Interaction between a DNA oligonucleotide and a dinuclear iron(II) supramolecular cylinder; an NMR and molecular dynamics study

Moldrheim, Erlend; Hannon, Michael J.; Meistermann, Isabelle; Rodger, Alison; Sletten, Einar

doi:10.1007/s00775-002-0354-2

Cited by 40 publications

(33 citation statements)

References 36 publications

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“…This addition results in a dramatic enlargement of the diameter of the cylinder so that it is unlikely that such a cylinder would fit into the central cavity of the three-way junction. Consistent with this, the results shown in Figure 4 (lanes 5,6) …”

Section: Resultssupporting

confidence: 87%

“…[1][2][3] The binding of this agent to natural polymeric DNAs and the intramolecular DNA coiling that results have been described previously [1,2] and appears to be through majorgroove recognition. [4,5] Recently, the agent in a complex with the palidromic hexanucleotide 5'-dA C H T U N G T R E N N U N G (CGTACG)-3' was crystallised. [6] Surprisingly, molecular recognition not of duplex DNA, but rather of a three-way junction was observed.…”

Section: Introductionmentioning

confidence: 99%

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Recognition of DNA Three‐Way Junctions by Metallosupramolecular Cylinders: Gel Electrophoresis Studies

Malina

Hannon

Brabec

2007

Chemistry A European J

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The interaction of metallosupramolecular cylinders with DNA three-way junctions has been studied by gel electrophoresis. A recent X-ray crystal structure of a palindromic oligonucleotide forming part of a complex with such a cylinder revealed binding at the heart of a three-way junction structure. The studies reported herein confirm that this is not solely an artefact of crystallisation and reveal that this is a potentially very powerful new mode of DNA recognition with wide scope. The cylinders are much more effective at stabilizing three-way junctions than simple magnesium di-cations or organic or metallo-organic tetra-cations, with the M cylinder enantiomer being more effective than P. The recognition is not restricted to three-way junctions formed from palindromic DNA with a central AT step at the junction; non-palindromic three-way junctions and those with GC steps are also stabilised. The cylinder is also revealed to stabilise other Y-shaped junctions, such as that formed at a fraying point in duplex DNA (for example, a replication fork), and other DNA three-way junction structures, such as those containing unpaired nucleotides, perhaps by opening up this structure to access the central cavity.

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Section: Resultssupporting

confidence: 87%

Section: Introductionmentioning

confidence: 99%

Recognition of DNA Three‐Way Junctions by Metallosupramolecular Cylinders: Gel Electrophoresis Studies

Malina

Hannon

Brabec

2007

Chemistry A European J

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“…An example of this is the use of molecular dynamics restraints obtained from 550 NOESY data to determine features of the iron helicate mentioned above with a DNA decamer. 38 The accurate interpretation of NOESY spectra, or related techniques such as correlation spectroscopy (COSY) 31 and rotating frame Ovehauser enhancement spectroscopy (ROESY) 31 rely on 555 molecular modelling to elucidate the correct molecular structure between multiple possible arrangements.…”

Section: Nuclear Magnetic Resonance Spectroscopymentioning

confidence: 99%

Synthetic metallomolecules as agents for the control of DNA structure

2007

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DNA is often referred to as the molecule of life, since it contains the instructions for making the required proteins. However, it is not simply a (genetic) code to be read; its structure has an important role in determining when and how much of a particular 5 protein is made at any point in time. Furthermore, there are a range of special DNA structures, e.g. Holliday junctions, which play essential roles for the existence of life as we know it or as it will become. In this tutorial review the normal B-DNA structure is summarised and metallomolecule binding modes discussed then used as a basis for examining DNA structures which can be induced by molecules containing metallic cations. The effects of aquated metal ions, cobalt ammine and ruthenium octahedral metal complexes, metallo helicates and platinum complexes such as cis-platin are discussed alongside techniques such as NMR, 10 X-ray crystallography, gel electrophoresis, circular dichroism, linear dichroism and molecular dynamics.

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“…[16] NMR data have confirmed a major groove-binding mode for the M cylinder. [19] From all the experimental data it is clear that the cylinder binds in the major groove and is able to induce dramatic conformational changes in the DNA. However, gaining molecular level information about the effects and interactions which lead to this remarkable supramolecular event is challenging.…”

Section: Introductionmentioning

confidence: 97%

Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove

Khalid

Hannon

Rodger

et al. 2006

Chemistry A European J

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In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(C25H20N4)3]4+, and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC) d(GGAAAAAGGGGG) dodecamer; one of this DNA complexed with the cylinder molecule; and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.

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Interaction between a DNA oligonucleotide and a dinuclear iron(II) supramolecular cylinder; an NMR and molecular dynamics study

Cited by 40 publications

References 36 publications

Recognition of DNA Three‐Way Junctions by Metallosupramolecular Cylinders: Gel Electrophoresis Studies

Recognition of DNA Three‐Way Junctions by Metallosupramolecular Cylinders: Gel Electrophoresis Studies

Synthetic metallomolecules as agents for the control of DNA structure

Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove

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