Probing the structure of long DNA molecules in solution using synchrotron radiation linear dichroism

Rittman, Martyn; Hoffmann, Søren Vrønning; Gilroy, Emma; Hicks, Matthew R.; Finkenstädt, Bärbel; Rodger, Alison

doi:10.1039/c1cp22371b

Cited by 13 publications

(12 citation statements)

References 41 publications

(56 reference statements)

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“…Recent work suggests that use of linear dichroism has good potential for understanding the effects of ionic strength and temperature on the flexibility of different DNA sequences, and should help to understand these phenomena better in future. 66 At present, predicting the ability of DNA to adapt to small molecule binding, and correlating the conformational deformability of base-pair steps with large scale sequence specific conformational plasticity is not straightforward. Nevertheless, we consider that DNA conformational adaptability plays a critical role in determining binding geometries.…”

Section: Dalton Transactions Papermentioning

confidence: 99%

Sensitivity of [Ru(phen)2dppz]2+ light switch emission to ionic strength, temperature, and DNA sequence and conformation

2013

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The luminescence of DNA-bound [Ru(phen)(2)dppz](2+) is shown to be highly sensitive to environmental conditions such as ionic strength, temperature, and the sequence and secondary structure of the nucleic acid, although not to bulky DNA substituents in the major groove. Each enantiomer has two characteristic lifetimes with any polynucleotide and their relative amplitudes vary as a function of binding ratio. For [poly(dA-dT)](2) as a model sequence, the longer lifetime for Δ-[Ru(phen)(2)dppz](2+) has been assigned to canted intercalation of the complex and the shorter lifetime is ascribed to symmetric intercalation. At a fixed binding ratio, the longer lifetime amplitude increases with increasing ionic strength, without significant change in lifetimes. Increasing temperature has a similar effect, but also affects lifetimes. In general, emission is strongest with AT-rich polynucleotides and with higher-order secondary structures, with intensity increasing as single-stranded < duplex < triplex. However, sequence-context and secondary duplex structure also influence the photophysics since emission with [poly(dA)]·[poly(dT)] is significantly higher than with [poly(dA-dT)](2) or [poly(rA)]·[poly(rU)]. The strong influence of different environmental conditions on the emission of nucleic acid-bound [Ru(phen)(2)dppz](2+) reflects subtle heterogeneities that are inherent elements of DNA recognition by small molecules, amplified by large changes in photophysics caused by differential exposure of the dppz nitrogens to groove hydration.

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Section: Dalton Transactions Papermentioning

confidence: 99%

Sensitivity of [Ru(phen)2dppz]2+ light switch emission to ionic strength, temperature, and DNA sequence and conformation

2013

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“…To improve these estimates we need better absorbance data and to deconvolve the LD spectrum into component bands. 37 The calculated dependence of S N on shear rate at 37 C for a rigid, rodlike particle with the dimensions of a DNA plasmid variant of pC3.1 (6882 base pairs in length, a ¼ 1170 nm, b ¼ 1.2 nm, r ¼ 975) 33 is also shown in Fig. 3.…”

Section: Steady-state Orientation Parameter As a Function Of Shear Ratementioning

confidence: 98%

Calculations of flow-induced orientation distributions for analysis of linear dichroism spectroscopy

et al. 2013

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Spectroscopic techniques involving flow-oriented samples and polarised light, such as linear dichroism (LD), are becoming increasingly useful to probe biomacromolecular assemblies. However, the magnitude of the signal and in some cases the shape of the spectrum are dependent on the distribution of the orientations of the molecules in the sample. Despite great progress in the modelling of dilute and semi-dilute suspension mechanics, these theories have had remarkably little impact on the community practising LD.We perform calculations with a model combining Brownian effects and rotations in a steady shear flow of a dilute suspension of rigid, rodlike particles. We calculate the time-dependent probability density functions for the orientation distributions of three biomolecular assemblies: M13 bacteriophage, DNA molecules of well-defined length, and FtsZ protofilaments. Our calculations allow us to compute directly (rather than infer from experiment) the LD orientation parameter, S, for such assemblies. The results from the model are consistent with experiment for M13 bacteriophage and allow us to estimate S empirically for reasonably short DNA molecules. In analysing the particle size distribution for the process of FtsZ polymerisation, we find that results from the model aid our understanding of the process.

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“…A synchrotron light source is one solution to this problem. 34,[38][39][40][41] Sometimes shorter path lengths or diluting with a transparent solvent or using F − salts rather than Cl − are options.…”

Section: Sample Absorbancementioning

confidence: 99%

Linear dichroism as a probe of molecular structure and interactions

Rodger

Dorrington

Ang

2016

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Linear dichroism (LD) spectroscopy involves measuring the wavelength (or energy) dependence of the difference in absorption of light parallel and perpendicular to an orientation direction. It requires samples to have a net orientation. The aim of this review is to summarise some UV-visible linear dichroism (LD) methods that can be usefully applied to increase our understanding of biomacromolecules and their complexes that have a high aspect ratio. LD shares the advantages of most spectroscopic techniques including the fact that data collection is fairly straightforward and many sample types can be investigated. Conversely, LD shares the disadvantage that the measured signal is an average over all species in the sample on which the light beam is incident. LD mitigates this disadvantage somewhat in that only species which are oriented give a net signal. How the data can be analysed to give structural information about small molecules in stretched films and membrane systems or bound to biomacromolecules and directly about biomacromolecules such as DNA and protein fibres forms part of this review. In the UV-visible region LD often suffers noticeably from light scattering since the samples tend to be large relative to the wavelength of the incident light, so consideration is also given to data analysis challenges including removal of scattering contributions to an observed signal. Brief mention is made of fluorescence detected LD.

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Probing the structure of long DNA molecules in solution using synchrotron radiation linear dichroism

Cited by 13 publications

References 41 publications

Sensitivity of [Ru(phen)2dppz]2+ light switch emission to ionic strength, temperature, and DNA sequence and conformation

Sensitivity of [Ru(phen)2dppz]2+ light switch emission to ionic strength, temperature, and DNA sequence and conformation

Calculations of flow-induced orientation distributions for analysis of linear dichroism spectroscopy

Linear dichroism as a probe of molecular structure and interactions

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