Patchiness of ion-exchanged mica revealed by DNA binding dynamics at short length scales

Billingsley, Daniel J.; Lee, A J; Johansson, N. A. B.; Walton, Alex S.; Stanger, Leigh Russell; Crampton, Neal; Bonass, William A.; Thomson, Neil H.

doi:10.1088/0957-4484/25/2/025704

Cited by 10 publications

(19 citation statements)

References 33 publications

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“…Billingsley et al found that sufficiently short dsDNA molecules (< 800 base pairs, or 260 nm long) deviated from the expected average binding conformation on Ni-mica [205]. These molecules were characterised by surface-equilibrated conformations rather than being kinetically trapped, which provided evidence that the surface distribution of Ni 2+ on the mica was not homogeneous.…”

Section: Adsorption Of Dna To Micamentioning

confidence: 99%

The nature of the air-cleaved mica surface

Christenson

Thomson

2016

Surface Science Reports

115

102

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The accepted image of muscovite mica is that of an inert and atomically smooth surface, easily prepared by cleavage in an ambient atmosphere. Consequently, mica is extensively used a model substrate in many fundamental studies of surface phenomena and as a substrate for AFM imaging of biomolecules. In this review we present evidence from the literature that the above picture is not quite correct. The mica used in experimental work is almost invariably cleaved in laboratory air, where a reaction between the mica surface, atmospheric CO2 and water occurs immediately after cleavage. The evidence suggests very strongly that as a result the mica surface becomes covered by up to one formula unit of K2CO3 per nm 2 , which is mobile under humid conditions, and crystallizes under drier conditions. The properties of mica in air or water vapour cannot be fully understood without reference to the surface K2CO3, and many studies of the structure of adsorbed water on mica surfaces may need to be revisited. With this new insight, however, the air-cleaved mica should provide exciting opportunities to study phenomena such as two-dimensional ion diffusion, electrolyte effects on surface conductivity, and two-dimensional crystal nucleation.

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Section: Adsorption Of Dna To Micamentioning

confidence: 99%

The nature of the air-cleaved mica surface

Christenson

Thomson

2016

Surface Science Reports

115

102

View full text Add to dashboard Cite

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Section: Introductionmentioning

confidence: 98%

“…As a consequence, Mg 2+ only mediates a relatively weak and diffuse adhesion between DNA and the mica surface, allowing DNA molecules to adopt an equilibrated form [22,[31][32][33]. This complex spatial distribution has been rationalized by others [31,33] . Previous work has taken advantage of this difference in binding capacities by adjusting the ratio between different monovalent and monovalent-to-divalent ion concentrations in the deposition buffer to alter the surface adhesion of DNA in air [20,34,35].…”

Section: Introductionmentioning

confidence: 98%

“…These alternative methods either put significant constraints on the experimental setup or do not provide the required functionality, and therefore pre-incubation of mica with divalent cations remains the common practice. [22,30], leading to phase-separated domains of positive surface charge [31]. Where transition metal cations are utilized, a strong adhesion between DNA and mica is achieved due to directional bonding of the d-orbitals of the divalent cation.…”

Section: Introductionmentioning

confidence: 99%

“…Where transition metal cations are utilized, a strong adhesion between DNA and mica is achieved due to directional bonding of the d-orbitals of the divalent cation. Such deposited DNA molecules adopt a kinetically trapped form [31], sufficient for high-resolution imaging in aqueous buffer.…”

Section: Introductionmentioning

confidence: 99%

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Tuning the translational freedom of DNA for high speed AFM

et al. 2015

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Direct observation is arguably the preferred way to investigate the interactions between two molecular complexes. With the development of high speed atomic force microscopy (AFM), it is becoming possible to observe directly DNA-protein interactions with relevant spatial and temporal resolutions. These interactions are of central importance to biology, bionanotechnology, and functional biologically inspired materials. As in all microscopy studies, sample preparation plays a central role in AFM observation and minimal perturbation of the sample is desired. Here, we demonstrate the ability to tune the interactions between DNA molecules and the surface to create an association strong enough to enable high-resolution AFM imaging while also providing sufficient translational freedom to allow the relevant protein-DNA interactions to take place. Furthermore, we describe a quantitative method for measuring DNA mobility, while also determining the individual forces contributing to DNA movement. We found that for a weak surface association, a significant contribution to the movement arises from the interaction of the AFM tip with the DNA. In combination, these methods enable the tuning of the surface translational freedom of DNA molecules to allow the direct study of a wide range of nucleo-protein interactions by high speed atomic force microscopy.

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