Metal‐Containing Nucleic Acid Structures Based on Synergetic Hydrogen and Coordination Bonding

He, Wei; Franzini, Raphael M.; Achim, Catalina

doi:10.1002/9780470144428.ch8

Cited by 30 publications

(30 citation statements)

References 173 publications

(257 reference statements)

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“…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][3][4][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.…”

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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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“…[41] In such a base pair, the natural nucleobases are replaced by ligands with a high affinity towards metal ions. [42][43][44][45][46] Hence, the base pair is no longer mediated by hydrogen bonds but rather by coordinative bonds to a central metal ion. This leads to a functionalization of the nucleic acids difficult to obtain otherwise: The metal ions can be arrayed in a geometrical fashion pre-defined by the choice of the oligonucleotide sequence.…”

Section: Introductionmentioning

confidence: 99%

Metal‐Ion‐Mediated Base Pairs in Nucleic Acids

Müller

2008

Eur J Inorg Chem

159

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Nucleic acids and their analogues raise more and more interest in research areas outside biology and biochemistry. The functionalization of these evolutionary optimized self-assembling macromolecules with metal ions widens their applicability even further. Previous efforts to incorporate metal ions site-specifically into nucleic acids focused on the covalent attachment of appropriate ligands to either the sugar phosphate backbone or the nucleobases. More recently, the

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“…It may be possible to metalize other nucleic acids in similar ways and thus converting them into a plausible conducting nanowire [ 76 ]. But the issue with using anything other than DNA is (1) how to control metallization in a location or sequence specific manner, and (2) how to make nano-scaffolds using that nucleic acid.…”

Section: Reca With Pna and Possibly Other Nucleic Acidsmentioning

confidence: 99%

“…Because PNA is initially neutral, perhaps this can be metallized in pH ranges that are more amenable to the use of RecA [ 76 ]. Apparently RecA-ssDNA strands can facilitate strand exchange in PNA and other nucleic acids as well [86].…”

Section: Reca With Pna and Possibly Other Nucleic Acidsmentioning

confidence: 99%

“…Results from mathematical models show that changes in the angle of hydrogen bonding is usually less than 5°, and the hydrogen bond length usually is reduced by 0.008 nm (see Figure 40) [73]. The biological systems, the purpose of M-DNA is to make some DNA less amenable to enzymatic Although GC content was predicted to be an indicator of M-DNA stability [76]. So we also need to choose metal ions based on this phenomenon as well.…”

Section: B M-dnamentioning

confidence: 99%

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Nucleic Acid Electronics: from Chemistry to Circuits

Verma

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Metal‐Containing Nucleic Acid Structures Based on Synergetic Hydrogen and Coordination Bonding

Cited by 30 publications

References 173 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

Metal‐Ion‐Mediated Base Pairs in Nucleic Acids

Nucleic Acid Electronics: from Chemistry to Circuits

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