Conformational transition in DNA on a cold surface

Feng, Xi Z.; Bash, R.; Balagurumoorthy, Pichumani; Lohr, D.; Harrington, R. M.; Lindsay, Stuart

doi:10.1093/nar/28.2.593

Cited by 22 publications

(14 citation statements)

References 24 publications

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“…The Co(phen) 3 3 + consisted of three vertical tris(1,10‐phenanthroline) and one Co 2+ ion, and could associate with the DNA by groove binding (Coury et al , 1997). The association of a few Co(phen) 3 3 + with DNA molecules did not alter the conformation of DNA but enhanced the adsorption of DNA on the mica surface (Feng et al , 2000). However, the association of a large number of Co(phen) 3 3 + molecules with DNA condensed the DNA molecules, as shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…However, the emphases of these theoretical studies were only focussed on the structure of molecules on a surface, and the relationship of the molecules on a surface and in a solution. Actually, the surface could not only alter the conformations of molecules in a solution but also affect the interaction between DNA and protein or small molecules, even if the complex was disassembled (Feng et al , 2000; Nagami et al , 2002).…”

Section: Introductionmentioning

confidence: 99%

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Disassembly of DNA–ligand on mica surface: atomic force microscopy studies

Song¹,

Wang²,

Zhao³

et al. 2009

Journal of Microscopy

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SummaryDisassembly of DNA-ligands, including DNA-methylene blue (MB) complex and DNA-Co(phen) 3 3+ complex on mica surface, were investigated by atomic force microscopy (AFM). The disassembly of these complexes occurred after they were immersed in ultra-pure water. AFM results showed that the disassembly depended strongly on bridge ions that were used to immobilize the complex onto mica surface, DNA species and ligands. When Mg 2+ was used as the bridge ion, the DNA-MB complex was completely disassembled because of the weak interactions between Mg 2+ and DNA's bases or mica surface. Although if Co 2+ was used as the bridge ion, the disassembly of the DNA-MB complex mainly depended on the species and shape of DNA. For plasmid DNA pBR 322, plasmid DNA pUC 18 and the linear DNA pBR 322/PstI, the degree of disassembly was gradually increased. Whereas if Co(phen) 3 3+ was chosen as the ligand, the disassembly of the DNA-Co(phen) 3 3+ complex was almost blocked because Co(phen) 3 3+ could hardly diffuse into the ultra-pure water. This obtained information may be useful for practical application of the AFM imaging of biological molecules, especially in liquid.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Disassembly of DNA–ligand on mica surface: atomic force microscopy studies

Song¹,

Wang²,

Zhao³

et al. 2009

Journal of Microscopy

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“…The various conformations of DNA (Lyubchenko and Shlyakhtenko, 1997;Oussatcheva et al, 2004;Zheng et al, 2002), conformational changes (Bussiek et al, 2003;Feng et al, 2000) as well as their complexes with other molecules (Dame et al, 2000;Lysetska et al, 2002;Tseng et al, 2005) have been imaged by AFM on a mica surface or a functionalized mica surface. It is also important to image DNA binding to a gold surface or a functionalized gold surface so that in future the effect of an applied electric field on the DNA surface conformation can be studied (Wackerbarth et al, 2004), since gold surfaces or functionalized gold surfaces have been extensively employed to construct DNA microchips.…”

Section: Introductionmentioning

confidence: 99%

Immobilization of DNA on 11‐mercaptoundecanoic acid‐modified gold (111) surface for atomic force microscopy imaging

Song

Liu

et al. 2005

Microscopy Res & Technique

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Immobilized DNA on preformed 11-mercaptoundecanoic acids (MUDA) self-assembled monolayers (SAMs) on a gold (111) surface was bound by a divalent cation bridges was imaged by atomic force microscopy (AFM). The DNA immobilization was attributed to the formation of ionic bridges between the carboxylate groups of MUDA and the phosphate groups of DNA. AFM images revealed that DNA molecules could be immobilized strongly enough to permit stable and reproducible imaging. The effect of different bridge cations, such as Mg(2+), Zn(2+) and Cu(2+), and the pH of DNA assembled solution on immobilization and conformation of DNA was studied. Plasmid DNA pBR 322/Pst I molecules were straightened by using a molecular combing technique on the MUDA surface.

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“…13 Imaging with these methods also generally requires mounting the sample on a surface, which likely alters the conformation of the DNA and its attached particles. 20 For sampling in solution, direct imaging is not usually feasible, but dimensional characterization is still achievable using spectroscopy and, in particular, by monitoring Förster resonance energy transfer (FRET) between chromophores attached to the DNA. Many studies of DNA utilizing FRET have been reported in the literature, although typically it is used in a stand-alone mode as a spatial characterization method.…”

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confidence: 99%

Multimodal Characterization of a Linear DNA-Based Nanostructure

Buckhout‐White

Ancona²,

et al. 2012

ACS Nano

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Designer DNA structures have garnered much interest as a way of assembling novel nanoscale architectures with exquisite control over the positioning of discrete molecules or nanoparticles. Exploiting this potential for a variety of applications such as light-harvesting, molecular electronics, or biosensing is contingent on the degree to which various nanoarchitectures with desired molecular functionalizations can be realized, and this depends critically on characterization. Many techniques exist for analyzing DNA-organized nanostructures; however, these are almost never used in concert because of overlapping concerns about their differing character, measurement environments, and the disparity in DNA modification chemistries and probe structure or size. To assess these concerns and to see what might be gleaned from a multimodal characterization, we intensively study a single DNA nanostructure using a multiplicity of methods. Our test bed is a linear 100 base-pair double-stranded DNA that has been modified by a variety of chemical handles, dyes, semiconductor quantum dots, gold nanoparticles, and electroactive labels. To this we apply a combination of physical/optical characterization methods including electrophoresis, atomic force microscopy, transmission electron microscopy, dynamic light scattering, Förster resonance energy transfer, voltammetry, and structural modeling. In general, the results indicate that the differences among the techniques are not so large as to prevent their effective use in combination, that the data tend to be corroborative, and that differences observed among them can actually be quite informative.

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Conformational transition in DNA on a cold surface

Cited by 22 publications

References 24 publications

Disassembly of DNA–ligand on mica surface: atomic force microscopy studies

Disassembly of DNA–ligand on mica surface: atomic force microscopy studies

Immobilization of DNA on 11‐mercaptoundecanoic acid‐modified gold (111) surface for atomic force microscopy imaging

Multimodal Characterization of a Linear DNA-Based Nanostructure

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