Influence of charged surfaces on the morphology of DNA condensed with multivalent ions

Besteman, K.; Eijk, K. Van; Vilfan, Igor D.; Ziese, Ulrike; Lemay, Serge G.

doi:10.1002/bip.20806

Cited by 11 publications

(14 citation statements)

References 34 publications

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“…Accordingly, with the increase of spermidine concentration, less and less DNA molecules exist as coils in solu- tion and thus less and less flat patterns can be observed on mica surfaces. This well explains why toroids are often observed in electron microscopy experiments [9] whereas only flat patterns can be observed in AFM experiments [15,16] .…”

Section: Dna Condensation By Spermidinementioning

confidence: 58%

“…As we have observed, above 400 µM spermidine, hardly any DNA condensation forms on mica surfaces. It is thus impossible that the flat disk is the opening of the three-dimensional compact toroid formed in solution, since toroids or globules still remain the same in solution even under high spermidine concentrations [16] . The assumption of intermediates for condensates into toroids is also questionable [15] , because even we increased the spermidine concentration up to 5 mM, no toroid or globule was observed.…”

Section: Discussionmentioning

confidence: 99%

“…Fang and Hoh [15] reported the flowerlike patterns of spermidine-induced DNA condensation on mica surfaces which were interpreted as early intermediates of free toroids in solutions. In 2007, the influence of charged surface on morphologies of spermidine-induced DNA condensates was investigated systemically [16] . Again, flowerlike shapes of a single layer were formed on mica surfaces.…”

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confidence: 99%

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Spermidine-induced two-dimensional DNA condensations on mica surfaces: A different pathway from condensations in solution

Zhang

Hou

et al. 2009

Chin. Sci. Bull.

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With atomic force microscopy (AFM) we systematically studied the DNA condensations on mica surfaces induced by multivalent cation spermidine. The pattern of the DNA condensates is a flat single layer, with a core in the centre and DNA wrapping around it at high density. We assume this to be a two-dimensional condensation of free coiled DNA onto negatively charged mica surfaces by the multivalent cation. The DNA molecules condense on mica surfaces via a pathway different from the formation of toroids, rods or globules in bulk solutions. We give an explanation to why toroid structures are difficult to be observed by AFM, and further discuss the relationship between DNA condensations in solutions and on mica surfaces. The present work will be helpful for understanding the behaviors of DNA on charged surfaces, which might be significantly different from that in solutions. DNA condensation, spermidine, two-dimension, condensing pathway, AFMThe condensation of DNA has become a fascinating research subject. Studies on DNA condensations are beneficial to the understanding of the physical behaviors of charged biopolymers and the process of virus packing in vivo, as well as to the development of technologies for gene therapy [1,2] . Experimental evidence has shown that DNA condensation occurs when ~90% of its charge is neutralized by multivalent cations, leading to a weak short range attractive force between different DNA segments [3] . DNA condensing agents include spermidine, spermine, cobalt hexamine and proteins such as protamine. The condensation can also be induced by crowding polymers such as PEG or weak electrolyte such as ethanol [4,5] . Although appearing as being continuous in ensemble assays, the coil-globule transition of DNA is markedly discrete for individual molecules, which is considered as a first-order phase transition [6] . In other words, each DNA molecule exists either in coiled or folded states. Fluorescence microscopy observations have revealed that, in bulk solutions, DNA molecules are mainly elongated when the spermidine concentration is less than 100 µM; elongated coils and folded compact states coexist in 150 µM spermidine; and all DNA molecules are in folded state when the spermidine concentration is increased to 200 µM [7] .Toroid is the most frequently observed folded structure of DNA condensates in solutions [8] . The size of the toroids is largely independent of the DNA length, reflecting that several DNA molecules may be incorporated into a single particle. Toroids are usually observed with electron microscopy. In such an observation, DNA is condensed in solution in advance, and then deposited onto a hydrophobic carbon grid and fixed with ethanol [9] . Some very well developed toroids have been recorded using this method.As a convenient and high-resolution instrument, AFM

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Section: Dna Condensation By Spermidinementioning

confidence: 58%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Spermidine-induced two-dimensional DNA condensations on mica surfaces: A different pathway from condensations in solution

Zhang

Hou

et al. 2009

Chin. Sci. Bull.

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“…Similar effects on the appearance of parallel ordering have been described in previous reports. [56][57][58] However, the degree of parallel ordering has not yet been fully analyzed quantitatively at the single-molecule level.…”

Section: Discussionmentioning

confidence: 99%

Critical behavior of megabase-size DNA toward the transition into a compact state

Yoshikawa

Suzuki

Yamada

et al. 2011

The Journal of Chemical Physics

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Naturally occurring branched-chain polyamines induce a crosslinked meshwork structure in a giant DNA The Journal of Chemical Physics 145, 235103 (2016) We studied the changes in the higher-order structure of a megabase-size DNA (S120-1 DNA) under different spermidine (SPD) concentrations through single-molecule observations using fluorescence microscopy (FM) and atomic force microscopy (AFM). We examined the difference between the folding transitions in S120-1 DNA and sub-megabase-size DNA, T4 DNA (166 kbp). From FM observations, it is found that S120-1 DNA exhibits intra-chain segregation as the intermediate state of transition, in contrast to the all-or-none nature of the transition on T4 DNA. Large S120-1 DNA exhibits a folding transition at lower concentrations of SPD than T4 DNA. AFM observations showed that DNA segments become aligned in parallel on a two-dimensional surface as the SPD concentration increases and that highly intense parallel alignment is achieved just before the compaction. S120-1 DNA requires one-tenth the SPD concentration as that required by T4 DNA to achieve the same degree of parallel ordering. We theoretically discuss the cause of the parallel ordering near the transition into a fully compact state on a two-dimensional surface, and argue that such parallel ordering disappears in bulk solution.

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“…The mechanism of DNA interaction with the microsphere surface can be more complicated. It was found out that PEG adsorbs through hydrogen bonds to the silica surface silanol groups . PEG is essentially non‐polar and PEG‐covered surfaces have been widely used as passivation layers to avoid non‐specific adsorption of proteins .…”

Section: Applications Of Magnetic Particles In Dna Separationsmentioning

confidence: 99%

SPE and purification of DNA using magnetic particles

Rittich

Španová

2013

J of Separation Science

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Superparamagnetic particles have been attractive for molecular diagnostics and analytical chemistry applications due to their unique magnetic properties and their ability to interact with various biomolecules of interest. This paper presents a critical overview of magnetic nano- and microparticles used as a solid phase for extraction and purification of DNAs. The mechanisms of DNA binding to the surface of functionalised magnetic particles are described. The most widely used materials including silica supports, organic polymers and other materials, mostly containing magnetite or paramagnetic metallic elements are reviewed. The main application areas of magnetic particles for DNA separation are briefly described.

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Influence of charged surfaces on the morphology of DNA condensed with multivalent ions

Cited by 11 publications

References 34 publications

Spermidine-induced two-dimensional DNA condensations on mica surfaces: A different pathway from condensations in solution

Spermidine-induced two-dimensional DNA condensations on mica surfaces: A different pathway from condensations in solution

Critical behavior of megabase-size DNA toward the transition into a compact state

SPE and purification of DNA using magnetic particles

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