Silver (I) as DNA glue: Ag+-mediated guanine pairing revealed by removing Watson-Crick constraints

Swasey, Steven M.; Espinosa-Leal, Leonardo; Lopez-Acevedo, Olga; Pavlovich, J.; Gwinn, E. G.

doi:10.1038/srep10163

Cited by 142 publications

(235 citation statements)

References 54 publications

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“…This is not unexpected and can probably be attributed to an electrostatic interaction between the Ag(I) cations and the negatively charged DNA backbone 28 or to additional weaker binding to the canonical nucleobases. 29 To rule out the inadvertent formation of G−Ag(I)−C Hoogsteen-type base pairs (as previously established within a triple helix) 30 . Melting profile of the DNA duplex under slightly acidic conditions (pH 5.5) depending on the added equivalents of AgNO 3 , monitored at 260 nm (black, 0 equiv; red, 0.5 equiv; blue, 1 equiv; green, 2 equiv; orange, 3 equiv).…”

Section: ■ Introductionmentioning

confidence: 99%

Metal-Mediated Assembly of 1,N⁶-Ethenoadenine: From Surfaces to DNA Duplexes

Mandal¹,

Wang

Prajapati

et al. 2016

Inorg. Chem.

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The design of multinuclear metal complexes requires a match of the ligand-to-metal vectors and the preferred coordination geometries of the metal ions. Only a few ligands are known with a parallel orientation of N→M vectors that brings the metal ions into close proximity. We establish here the adenine derivative 1,N(6)-ethenoadenine (εA) as an ideal bis(monodentate) ligand. Scanning tunneling microscope images of alkylated εA on graphite surface clearly indicate that these ligands bind to Ag(I) ions. The molecular structures of [Ag2(1)2](ClO4)2 and [Ag2(2)2](ClO4)2 (1, 9-ethyl-1,N(6)-ethenoadenine; 2, 9-propyl-1,N(6)-propylenoadenine) confirm that dinuclear complexes with short Ag···Ag distances are formed (3.0256(3) and 2.984(1) Å, respectively). The structural motif can be extended to divalent metal ions, as was shown by determining the molecular structure of [Cu2(1)2(CHO2)2(OH2)2](NO3)2·2H2O with a Cu···Cu distance of 3.162(2) Å. Moreover, when introducing the 1,N(6)-ethenoadenine deoxyribonucleoside into parallel-stranded DNA duplexes, even dinuclear Ag(I)-mediated base pairs are formed, featuring the same transoid orientation of the glycosidic bonds as the model complexes. Hence, 1,N(6)-ethenoadenine and its derivatives are ideally suited as bis(monodentate) ligands with a parallel alignment of the N→M vectors for the construction of supramolecular metal complexes that require two metal ions at close distance.

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Section: ■ Introductionmentioning

confidence: 99%

Metal-Mediated Assembly of 1,N⁶-Ethenoadenine: From Surfaces to DNA Duplexes

Mandal¹,

Wang

Prajapati

et al. 2016

Inorg. Chem.

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“…54 In all calculations the TS09 pair-wise van der Waals (vdW) correction 55 was included to improve the accuracy of the results. 21 It is worth to mention that the inclusion of the vdW correction is extremely important to obtain a stable layered structure, only with PBE 56 without correction the planes are not stable to form a crystal.…”

Section: Figurementioning

confidence: 99%

“…The mechanism underlying this switch is used for designing biosensors and metal-ion-stimulated DNA switches. 19 For example, in the particular case of noble metals, the assembly of metal-mediated DNA strands in single or double strands is highly base-specific, 20,21 with the final structures resulting from an interplay between the metal-base-solvent interactions. These interactions include not only covalent but also 2 dispersion interactions that can be accurately simulated within the van der Waals corrected density functional theory.…”

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confidence: 99%

Three-Dimensional Uracil Network with Sodium as a Linker

et al. 2016

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Here we show that uracil and sodium form a three-dimensional metal-mediated nucleic acid network; it is grown in atomic/molecular layer-by-layer manner using the atomic/molecular layer deposition (ALD/MLD) thin-film technique. The long-range ordered Na-uracil crystalline structure is evidenced as sharp Bragg reflections. Based on density functional theory (DFT) calculations, a tetrameric-like crystal structure is proposed. Na-uracil thin films are fluorescent with a lifetime three orders of magnitude higher than commonly seen for nucleic acid molecules. Our method provides a new approach to designing 3D nucleic acid-metal nanostructures.

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“…41 In a combined experimental-theoretical study, Gwinn, Lopez-Acevedo, and coworkers have shown a higher stability in Ag + -mediated pairing of guanine homo-base strands than canonical guanine-cytosine pairing. 42 Kononov's group has investigated the excitation and emission properties of several DNA-AgNCs using time dependent DFT and QM/MM calculations. 43,44 The structural sensitivity of the chiroptical activity of DNA-AgNCs has been studied by Gwinn, Aikens, and coworkers to suggest cluster structures.…”

Section: Introductionmentioning

confidence: 99%

Research Update: Density functional theory investigation of the interactions of silver nanoclusters with guanine

2017

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Bare and guanine-complexed silver clusters Ag n z (n = 2-6; z = 0-2) are examined using density functional theory to elucidate the geometries and binding motifs that are present experimentally. Whereas the neutral systems remain planar in this size range, a 2D-3D transition occurs at Ag 5 + for the cationic system and at Ag 4 2+ for the dicationic system. Neutral silver clusters can bind with nitrogen 3 or with the pi system of the base. However, positively charged clusters interact with nitrogen 7 and the neighboring carbonyl group. Thus, the cationic silver-DNA clusters present experimentally may preferentially interact at these sites. © 2017 Author (s)

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Silver (I) as DNA glue: Ag+-mediated guanine pairing revealed by removing Watson-Crick constraints

Cited by 142 publications

References 54 publications

Metal-Mediated Assembly of 1,N⁶-Ethenoadenine: From Surfaces to DNA Duplexes

Metal-Mediated Assembly of 1,N⁶-Ethenoadenine: From Surfaces to DNA Duplexes

Three-Dimensional Uracil Network with Sodium as a Linker

Research Update: Density functional theory investigation of the interactions of silver nanoclusters with guanine

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Silver (I) as DNA glue: Ag+-mediated guanine pairing revealed by removing Watson-Crick constraints

Cited by 142 publications

References 54 publications

Metal-Mediated Assembly of 1,N6-Ethenoadenine: From Surfaces to DNA Duplexes

Metal-Mediated Assembly of 1,N6-Ethenoadenine: From Surfaces to DNA Duplexes

Three-Dimensional Uracil Network with Sodium as a Linker

Research Update: Density functional theory investigation of the interactions of silver nanoclusters with guanine

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Metal-Mediated Assembly of 1,N⁶-Ethenoadenine: From Surfaces to DNA Duplexes

Metal-Mediated Assembly of 1,N⁶-Ethenoadenine: From Surfaces to DNA Duplexes