Programmable self-assembly of metal ions inside artificial DNA duplexes

Tanaka, Kentaro; Clever, Guido H.; Takezawa, Yusuke; Yamada, Yasuyuki; Kaul, Corinna; Shionoya, Mitsuhiko; Carell, Thomas

doi:10.1038/nnano.2006.141

Cited by 322 publications

(208 citation statements)

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“…Even if focussing only on the use of artificial nucleosides, examples exist for DNA duplexes containing one or two metal-mediated base pairs interspersed between natural ones, [6][7][8] DNA double helices with continuous stretches of metalated base pairs, [9][10][11] and DNA duplexes with different metalmediated base pairs at pre-defined positions. 12 When including also metal-mediated base pairs from natural nucleosides, [13][14][15] even more combinations can be envisaged.…”

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confidence: 99%

Solution structure of a DNA double helix with consecutive metal-mediated base pairs

et al. 2010

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Metal-mediated base pairs represent a powerful tool for the site-specific functionlization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre. In the absence of transition-metal ions, a hairpin structure is adopted with the artifical nucleotides forming the loop. In the presence of Ag(I) ions, a duplex comprising three imidazoleAg+-imidazole base pairs is formed. Direct proof for the formation of metal-mediated base pairs was obtained from (1) AbstractMetal-mediated base pairs represent a powerful tool for the site-specific functionalization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre: In the absence of transition metal ions, a hairpin structure is adopted with the artificial nucleotides forming the loop. In the presence of silver(I) ions, a duplex comprising three imidazole-Ag + -imidazole base pairs is formed.Direct proof for the formation of metal-mediated base pairs was obtained from 1 J( 15 N, 107/109 Ag) couplings upon incorporation of 15 N-labelled imidazole. The duplex adopts a B-type conformation with only minor deviations in the region of the artificial base pairs. This structure represents the first example of a metal-modified nucleic acid with a continuous stretch of metal-mediated base pairs.3 Nucleic acids such as DNA are becoming increasingly popular as versatile building blocks in nanobiotechnology as a result of their superb, predictable self-assembling properties and the high rigidity of their double helices on the nanoscale. 1 Their applicability can be extended even further by the introduction of functional groups such as metal ions. One recently established method for the site-specific functionalization of nucleic acids with metal ions is based on the use of metal-mediated base pairs. 2-5 Such base pairs comprise natural or artificial nucleobases and rely on coordinative bonds to a central metal ion instead of (or in addition to) hydrogen bonds. Depending on the choice of nucleosides, metal ions, and oligonucleotide sequence, a plethora of metal-modified double helices can be generated. Even if focussing only on the use of artificial nucleosides, examples exist for DNA duplexes containing one or two metal-mediated base pairs interspersed between natural ones, 6-8 DNA double helices with continuous stretches of metalated base pairs, 9-11 and DNA duplexes with different metalmediated base pairs at pre-defined positions. 12 When including also metal-mediated base pairs from natural nucleosides, 13-15 even more combinations can ...

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Solution structure of a DNA double helix with consecutive metal-mediated base pairs

et al. 2010

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“…in our laboratory, the aim is to construct nanodevices with particular electric, magnetic and sensing properties. [47,48] …”

