Published online 31 May 2006
© 2006 The Author(s)
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Structural analysis of hyperperiodic DNA from Caenorhabditis elegans
Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology Lorentzweg 1, 2628 CJ Delft, The Netherlands 1 Department of Pathology, Stanford University School of Medicine 300 Pasteur Drive, Room L235, Stanford, CA 94305-5324, USA 2 Department of Genetics, Stanford University School of Medicine 300 Pasteur Drive, Room L235, Stanford, CA 94305-5324, USA
*To whom correspondence should be addressed. Tel: +31 0 15 278 3219; Fax: +31 0 15 278 1202; Email: Nynke.Dekker{at}mb.tn.tudelft.nl
Received April 11, 2006. Revised May 11, 2006. Accepted May 11, 2006.
Several bioinformatics studies have identified an unexpected but remarkably prevalent 
10 bp periodicity of AA/TT dinucleotides (hyperperiodicity) in certain regions of the Caenorhabditis elegans genome. Although the relevant C.elegans DNA segments share certain sequence characteristics with bent DNAs from other sources (e.g. trypanosome mitochondria), the nematode sequences exhibit a much more extensive and defined hyperperiodicity. Given the presence of hyperperiodic structures in a number of critical C.elegans genes, the physical characteristics of hyperperiodic DNA are of considerable interest. In this work, we demonstrate that several hyperperiodic DNA segments from C.elegans exhibit structural anomalies using high-resolution atomic force microscopy (AFM) and gel electrophoresis. Our quantitative analysis of AFM images reveals that hyperperiodic DNA adopts a significantly smaller mean square end-to-end distance, hence a more compact coil structure, compared with non-periodic DNA of similar length. While molecules remain capable of adopting both bent and straight (rod-like) configurations, indicating that their flexibility is still retained, examination of the local curvatures along the DNA contour length reveals that the decreased mean square end-to-end distance can be attributed to the presence of long-scale intrinsic bending in hyperperiodic DNA. Such bending is not detected in non-periodic DNA. Similar studies of shorter, nucleosome-length DNAs that survived micrococcal nuclease digestion show that sequence hyperperiodicity in short segments can likewise induce strong intrinsic bending. It appears, therefore, that regions of the C.elegans genome display a significant correlation between DNA sequence and unusual mechanical properties.
Present address: Ralf Seidel, BioTechnological Center, University of Technology Dresden, Tatzberg 47-51, D-01307 Dresden, Germany
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