Stabilisation of non-canonical structures of nucleic acids by metal ions and small molecules

Biver, Tarita

doi:10.1016/j.ccr.2013.04.016

Cited by 41 publications

(26 citation statements)

References 314 publications

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“…One possible source of this discrepancy is the ability of two poly(rA):poly(rU) duplexes to convert back and forth to triplex poly(rA):poly(rU):poly(rU) and a poly(rA) strand, as reported in previous studies (45)(46)(47). We have no direct measure of such a duplex-to-triplex conversion; this speculation is based on those previous reports.…”

Section: Mechanism Of Poly(ra):poly(ru) Condensationmentioning

confidence: 68%

Spermine Condenses DNA, but Not RNA Duplexes

Katz

Tolokh

Pabit

et al. 2017

Biophysical Journal

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Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA and some RNAs, such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA, and compare our findings with predictions of molecular-dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence containing a mixture of 14 GC pairs and 11 AU pairs resists condensation relative to DNA of an equivalent sequence or to 25 bp poly(rA):poly(rU) RNA. A comparison of wide-angle x-ray scattering profiles with simulation results suggests that spermine is sequestered deep within the major groove of mixed-sequence RNA. This prevents condensation by limiting opportunities to bridge to other molecules and stabilizes the RNA by locking it into a particular conformation. In contrast, for DNA, simulations suggest that spermine binds externally to the duplex, offering opportunities for intermolecular interaction. The goal of this study is to explain how RNA can remain soluble and available for interaction with other molecules in the cell despite the presence of spermine at concentrations high enough to precipitate DNA.

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Section: Mechanism Of Poly(ra):poly(ru) Condensationmentioning

confidence: 68%

Spermine Condenses DNA, but Not RNA Duplexes

Katz

Tolokh

Pabit

et al. 2017

Biophysical Journal

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“…The selective accumulation of metal ions, such as heavy and rare-earth metal ions, has been reported by DNA-inorganic hybrid materials. 22 These results suggested that the DNA-Fe-particles selectively Generally, since the metal ions interact with the nucleic acid bases and the phosphate group in DNA, [40][41][42][43] the DNA materials can accumulate the metal ions in their structures. Especially, the DNA materials indicate the metal ion selectivity for heavy and rare earth metal ions.…”

Section: E Reuse Of Metal Ion-accumulated Dna-feparticlesmentioning

confidence: 99%

Preparation of DNA-immobilized magnetic particles and their utilization as an accumulative material of metal ions

et al. 2016

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DNA-immobilized Fe 3 O 4 particles (DNA-Fe-particles) were prepared by mixing DNA, magnetic Fe 3 O 4 particles, and the silane coupling reagent, bis [3-(trimethoxysilyl)propyl]amine. The DNA-inorganic hybrid material was uniformly immobilized onto magnetic Fe 3 O 4 particles with the diameters of approximately 450 nm. These DNA-Fe-particles were stable in water. Additionally, we could simply collect the DNA-Fe-particles by a magnet from an aqueous solution. Therefore, we demonstrated the accumulation of various metal ions, such as heavy and rare-earth metal ions, by the DNA-Fe-particles. As a result, although these DNA-Fe-particles could selectively accumulate heavy and rare-earth metal ions, these materials could not accumulate the light metal ions, such as Mg(II) and Ca(II) ions. Furthermore, the metal ion-accumulated DNA-Fe-particles could be recycled by washing them with an aqueous ethylenediaminetetraacetic acid solution.

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“…Moreover, it has been demonstrated that cytosine–cytosine base‐pair mismatches bind Ag I ions with high specificity in DNA duplexes . The number of related studies and applications, using also non‐natural bases, has increased exponentially . Among them, the NMR solved structure of three consecutive imidazol‐silver‐imidazol base‐pairs must be highlighted.…”

Section: Introductionmentioning

confidence: 99%

X‐ray Crystal Structure of a Metalled Double‐Helix Generated by Infinite and Consecutive C‐Ag^I‐C (C*:N¹‐Hexylcytosine) Base Pairs through Argentophilic and Hydrogen Bond Interactions

Terrón

Moreno-Vachiano

Bauzá

et al. 2017

Chemistry A European J

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The synthesis of a metalled double-helix containing exclusively silver-mediated C*-C* base pairs is reported herein (C*=N hexylcytosine). Remarkably, it is the first crystal structure containing infinite and consecutive C*-Ag -C* base pairs that form a double helix. The Ag ion occupies the center between two C* residues with N(3)-Ag bond lengths of 2.1 Å and short Ag -Ag distances (3.1 Å) suggesting an interesting argentophilic attraction as a stabilization source of the helical disposition. The solid-state structure is further stabilized by metal-mediated base-pairs, hydrogen bonding and π-stacking interactions. Moreover, the angle N(3)-Ag-N(3) is almost linear in the [Ag(N hexylcytosine) ] motif and the bases are not coplanar, thus generating a double-strand helical aggregate in the solid state. The noncovalent and argentophilic interactions have been rationalized based on DFT calculations.

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Stabilisation of non-canonical structures of nucleic acids by metal ions and small molecules

Cited by 41 publications

References 314 publications

Spermine Condenses DNA, but Not RNA Duplexes

Spermine Condenses DNA, but Not RNA Duplexes

Preparation of DNA-immobilized magnetic particles and their utilization as an accumulative material of metal ions

X‐ray Crystal Structure of a Metalled Double‐Helix Generated by Infinite and Consecutive C‐Ag^I‐C (C*:N¹‐Hexylcytosine) Base Pairs through Argentophilic and Hydrogen Bond Interactions

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Stabilisation of non-canonical structures of nucleic acids by metal ions and small molecules

Cited by 41 publications

References 314 publications

Spermine Condenses DNA, but Not RNA Duplexes

Spermine Condenses DNA, but Not RNA Duplexes

Preparation of DNA-immobilized magnetic particles and their utilization as an accumulative material of metal ions

X‐ray Crystal Structure of a Metalled Double‐Helix Generated by Infinite and Consecutive C*‐AgI‐C* (C*:N1‐Hexylcytosine) Base Pairs through Argentophilic and Hydrogen Bond Interactions

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X‐ray Crystal Structure of a Metalled Double‐Helix Generated by Infinite and Consecutive C‐Ag^I‐C (C*:N¹‐Hexylcytosine) Base Pairs through Argentophilic and Hydrogen Bond Interactions