Section: Metal Ion-assisted Folding Of Large Rnasmentioning

confidence: 99%

Shaping RNA Structures with Metal Ions and Metal Ion Complexes

Sigel

Gallo²

2010

Chimia

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The research in our laboratory focuses on the role of metal ions and their complexes in structure formation and folding of nucleic acids. Large catalytic RNAs, like group II introns and some riboswitches, as well as shorter RNAs and DNAs containing modified nucleotides for the assembly of nanodevices are examined. Abundant metal ions like Mg2+ or natural metabolites like coenzyme B-12 are in the center of interest, but also other metal ions, complexes thereof and B-12 derivatives are applied with the aim to understand the largely unknown and manifold non-covalent interactions with nucleic acids. We apply a multitude of techniques, including potentiometric pH titrations, NMR spectroscopy, X-ray crystallography, gel electrophoresis and single molecule FRET experiments. Here we briefly summarize each of our research topics emphasizing the interaction of coenzyme B-12 and its derivatives with the btuB riboswitch of E. coli. This highly conserved sequence, found in the 5'-untranslated region (5'-UTR) of the btuB mRNA, is involved in the regulation of the btuB protein expression. After a summary on the historical discovery of such riboswitches and their mechanism of action, we shortly focus on our own contributions to understand the structural equilibrium, high affinity and selectivity of the interaction between this specific RNA sequence and the largest and most complex cellular metabolite, coenzyme B-12. or natural metabolites like coenzyme B 12 are in the center of interest, but also other metal ions, complexes thereof and B 12 derivatives are applied with the aim to understand the largely unknown and manifold non-covalent interactions with nucleic acids. We apply a multitude of techniques, including potentiometric pH titrations, NMR spectroscopy, X-ray crystallography, gel electrophoresis and single molecule FRET experiments. Here we briefly summarize each of our research topics emphasizing the interaction of coenzyme B 12 and its derivatives with the btuB riboswitch of E. coli. This highly conserved sequence, found in the 5'-untranslated region (5'-UTR) of the btuB mRNA, is involved in the regulation of the btuB protein expression. After a summary on the historical discovery of such riboswitches and their mechanism of action, we shortly focus on our own contributions to understand the structural equilibrium, high affinity and selectivity of the interaction between this specific RNA sequence and the largest and most complex cellular metabolite, coenzyme B 12 .

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“…The base pairing properties of DNA can be altered by incorporating metal ions in the center of two opposite nucleobases, allowing the double strand to implement non-natural base pairs held together through coordinative forces rather than hydrogen bonds. [10,11] For example a thymine-thymine (T-T) mismatch base pair is stabilized by addition of Hg 2+ , which replaces the H(3) protons of the two opposite pyrimidine bases (Fig. 2D).…”

Section: Artificial Metal Ions-nucleic Acids Systemsmentioning

confidence: 99%

“…What makes this story even more interesting (and at the same time also more challenging) is that many more metal ions than just Na + and Mg 2+ can be involved with nucleic acids: i) Redox active metal ions are used in combination with specific sequences or modified oligonucleotides to build up electronic molecular devices for nanotechnology. [10][11][12] ii) Other metal ions than Mg 2+ are used for in vitro studies of, e.g. ribozymes, to localize binding sites and elucidate the functional roles of these ions.…”

Section: Introductionmentioning

confidence: 99%

Exploring Metal Ion Coordination to Nucleic Acids by NMR

Johannsen¹,

Korth²,

Schnabl³

et al. 2009

Chimia

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Metal ions play a crucial role in charge compensation, folding and stabilization of tertiary structures of large nucleic acids. In addition, they may be directly involved in the catalytic mechanism of ribozymes. Most metal ions applied in the context of nucleic acids in vivo and in vitro bind in a kinetically labile fashion. Hence, the detection of metal ion binding sites, not to mention the elucidation of the specific coordination sphere, still poses largely unresolved problems. Here we describe the different strategies applied and the progress made over the last years to characterize metal ion coordination to large nucleic acids by NMR. Metal ions play a crucial role in charge compensation, folding and stabilization of tertiary structures of large nucleic acids. In addition, they may be directly involved in the catalytic mechanism of ribozymes. Most metal ions applied in the context of nucleic acids in vivo and in vitro bind in a kinetically labile fashion. Hence, the detection of metal ion binding sites, not to mention the elucidation of the specific coordination sphere, still poses largely unresolved problems. Here we describe the different strategies applied and the progress made over the last years to characterize metal ion coordination to large nucleic acids by NMR.

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Programmable self-assembly of metal ions inside artificial DNA duplexes

Cited by 322 publications

References 15 publications

Solution structure of a DNA double helix with consecutive metal-mediated base pairs

Solution structure of a DNA double helix with consecutive metal-mediated base pairs

Shaping RNA Structures with Metal Ions and Metal Ion Complexes

Exploring Metal Ion Coordination to Nucleic Acids by NMR

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