairing and highlights recent developments in the field.

[1]  F. Seela,et al.  6-aza-2'-deoxyisocytidine: synthesis, properties of oligonucleotides, and base-pair stability adjustment of DNA with parallel strand orientation. , 2003, The Journal of organic chemistry.

[2]  M. Gait,et al.  Oligonucleotide synthesis : a practical approach , 1984 .

[3]  E. Meggers,et al.  Duplex Structure of a Minimal Nucleic Acid , 2008, Journal of the American Chemical Society.

[4]  Masayuki Endo,et al.  Chemical Approaches to DNA Nanotechnology , 2009, Chembiochem : a European journal of chemical biology.

[5]  T. Carell,et al.  Programmable self-assembly of metal ions inside artificial DNA duplexes , 2006, Nature nanotechnology.

[6]  P. Schultz,et al.  Structure of a copper-mediated base pair in DNA. , 2001, Journal of the American Chemical Society.

[7]  James Hone,et al.  Conductivity of a single DNA duplex bridging a carbon nanotube gap. , 2008, Nature nanotechnology.

[8]  Christof M Niemeyer,et al.  Nanomechanical devices based on DNA. , 2002, Angewandte Chemie.

[9]  T. Carell,et al.  Metal-salen-base-pair complexes inside DNA: complexation overrides sequence information. , 2006, Chemistry.

[10]  Kentaro Tanaka,et al.  Efficient incorporation of a copper hydroxypyridone base pair in DNA. , 2002, Journal of the American Chemical Society.

[11]  T. Carell,et al.  Controlled stacking of 10 transition-metal ions inside a DNA duplex. , 2007, Angewandte Chemie.

[12]  P. Schultz,et al.  A second-generation copper(II)-mediated metallo-DNA-base pair. , 2004, Bioorganic chemistry.

[13]  Michael Famulok,et al.  A versatile toolbox for variable DNA functionalization at high density. , 2005, Journal of the American Chemical Society.

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

[15]  Chojiro Kojima,et al.  15N-15N J-coupling across Hg(II): direct observation of Hg(II)-mediated T-T base pairs in a DNA duplex. , 2007, Journal of the American Chemical Society.

[16]  Luigi G. Marzilli,et al.  Mercury(II) Site-Selective Binding to a DNA Hairpin. Relationship of Sequence-Dependent Intra- and Interstrand Cross-Linking to the Hairpin-Duplex Conformational Transition. , 1996, Inorganic chemistry.

[17]  E. Buncel,et al.  Metal ion-biomolecule interactions. XII. 1H and 13C NMR evidence for the preferred reaction of thymidine over guanosine in exchange and competition reactions with Mercury(II) and Methylmercury(II) , 1985 .

[18]  P. Dumas,et al.  A crystallographic study of the binding of 13 metal ions to two related RNA duplexes. , 2003, Nucleic acids research.

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

[20]  Nadrian C Seeman,et al.  The Challenge of Structural Control on the Nanoscale: Bottom-Up Self-Assembly of Nucleic Acids in 3D. , 2005, International journal of nanotechnology.

[21]  Michal Hocek,et al.  C-nucleosides: synthetic strategies and biological applications. , 2009, Chemical reviews.

[22]  T. Carell,et al.  A highly DNA-duplex-stabilizing metal-salen base pair. , 2005, Angewandte Chemie.

[23]  Kentaro Tanaka,et al.  A Discrete Self-Assembled Metal Array in Artificial DNA , 2003, Science.

[24]  C. Papadopoulos,et al.  Metallic conduction through engineered DNA: DNA nanoelectronic building blocks. , 2001, Physical review letters.

[25]  C. Niemeyer REVIEW Nanoparticles, Proteins, and Nucleic Acids: Biotechnology Meets Materials Science , 2022 .

[26]  Peter G. Schultz,et al.  A Novel Copper-Mediated DNA Base Pair , 2000 .

[27]  Faisal A. Aldaye,et al.  Assembling Materials with DNA as the Guide , 2008, Science.

[28]  Hao Yan,et al.  Nucleic Acid Nanotechnology , 2004, Science.

[29]  A. Houlton,et al.  DNA-based routes to semiconducting nanomaterials. , 2009, Chemical communications.

[30]  Kurt V Gothelf,et al.  DNA-programmed assembly of nanostructures. , 2005, Organic & biomolecular chemistry.

[31]  Takashi Fujimoto,et al.  MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes. , 2006, Journal of the American Chemical Society.

[32]  C. Switzer,et al.  A pyrimidine-like nickel(II) DNA base pair. , 2005, Chemical communications.

