Accurate nanoscale flexibility measurement of DNA and DNA–protein complexes by atomic force microscopy in liquid

Murugesapillai, Divakaran; Bouaziz, Serge; Maher, L. James; Israeloff, N. E.; Cameron, Craig Ε.; Williams, Mark C.

doi:10.1039/c7nr04231k

Cited by 38 publications

(44 citation statements)

References 56 publications

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“…The crystal structure of proteins bound to DNA also informs us that Abf2p protein are able to mediate loops (228). To further characterize the extent of the looping we imaged linear pUC18 (1650 bp) (232,233) in the presence of varying concentration of Abf2p proteins (Fig. 5.3B).…”

Section: Abf2p Loops Dnamentioning

confidence: 95%

“…Nanoscope Analysis software was used for image processing. The scan range was varied from 500 nm X 500 nm to 2um X 2um at 512 × 512 (232,233).…”

Section: Characterization Of Abf2p-dna Interactions Using Atomic Forcmentioning

confidence: 99%

“…To determine the persistence length p in the absence and presence of Abf2p proteins we fit the data to the 3D wormlike chain (WLC) model (232,233):…”

Section: Characterization Of Dna Flexibilitymentioning

confidence: 99%

“…We characterize the persistence length p, in the absence and in the presence of proteins. We measure orientation differences, θ, for different locations along the DNA as a function of contour length, L. The results were then fit to the 2D worm-like chain (WLC) model (48,98,184,232,233).…”

Section: Atomic Force Microscopymentioning

confidence: 99%

“…We have shown in our previous studies using both optical tweezers and AFM that the DNA persistence length is increased upon Vpr binding (233). Here we use AFM to image and measure the persistence length of the DNA over a broad range of concentrations, which represents the extent of the flexibility of the molecule under different conditions.…”

Section: Vpr Increases the Persistence Length Of The Dnamentioning

confidence: 99%

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Single molecule studies of DNA bending, looping and compacting proteins using optical tweezers and atomic force microscopy

Murugesapillai¹

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They have been instrumental in making the lab a fun environment to do research. And also a special thanks to Prof Stepanyants and Prof Nathan Israeloff who have helped me throughout my PhD. I would also like thank my committee members for their constructive criticism during on my research work, Prof Stepanyants, Prof Meni Wanunu, Prof Bryan Spring and Prof Wesley Wong. I would like to thank my family, my mom, my dad, Gobu, Sayida, Arasy and Gobi for their unconditional support all those long years. Also, I would like to thank my wife, my uncles, aunts, my cousins and my late grandparents. Throughout all of my school years I have never forgotten how lucky I am to have escaped and survived the civil war in Sri Lanka by finding refuge in France, and then to study science. Coming from a working-class background, this long journey would have been impossible without the support and help of so many dedicated teachers, public servants and regular people who provided their generous help to see us succeed. I would like to thank: Mme Desjardin, Mme

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Section: Abf2p Loops Dnamentioning

confidence: 95%

“…Nanoscope Analysis software was used for image processing. The scan range was varied from 500 nm X 500 nm to 2um X 2um at 512 × 512 (232,233).…”

Section: Characterization Of Abf2p-dna Interactions Using Atomic Forcmentioning

confidence: 99%

“…To determine the persistence length p in the absence and presence of Abf2p proteins we fit the data to the 3D wormlike chain (WLC) model (232,233):…”

Section: Characterization Of Dna Flexibilitymentioning

confidence: 99%

Section: Atomic Force Microscopymentioning

confidence: 99%

Section: Vpr Increases the Persistence Length Of The Dnamentioning

confidence: 99%

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Single molecule studies of DNA bending, looping and compacting proteins using optical tweezers and atomic force microscopy

Murugesapillai¹

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Survival of environmental DNA in sediments: Mineralogic control on DNA taphonomy

Freeman,

Dieudonné,

Agbaje

et al. 2023

Environmental DNA

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The extraction of environmental DNA (eDNA) from sediments is providing ground‐breaking views of past ecosystems and biodiversity. Despite this rich source of information, it is still unclear which sediments favor preservation and why. Here, we used atomic force microscopy and molecular dynamics simulations to explore the DNA‐mineral interaction to assess how mineralogy and interfacial geochemistry play a role in the preservation of environmental DNA on mineral substrates. We demonstrate that mineral composition, surface topography, and surface charge influence DNA adsorption behavior as well as preservation. Modeling and experimental data show that DNA damage can be induced by mineral binding if there is a strong driving force for adsorption. The study shows that knowledge of the mineralogical composition of a sediment and the environmental conditions can be useful for assessing if a deposit is capable of storing extracellular DNA and to what extent the DNA would be preserved. Our data adds to the understanding of eDNA taphonomy and highlights that, for some mineral systems, fragmented DNA may not represent old DNA.

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Environment‐Dependent Stability and Mechanical Properties of DNA Origami Six‐Helix Bundles with Different Crossover Spacings

Yang

Piskunen

Suma

et al. 2022

Small

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The internal design of DNA nanostructures defines how they behave in different environmental conditions, such as endonuclease‐rich or low‐Mg2+ solutions. Notably, the inter‐helical crossovers that form the core of such DNA objects have a major impact on their mechanical properties and stability. Importantly, crossover design can be used to optimize DNA nanostructures for target applications, especially when developing them for biomedical environments. To elucidate this, two otherwise identical DNA origami designs are presented that have a different number of staple crossovers between neighboring helices, spaced at 42‐ and 21‐ basepair (bp) intervals, respectively. The behavior of these structures is then compared in various buffer conditions, as well as when they are exposed to enzymatic digestion by DNase I. The results show that an increased number of crossovers significantly improves the nuclease resistance of the DNA origami by making it less accessible to digestion enzymes but simultaneously lowers its stability under Mg2+‐free conditions by reducing the malleability of the structures. Therefore, these results represent an important step toward rational, application‐specific DNA nanostructure design.

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Accurate nanoscale flexibility measurement of DNA and DNA–protein complexes by atomic force microscopy in liquid

Abstract: We obtain accurate three-dimensional persistence length measurements for DNA and DNA–protein complexes using liquid AFM imaging, validated by optical tweezers.

Cited by 38 publications

References 56 publications

Single molecule studies of DNA bending, looping and compacting proteins using optical tweezers and atomic force microscopy

Single molecule studies of DNA bending, looping and compacting proteins using optical tweezers and atomic force microscopy

Survival of environmental DNA in sediments: Mineralogic control on DNA taphonomy

Environment‐Dependent Stability and Mechanical Properties of DNA Origami Six‐Helix Bundles with Different Crossover Spacings

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