A Lead-Filled G-Quadruplex:  Insight into the G-Quartet's Selectivity for Pb<sup>2+</sup> over K<sup>+</sup>

Kotch, Frank W.; Fettinger, James C.; Davis, Jeffery T.

doi:10.1021/ol0065120

Cited by 160 publications

(184 citation statements)

References 50 publications

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“…Multiple scattering analysis of the EXAFS data for the Pb 2+ -G1 system, in conjunction with the known crystal structure illustrated in Figure 2B (17), employed three shells of atoms surrounding the metal. The first, located at 2.65 Å, corresponds to the eight O6 atoms, one from each guanine in both quartets surrounding the metal ion.…”

Section: Resultsmentioning

confidence: 99%

Pb EXAFS Studies on DNA Quadruplexes: Identification of Metal Ion Binding Site

et al. 2002

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Nucleic acid quadruplexes are composed of guanine quartets stabilized by specific metal ions. X-ray diffraction can provide high-resolution information on the structure and metal binding properties of quadruplexes, but only if they can be crystallized. NMR can provide detailed information on the solution structure of such quadruplexes but little quantitative data concerning the metal binding site. Here we apply extended X-ray absorption fine structure (EXAFS) measurements to characterize the metal ion binding site, in frozen solution, of the unimolecular quadruplex formed by the thrombin binding aptamer, d(G 2 T 2 G 2 TGTG 2 T 2 G 2 ) (TBA), in the presence of Pb 2+ ions. The Pb L III -edge X-ray absorption spectrum of this metal-DNA complex is very similar to that we obtain for a Pb 2+ -stabilized quartet system of known structure constructed from a modified guanine nucleoside (G1). The Fourier transforms of the Pb 2+ complexes with both TBA and G1 show a first-shell interaction at about 2.6 Å, and a weaker, broader shell at 3.5-4.0 Å. Quantitative analysis of the EXAFS data reveals the following: (i) very close agreement between interatomic distances at the metal coordination site for the Pb 2+ -G1 complex determined by EXAFS and by X-ray crystallography; (ii) similarly close agreement between interatomic distances measured by EXAFS for the Pb 2+ -G1 and Pb 2+ -TBA complexes. These results provide strong evidence for binding of the Pb 2+ ion in the region between the two quartets in the Pb 2+ -TBA complex, coordinated to the eight surrounding guanine O6 atoms. The specific binding of Pb 2+ to DNA examined here may be relevant to the genotoxic effects of this environmentally important heavy metal. Furthermore, these results demonstrate the utility of EXAFS as a method for quantitative characterization of specific metal binding sites in nucleic acids in solution.Metal ion-DNA interactions are important in nature, often impacting the genetic material's structure and function. To better understand the molecular details of these interactions, it is essential that we have a reliable picture of the metal ion coordination site. This is not always so straightforward. Thus, X-ray diffraction can provide high-resolution information on the structure and metal binding properties of nucleic acids, but only if diffraction-quality crystals can be obtained. NMR can provide detailed information on solution structure, but usually little quantitative data concerning the metal binding site. This paper describes how extended X-ray absorption fine structure (EXAFS) 1 measurements can be used to gain detailed information about a Pb 2+ binding site within a folded DNA oligonucleotide.DNA and RNA can form quadruplex structures in the presence of certain metal ions, based on the guanine quartet, which is shown in Figure 1A. Only a small number of X-ray crystal structure determinations on quadruplexes have been reported, and these have located the metal binding site in the region between two quartet stacks, or coplanar with one...

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Section: Resultsmentioning

confidence: 99%

Pb EXAFS Studies on DNA Quadruplexes: Identification of Metal Ion Binding Site

et al. 2002

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“…These one-dimensional polymers act as prospective candidates for bio-molecular electronics because, due to the low ionization potential of guanine (the lowest among nucleicacid bases), they might be suitable to mediate charge transport by hole conduction along the helix, and have even been suggested as nano-mechanical extension-contraction machines [35]. In the presence of appropriate metal cations (especially K + and Na + ), solutions of homoguanylic strands in water [36,37] as well as lipophilic guanosine monomers in organic solvents [38], self-assemble in right-handed quadruple helices. Recent investigations has been carried out for the G4-nanowires, but the conduction properties of these nanowires are basically unknown and a direct measurement of electrical properties of G4-wires is still missing.…”

Section: G4-wires Dna As Nanowirementioning

confidence: 99%

Biomolecules and Pure Carbon Aggregates: An Application Towards “Green Electronics”

Srivastava¹

2018

Green Electronics

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Abstract"Green electronics" is a novel scientific term which aims to identify the compounds of natural origin (economically safe and biodegradable) and establish economically efficient route for production of synthetic materials. The purpose of green electronics is to create path for the production of human and environmental friendly electronics and the integration of electronics with living tissue in particular. These researches may help to fulfill not only the organic electronics to deliver low cost energy efficient materials and devices, but also achieve unimaginable functionalities for electronics. In this chapter we have considered the molecular electronic devices biomolecules: deoxyribonucleic acid (DNA) and pure carbon aggregates: (carbon nanotubes (CNTs)/graphene), their properties and applications.

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“…Since the ionic radius of Zn 2+ (r = 0.74 Å) is much smaller than Pb 2+ (r = 1.29 Å) and K + (r = 1.51 Å) (inset in Scheme 1(B)), 56 G4s mediated by a smaller ion have been demonstrated to show more compact structures and are unfavorable for the binding to the G4 specific dyes. 57,58 Besides H22, five most-reported G4 sequences (Table S1, Supporting Information) were also employed to further validate the principle of the Zn 2+ -induced fluorescence decrease. As shown in Fig.…”

Section: Principle Of Operationmentioning

confidence: 99%

Label-free Detection of Zn2+ Based on G-quadruplex

et al. 2015

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Herein, we developed a sensing strategy for the label-free detection of Zn 2+ based on G-quadruplex. In the absence of Zn 2+ , there was a fluorescence enhancement of thioflavin T by interaction with human telomere sequence. On the addition of Zn 2+ , Zn 2+ induced a more compact G-quadruplex structure to release thioflavin T, resulting in a fluorescence decrease. This simple "mix-then-detect" method gave the detection limit of 0.91 μM with linear dynamic ranges from 0 to 10 μM. Because it does not require the use of expensive and unstable DNAzyme systems, or need synthesis and modification of nanomaterials, this label-free biosensor is simple, fast, cost-effective and applicable for real samples taken from lake water.

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A Lead-Filled G-Quadruplex: Insight into the G-Quartet's Selectivity for Pb²⁺ over K⁺

Cited by 160 publications

References 50 publications

Pb EXAFS Studies on DNA Quadruplexes: Identification of Metal Ion Binding Site

Pb EXAFS Studies on DNA Quadruplexes: Identification of Metal Ion Binding Site

Biomolecules and Pure Carbon Aggregates: An Application Towards “Green Electronics”

Label-free Detection of Zn2+ Based on G-quadruplex

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A Lead-Filled G-Quadruplex: Insight into the G-Quartet's Selectivity for Pb2+ over K+

Cited by 160 publications

References 50 publications

Pb EXAFS Studies on DNA Quadruplexes: Identification of Metal Ion Binding Site

Pb EXAFS Studies on DNA Quadruplexes: Identification of Metal Ion Binding Site

Biomolecules and Pure Carbon Aggregates: An Application Towards “Green Electronics”

Label-free Detection of Zn2+ Based on G-quadruplex

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A Lead-Filled G-Quadruplex: Insight into the G-Quartet's Selectivity for Pb²⁺ over K⁺