Adsorption of DNA to Mica, Silylated Mica, and Minerals: Characterization by Atomic Force Microscopy

Bezanilla, Magdalena; Manne, S.; Laney, Daniel E.; Lyubchenko, Yuri L.; Hansma, Helen G.

doi:10.1021/la00002a050

Cited by 249 publications

(195 citation statements)

References 7 publications

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“…Calculation of the concentration of all ionic species for all buffers is explained in Supplementary Note 1 and summarized in Supplementary Table 1). Since monovalent cations are known to weaken the binding of DNA to mica 31,32,35,36 , we implemented the diffusion step by exchanging the buffer to one whose predominant cation is Na þ (B700 mM NaCl). During the diffusion step, we also mildly heated samples at a constant temperature (40°C, for B4 h; while heating above room temperature appears to facilitate the process, it is not essential for the surface diffusion of origami; evidence provided later).…”

Section: Resultsmentioning

confidence: 99%

“…Thus divalent cations, such as Mg 2 þ and Ni 2 þ , are often described as mediating the binding of DNA to mica by bridging the negative charges on the DNA backbone and those on the mica 29,31,35,36,39 . This is a great simplification of divalent-cation-mediated DNA-mica binding, since the strength of binding for a particular cation concentration depends strongly on the identity of the cation, the size and geometry of the DNA object in question and the method of sample preparation.…”

Section: Control Experimentsmentioning

confidence: 99%

“…Further complicating matters, monovalent cations commonly present in buffer solutions such as Na þ , K þ or TrisH þ can decrease the interaction of divalent cations with DNA and mica. 31,32,35,36 For particular cations, for linear dsDNA, three studies by the same group have been successful in explaining strong-to-weak binding transitions of particular relevance to our system 31,32,40 .…”

Section: Control Experimentsmentioning

confidence: 99%

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Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion

2014

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DNA origami has proven useful for organizing diverse nanoscale components into patterns with 6 nm resolution. However for many applications, such as nanoelectronics, large-scale organization of origami into periodic lattices is desired. Here, we report the self-assembly of DNA origami rectangles into two-dimensional lattices based on stepwise control of surface diffusion, implemented by changing the concentrations of cations on the surface. Previous studies of DNA-mica binding identified the fractional surface density of divalent cationsñ s2 ð Þ as the parameter which best explains the behaviour of linear DNA on mica. We show that for n s2 between 0.04 and 0.1, over 90% of DNA rectangles were incorporated into lattices and that, compared with other functions of cation concentration,ñ s2 best captures the behaviour of DNA rectangles. This work shows how a physical understanding of DNA-mica binding can be used to guide studies of the higher-order assembly of DNA nanostructures, towards creating large-scale arrays of nanodevices for technology.

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Section: Resultsmentioning

confidence: 99%

Section: Control Experimentsmentioning

confidence: 99%

Section: Control Experimentsmentioning

confidence: 99%

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Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion

2014

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“…Using 0.05 % v/v (3-aminopropyl)triethoxysilane (APTES)-modified mica (APmica) [9] was found ideal for polymer adsorption and AFM imaging purposes. The negatively charged sulfate groups of the carrageenans (pK a = 2) [10] interact ionically with the positively charged surface aliphatic amino groups of the AP-mica (pK a = 10.6) [11] providing an efficient immobilization.High resolution AFM imaging reveals individual, well separated polymer chains in condition of no added salt (0 mm) with an average chain height of about 0.3 nm for iota-as well as lambda-carrageenan (Figure 1 a,e and Figure S2 and S3). Analogous heights of about 0.3 to 0.5 nm were previously reported, [12,13] which is also in accordance with the estimated longitudinal axis of 0.3 nm for a hexose unit in its most stable 4 C 1 chair conformation.…”

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confidence: 99%

mentioning

confidence: 99%

Unravelling Secondary Structure Changes on Individual Anionic Polysaccharide Chains by Atomic Force Microscopy

2014

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The structural conformations of the anionic carrageenan polysaccharides in the presence of monovalent salt close to physiological conditions are studied by atomic force microscopy. Iota-carrageenan undergoes a coil-helix transition at high ionic strength, whereas lambda-carrageenan remains in the coiled state. Polymer statistical analysis reveals an increase in persistence length from 22.6 AE 0.2 nm in the random coil, to 26.4 AE 0.2 nm in the ordered helical conformation, indicating an increased rigidity of the helical iota-carrageenan chains. The many decades-long debated issue on whether the ordered state can exist as single or double helix, is conclusively resolved by demonstrating the existence of a unimeric helix formed intramolecularly by a single polymer chain.Carrageenans are naturally occurring anionic polysaccharides extracted from red seaweed species and find application in food, cosmetic, and pharmaceutical product formulations where they serve as gelling agents, thickeners, stabilizers, and excipients. [1,2] Referring to a family of sulfated linear galactans, their principal disaccharide repeating unit consists of alternating b-(1!3)-and a-(1!4)-d-galactose or 3,6-anhydride residues. [1c] Following the traditional classification, iotaand lambda-carrageenan have two and three sulfate groups, respectively, with the former containing a 3,6-anhydridebridge. [1a] These chemical and structural varieties combined with the ionic environment control their conformation. [3] The sequence motif of lambda-carrageenan has been suggested to prevent the formation of any secondary structure and thus gel formation, whereas iota-carrageenan has been reported to be capable of undergoing a coil-helix transition as a first event of gelation. [4] For their thermoreversible gelation in aqueous solution, a two-step process involving an initial ion-induced helix formation followed by association into networks is generally accepted. Nonetheless, the mechanisms governing the conformational transition, ion-specificity effects, and the mode of molecular association into a percolating gel are still highly debated. [2] An ordered dimeric double helix with 1.3 nm diameter was initially proposed for iota-carrageenan based on fiber X-ray diffraction results, [5a] which was further supported by osmometry, [5b] stopped-flow polarimetry, [5c] sizeexclusion chromatography combined with light scattering, [5d, e] and differential scanning calorimetry.[5f] Strong indication for a single-stranded iota-carrageenan helix as the ordered conformation emerged, however, from other osmometry studies combined with measurements of optical rotation [4] and intrinsic viscosity, [6a] which were substantiated by light scattering data, [6b] leaving the nature of the ordered state a highly controversial issue.This study focuses on resolving the disorder-order conformational transition in molecular solutions of these anionic polysaccharides by atomic force microscopy (AFM) imaging. The conformational change from disordered carrageenans i...

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Nucleic Acid Organizations Visualized by Scanning Force Microscopy

Bohley

Matern

Bischoff

et al. 1997

Surf. Interface Anal.

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Both DNA and RNA domains and microdomains—to a certain degree comparable to self‐organizational mesophase areas—have been visualized as graphite surface adlayers by scanning force microscopy in contact force mode. More polar substrate surfaces, sharper tip geometries and tapping mode procedures proved less favourable, due to sample distortions and prevention of organization within the adlayer by dominant adhesive forces in the interface.© 1997 John Wiley & Sons, Ltd.

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Adsorption of DNA to Mica, Silylated Mica, and Minerals: Characterization by Atomic Force Microscopy

Cited by 249 publications

References 7 publications

Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion

Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion

Unravelling Secondary Structure Changes on Individual Anionic Polysaccharide Chains by Atomic Force Microscopy

Nucleic Acid Organizations Visualized by Scanning Force Microscopy

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