[33]  Metal‐Ion‐Mediated Base Pairs in Nucleic Acids , 2008 .

[34]  L. Delbaere,et al.  M-DNA: A complex between divalent metal ions and DNA which behaves as a molecular wire. , 1999, Journal of molecular biology.

[35]  P. Schultz,et al.  A novel silver(i)-mediated DNA base pair. , 2002, Journal of the American Chemical Society.

[36]  M. Famulok,et al.  Building objects from nucleic acids for a nanometer world. , 2008, Biochimie.

[37]  E. Meggers,et al.  Metal-mediated base pairing within the simplified nucleic acid GNA. , 2009, Organic and biomolecular chemistry.

[38]  Jens Müller Chemistry: Metals line up for DNA , 2006, Nature.

[39]  R. Sigel,et al.  Solution structure of a DNA double helix with consecutive metal-mediated base pairs. , 2010, Nature chemistry.

[40]  Jens Müller,et al.  An artificial base pair, mediated by hydrogen bonding and metal-ion binding. , 2007, Angewandte Chemie.

[41]  Faisal A. Aldaye,et al.  Modular construction of DNA nanotubes of tunable geometry and single- or double-stranded character. , 2009, Nature nanotechnology.

[42]  K. Hirao,et al.  Theoretical studies on sulfur and metal cation (Cu(II), Ni(II), Pd(II), and Pt(II))-containing artificial DNA. , 2009, The journal of physical chemistry. B.

[43]  M R Arkin,et al.  Long-range photoinduced electron transfer through a DNA helix. , 1993, Science.

[44]  R. Sigel,et al.  Using in vitro transcription to construct scaffolds for one-dimensional arrays of mercuric ions. , 2008, Journal of inorganic biochemistry.

[45]  A. Ono,et al.  Highly selective oligonucleotide-based sensor for mercury(II) in aqueous solutions. , 2004, Angewandte Chemie.

[46]  A. Okamoto,et al.  Pyrene-labeled base-discriminating fluorescent DNA probes for homogeneous SNP typing. , 2004, Journal of the American Chemical Society.

[47]  Christof M Niemeyer,et al.  Rational design of DNA nanoarchitectures. , 2006, Angewandte Chemie.

[48]  J. Gómez‐Herrero,et al.  Towards Molecular Wires Based on Metal‐Organic Frameworks , 2009 .

[49]  D. Levy,et al.  The Chemistry of C-Glycosides , 1995 .

[50]  J. Wengel,et al.  Nucleic acid nanotechnology-towards Angstrom-scale engineering. , 2004, Organic & biomolecular chemistry.

[51]  P. Fromherz,et al.  Signal transmission from individual mammalian nerve cell to field-effect transistor. , 2005, Small.

[52]  Erik Winfree,et al.  Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. , 2010, Nature nanotechnology.

[53]  T. Carell,et al.  DNA--metal base pairs. , 2007, Angewandte Chemie.

[54]  T. Majima,et al.  Charge separation in acridine- and phenothiazine-modified DNA. , 2008, The journal of physical chemistry. B.

[55]  M. Mehring,et al.  Differential reactivity of α and β 2′-deoxyribonucleosides towards protonation and metalation , 2007 .

[56]  Yasuyuki Yamada,et al.  Formation of silver(I)-mediated DNA duplex and triplex through an alternative base pair of pyridine nucleobases. , 2002, Journal of the American Chemical Society.

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

[58]  Benjamin Elias,et al.  Ping-pong electron transfer through DNA. , 2008, Angewandte Chemie.

[59]  Steven A Benner,et al.  Understanding nucleic acids using synthetic chemistry. , 2004, Accounts of chemical research.

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

[61]  I. Willner,et al.  Multiplexed analysis of Hg2+ and Ag+ ions by nucleic acid functionalized CdSe/ZnS quantum dots and their use for logic gate operations. , 2009, Angewandte Chemie.

[62]  Chad A. Mirkin,et al.  Programmed Materials Synthesis with DNA. , 1999, Chemical reviews.

[63]  Y. Kitagawa,et al.  Theoretical studies on magnetic interactions between Cu(II) ions in salen nucleobases , 2009 .

[64]  Kentaro Tanaka,et al.  Programmable metal assembly on bio-inspired templates , 2007 .

[65]  Yoav Eichen,et al.  Directed DNA metallization. , 2006, Journal of the American Chemical Society.

[66]  Á. Somoza,et al.  Evolution of DNA origami. , 2009, Angewandte Chemie.

[67]  Kentaro Tanaka,et al.  Synthesis of a Novel Nucleoside for Alternative DNA Base Pairing through Metal Complexation. , 1999, The Journal of organic chemistry.

