Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework

Malinovskii, Vladimir L.; Samain, Florent; Häner, Robert

doi:10.1002/anie.200700891

Cited by 145 publications

(85 citation statements)

References 66 publications

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“…[18] A critical issue for the optical properties of pyrene is the linkage between this chromophore and the oligonucleotide.…”

Section: Introductionmentioning

confidence: 99%

“…[11,12] Pyrenes have been widely used for nucleic acid labelling. [12][13][14][15][16][17][18] We used 5-(1-pyrenyl)-2Ј-deoxyuridine (1PydU, 1) and other pyrene-modified nucleosides as models for understanding electron transfer in DNA. [7,8] Furthermore, in 1PydU-modified DNA duplexes, photochemically induced electron transfer from the PydU group can be studied by chemical and spectroscopic techniques.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Synthesis of 5‐(2‐Pyrenyl)‐2′‐deoxyuridine as a DNA Modification for Electron‐Transfer Studies: The Critical Role of the Position of the Chromophore Attachment

Wanninger-Weiß

Wagenknecht

2007

Eur J Org Chem

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Keywords: Electron transfer / Fluorescence / Iridium / Oligonucleotides / Palladium / Pyrene 5-(2-Pyrenyl)-2Ј-deoxyuridine (2PydU, 2) has been prepared as a new thymidine analogue in which the 2-position of the pyrene chromophore is connected covalently to the 5-position of uridine through a single C-C bond. The synthesis of 2 starts with the conversion of pyrene (3) into 2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrene (4) by using an Ir catalyst that was prepared in situ from [IrCl(cod)] 2 and 4,4Ј-di-tert-butyl-2,2Ј-bipyridine (dtbpy) in the presence of NaOMe. The subsequent Suzuki-Miyaura cross-coupling of 4 with 5-iodo-2Ј-deoxyuridine (5) was performed by using 1,1Ј-bis[(diphenylphosphanyl)ferrocene]dichloropalladium-(II) as the catalyst in a THF/MeOH/H 2 O mixture as the solvent. The modified nucleoside 2 was characterized by absorption and fluorescence spectroscopy. The results were compared with the strongly electronically coupled 5-(1-pyrenyl)-2Ј-deoxyuridine (1PydU, 1). Finally, the nucleoside 2 was converted into the corresponding phosphoramidite 7 as a DNA building block. The DNA set 8a-8d was synthesized

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“…[18] A critical issue for the optical properties of pyrene is the linkage between this chromophore and the oligonucleotide.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Synthesis of 5‐(2‐Pyrenyl)‐2′‐deoxyuridine as a DNA Modification for Electron‐Transfer Studies: The Critical Role of the Position of the Chromophore Attachment

Wanninger-Weiß

Wagenknecht

2007

Eur J Org Chem

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“…There is a well-defined first solvation shell peak with a maximum at approximately 5.5 Å and first minimum at 7.5 Å. Using this distance to define the first solvation shell, calculation of the N(r) using eqn (5) shows that there are approximately 12.5 molecules in the first solvation shell. To further interrogate the local orientational structure we calculated the angular radial distribution function, g(r,y), where y is the angle between the aromatic cores (see Fig.…”

Section: View Article Onlinementioning

confidence: 99%

“…[1][2][3] Examples include protein-ligand complexation, 4 DNA base stacking, 5 supramolecular chemical recognition, [6][7][8] selectivity in chemical reactions, 9 aggregation and solvation of carbon nanostructures, 10 and petroleum phase behaviour. 11,12 Unlike other non-covalent interactions, such as hydrogen or halogen bonding, aromatic interactions do not arise from one single dominant interatomic mechanism.…”

Section: Introductionmentioning

confidence: 99%

The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions

Headen

Cullen

Patel

et al. 2018

Phys. Chem. Chem. Phys.

