Interactive measurement and characterization of DNA molecules by analysis of AFM images

Marek, Jozef; Demjénová, Erna; Tomori, Z; Janáček, Jiřı́; Zolotová, Iveta; Valle, Francesco; Favre, M.; Dietler, Giovanni

doi:10.1002/cyto.a.20105

Cited by 43 publications

(38 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…From similar images, the contour of 52 molecules was traced using the software ELLIPSE. 31 The average length of the molecules is found to be 1975 nm, which equals a length per base of 0.37 nm in agreement with a previous investigation where, depending on sequence, 0.32-0.52 nm was found. 6 Values for the height and width of the adsorbed molecules are similar to the reported values from other AFM studies, 0.3 and 7 nm, respectively.…”

Section: A Afm Imagessupporting

confidence: 91%

Persistence length and scaling properties of single-stranded DNA adsorbed on modified graphite

Rechendorff

Witz

Adamčík

et al. 2009

The Journal of Chemical Physics

View full text Add to dashboard Cite

We have characterized the polymer physics of single-stranded DNA ͑ssDNA͒ using atomic force microscopy. The persistence length ᐉ p of circular ssDNA adsorbed on a modified graphite surface was determined independently of secondary structure. At a very low ionic strength we obtained ᐉ p = 9.1 nm from the bond correlation function. Increasing the salt concentration lead to a decrease in ᐉ p ; at 1 mM NaCl we found ᐉ p = 6.7 nm, while at 10 mM NaCl a value ᐉ p = 4.6 nm was obtained. The persistence length was also extracted from the root-mean-square end-to-end distance and the end-to-end distance distribution function. Finally, we have investigated the scaling behavior using the two latter quantities, and found that on long length scales ssDNA behaves as a two-dimensional self-avoiding walk.

show abstract

Section: A Afm Imagessupporting

confidence: 91%

Persistence length and scaling properties of single-stranded DNA adsorbed on modified graphite

Rechendorff

Witz

Adamčík

et al. 2009

The Journal of Chemical Physics

View full text Add to dashboard Cite

show abstract

“…In spite of its simplicity, backbone contour length appears remarkably accurate for the molecule sizes tested (∼300-20 000 bp) [167,168,[186][187][188][189]. While the conditions varied among studies, single measurement sizing accuracy (defined here as population CV) better than ±2-5% was reported for most cases for distances larger than 1000 bp.…”

Section: Mathematical Analysismentioning

confidence: 97%

Single molecule transcription profiling with AFM

et al. 2006

View full text Add to dashboard Cite

Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from microdissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.

show abstract

“…In this respect it is necessary to mention polymers with ring topology. As it was shown in a series of the atomic force spectroscopy (AFM) experiments [33,34] biopolymers such as DNA very often present ring topology. Such situation takes place, for example, in the case of Escherichia coli (E.coli) bacteria with a chromosome which is not a linear polymer, but has a ring topology [35].…”

Section: The European Physical Journal Special Topicsmentioning

confidence: 99%

Linear and ring polymers in confined geometries

Usatenko

Kuterba

Chamati

et al. 2017

Eur. Phys. J. Spec. Top.

View full text Add to dashboard Cite

Abstract. A short overview of the theoretical and experimental works on the polymer-colloid mixtures is given. The behaviour of a dilute solution of linear and ring polymers in confined geometries like slit of two parallel walls or in the solution of mesoscopic colloidal particles of big size with different adsorbing or repelling properties in respect to polymers is discussed. Besides, we consider the massive field theory approach in fixed space dimensions d = 3 for the investigation of the interaction between long flexible polymers and mesoscopic colloidal particles of big size and for the calculation of the correspondent depletion interaction potentials and the depletion forces between confining walls. The presented results indicate the interesting and nontrivial behavior of linear and ring polymers in confined geometries and give possibility better to understand the complexity of physical effects arising from confinement and chain topology which plays a significant role in the shaping of individual chromosomes and in the process of their segregation, especially in the case of elongated bacterial cells. The possibility of using linear and ring polymers for production of new types of nano-and micro-electromechanical devices is analyzed.

show abstract

Interactive measurement and characterization of DNA molecules by analysis of AFM images

Cited by 43 publications

References 30 publications

Persistence length and scaling properties of single-stranded DNA adsorbed on modified graphite

Persistence length and scaling properties of single-stranded DNA adsorbed on modified graphite

Single molecule transcription profiling with AFM

Linear and ring polymers in confined geometries

Contact Info

Product

Resources

About