[68]  M. Fujita,et al.  Engineering discrete stacks of aromatic molecules. , 2009, Chemical Society reviews.

[69]  Y. Tor,et al.  2,2'-Bipyridine ligandoside: a novel building block for modifying DNA with intra-duplex metal complexes. , 2001, Journal of the American Chemical Society.

[70]  E. Meggers,et al.  An extremely stable and orthogonal DNA base pair with a simplified three-carbon backbone. , 2005, Journal of the American Chemical Society.

[71]  Jeremy S. Lee,et al.  A field-effect transistor from M-DNA , 2007 .

[72]  Sairam S. Mallajosyula,et al.  Conformational tuning of magnetic interactions in metal-DNA complexes. , 2009, Angewandte Chemie.

[73]  F. Simmel Three-dimensional nanoconstruction with DNA. , 2008, Angewandte Chemie.

[74]  Jens Müller,et al.  Conformational change induced by metal-ion-binding to DNA containing the artificial 1,2,4-triazole nucleoside. , 2007, Inorganic chemistry.

[75]  J. Wengel,et al.  Functionalized LNA (locked nucleic acid): high-affinity hybridization of oligonucleotides containing N-acylated and N-alkylated 2'-amino-LNA monomers. , 2003, Chemical communications.

[76]  S. Katz The Reversible Reaction of Sodium Thymonucleate and Mercuric Chloride , 1952 .

[77]  Kentaro Tanaka,et al.  Soft metal-mediated base pairing with novel synthetic nucleosides possessing an O,S-donor ligand. , 2008, The Journal of organic chemistry.

[78]  C. Switzer,et al.  A purine-like nickel(II) base pair for DNA. , 2005, Angewandte Chemie.

[79]  T. Carell,et al.  Investigation of the pathways of excess electron transfer in DNA with flavin-donor and oxetane-acceptor modified DNA hairpins. , 2006, Chemistry.

[80]  Y. Tor,et al.  Metal-Containing Oligonucleotides: Solid-Phase Synthesis and Luminescence Properties , 1998 .

[81]  A. Voityuk Electronic coupling mediated by stacked [Thymine-Hg-Thymine] base pairs. , 2006, The journal of physical chemistry. B.

[82]  A. Ono,et al.  Metal-ion selectivity of chemically modified uracil pairs in DNA duplexes. , 2009, Angewandte Chemie.

[83]  T. Carell,et al.  Synthesis of modified DNA by PCR with alkyne-bearing purines followed by a click reaction. , 2008, Organic letters.

[84]  S. Tagawa,et al.  Photogenerated hole mobility in DNA measured by time-resolved microwave conductivity. , 2006, Journal of the American Chemical Society.

[85]  Joshy Joseph,et al.  Long-distance radical cation hopping in DNA: the effect of thymine-Hg(II)-thymine base pairs. , 2007, Organic letters.

[86]  Kentaro Tanaka,et al.  Discrete self-assembly of iron(III) ions inside triple-stranded artificial DNA. , 2009, Angewandte Chemie.

[87]  S. Katz,et al.  The reversible reaction of Hg (II) and double-stranded polynucleotides. A step-function theory and its significance. , 1963, Biochimica et biophysica acta.

[88]  E. Kool,et al.  Redesigning the architecture of the base pair: toward biochemical and biological function of new genetic sets. , 2009, Chemistry & biology.

[89]  E. Scheer,et al.  Direct measurement of electrical transport through G-quadruplex DNA with mechanically controllable break junction electrodes. , 2010, Angewandte Chemie.

[90]  Jens Müller,et al.  Metal ion coordination to azole nucleosides. , 2005, Chemistry.

[91]  D. A. Megger,et al.  Silver(I)-Mediated Cytosine Self-Pairing is Preferred Over Hoogsteen-Type Base Pairs with the Artificial Nucleobase 1,3-Dideaza-6-Nitropurine , 2010, Nucleosides, nucleotides & nucleic acids.

[92]  E. Stulz,et al.  Duplex stabilization and energy transfer in zipper porphyrin-DNA. , 2009, Angewandte Chemie.

[93]  N. Araki,et al.  Silver ion unusually stabilizes the structure of a parallel-motif DNA triplex. , 2009, Journal of the American Chemical Society.

[94]  A. Ono,et al.  Specific interactions between silver(I) ions and cytosine-cytosine pairs in DNA duplexes. , 2008, Chemical communications.

[95]  T. Carell,et al.  Antiferromagnetic coupling of stacked Cu(II)-salen complexes in DNA. , 2010, Angewandte Chemie.