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Total neutron scattering has been used in conjunction with H/D and *N/ 15 N isotopic substitution to determine the detailed liquid-state structures of pyridine and naphthalene. Analysis of the data via an empirical potential-based structure refinement method has allowed us to interrogate the full six-dimensional spatial and orientational correlation surfaces in these systems, and thereby to deduce the fundamental effects of a heteroatom and aromatic core-size on intermolecular p-p interactions. We find that the presence of a nitrogen heteroatom, and concomitant dipole moment, in pyridine induces surprisingly subtle departures from the structural correlations observed in liquid benzene: in both cases the most probable local motif is based on perpendicular (edge-to-face) intermolecular contacts, while parallel-displaced configurations give rise to a clear shoulder in the correlation surface. However, the effect of the heteroatom is revealed through detailed analysis of the intermolecular orientational correlations. This analysis shows a tendency for neighbouring pyridine molecules to direct one meta-and one para-hydrogen towards the neighbouring aromatic p-orbitals in edge-to-face configurations, while head-to-tail alignment of adjacent nitrogen atoms is favoured in faceto-face configurations. In contrast to this, increasing aromatic core size from one to only two rings has a clear and profound effect on the p-p interactions and liquid structure. Our experiments show that naphthalenenaphthalene contacts are dominated by parallel-displaced configurations, akin to those found in graphite. This marks a fundamental difference with the structure of liquid benzene, in which perpendicular geometries are favoured. Furthermore, it is remarkable to note that in the systems studied, the most favoured spatioorientational configurations observed in the liquid state are not predicted from ab initio calculations and/or solid state crystallographic studies. This highlights the need for caution when extrapolating the results of crystallographic and computational studies to aromatic interactions in liquids and disordered systems.

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“…Twisted chains of molecules are commonly produced with biological polymers, such as DNA, collagen, and agar [4][5][6]. Inspired by the fact of helical structures as ubiquity in nature and the foundation of the genetic code, helical frameworks have been attracting increased attention in coordination chemistry and materials chemistry [7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Hydrothermal Synthesis, Crystal Structure and Spectroscopic Characterization of a Novel 2D → 2D Parallel Interpenetrated Coordination Polymer [Zn2(pdoa)2(bpp)2(H2O)]·4H2O

Zhao

et al. 2012

J Inorg Organomet Polym

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A novel 2D ? 2D parallel interpenetrated coordination polymer [Zn 2 (pdoa) 2 (bpp) 2 (H 2 O)]Á4H 2 O (1) [H 2 pdoa = 2,2 0 -(1,3-phenylenedioxy)bis(acetate), bpp = 1,3-bis (4-pyridyl)propane], has been synthesized by hydrothermal reaction of Zn(Ac) 2 Á2H 2 O, bpp and H 2 pdoa, and characterized by elemental analysis, IR spectra, PXRD, and singlecrystal X-ray diffraction. The structure determination reveals that 1 features a 2D parallel interpenetrated 4 4 -sql net generated by 2-crossing [2]-catenane motif, and pairs of interpenetrating 2D sheets show the same handedness. The overall structure, however, is achiral-in each layer of doubly interpenetrating nets, the two individual nets have the opposite handedness to the corresponding nets in the adjoining layers. Moreover, the thermal stabilities and photoluminescence properties of 1 were also discussed.

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Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework

Cited by 145 publications

References 66 publications

Synthesis of 5‐(2‐Pyrenyl)‐2′‐deoxyuridine as a DNA Modification for Electron‐Transfer Studies: The Critical Role of the Position of the Chromophore Attachment

Synthesis of 5‐(2‐Pyrenyl)‐2′‐deoxyuridine as a DNA Modification for Electron‐Transfer Studies: The Critical Role of the Position of the Chromophore Attachment

The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions

Hydrothermal Synthesis, Crystal Structure and Spectroscopic Characterization of a Novel 2D → 2D Parallel Interpenetrated Coordination Polymer [Zn2(pdoa)2(bpp)2(H2O)]·4H2O

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