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Reconstruction of DNA Shape from AFM Data

✍ Scribed by V. Ph. Pastushenko; R. Kaderabek; M. Šip; C. Borken; F. Kienberger; P. Hinterdorfer

Publisher
John Wiley and Sons
Year
2002
Tongue
English
Weight
515 KB
Volume
3
Category
Article
ISSN
1438-5163

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✦ Synopsis

DNA plasmid molecules modified with the antitumor drug cisplatin were imaged using dynamic force microscopy (DFM) in liquids. We have studied the positions of DNA kinks defined as points of abrupt change of the direction of the DNA double helix axis. The jumps of the direction were found using a method developed earlier for the idealization of electrical current through single ion channels (1). Raw AFM data were compensated for drift by joining adjacent scan lines of the image at flat portions of the sample surface. The quality of the reconstituted image is characterized quantitatively by an order parameter that describes the image wobble remaining after drift elimination. A new method for obtaining the molecule direction (central line) from contours of equal height based on the determination of central positions of circles inscribed between the inner and the outer contours of the molecule has been developed, leading to effective decrease of noise and drift. The positions of kinks are in good agreement with results of immediate analysis.

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