Nucleic Acids Research, 2006, Vol. 34, No. 10 3057–3066 doi:10.1093/nar/gkl397 Structural analysis of hyperperiodic DNA from Caenorhabditis elegans Fernando Moreno-Herrero, Ralf Seidel, Steven M. Johnson1,2, Andrew Fire1,2 and Nynke H. Dekker* Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands and 1Department of Pathology and 2Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Room L235, Stanford, CA 94305-5324, USA Received April 11, 2006; Revised and Accepted May 11, 2006 ABSTRACT Several bioinformatics studies have identified an unexpected but remarkably prevalent 10 bp peri- odicity of AA/TT dinucleotides (hyperperiodicity) in certain regions of the Caenorhabditis elegans gen- ome. Although the relevant C.elegans DNA seg- ments 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 consid- erable 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 dis- tance, hence a more compact coil structure, com- pared 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 seg- ments 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. INTRODUCTION DNA structures are frequently modeled as ﬂexible, isotropic rods both in solution and in their ability to contribute to native biological structures such as chromatin (1). Despite the utility of such models, it has been clear for some time that the sequence of a DNA molecule can contribute very speciﬁcally to its 3D structure, both in vitro (2,3) and in vivo (4). Particularly striking in their non-linear structure, certain sequences can introduce a stereo-speciﬁc bend in DNA. The most prominent sequence contributing to these structural anomalies are strings of three, four or more consec- utive A or T residues (A-tracts) (5,6), although other nucleot- ide segments can also induce structural anomalies (7). A-tract bending has been investigated using X-ray crystallography, gel electrophoresis, electric birefringence, circular dichroism and NMR [for reviews see (8,9)]. DNA curvature of non-genomic DNA has also been investigated with electron microscopy (10,11) and atomic force microscopy (AFM) (12–14). Many of the unusual DNA sequences that have been the subject of biophysical and modeling studies have involved relatively short (10–80 bases) bent regions either examined in isolation (15) or examined in the context of a longer frag- ment (13). This type of DNA structure is common in many genome sequences and in numerous cases has been associated with biological function, either in facilitating a speciﬁc protein interaction at the site of the bend as in the case of nuc- leosomes (16) or in facilitating a long-range interaction of two sites in the genome that otherwise might not be capable of interacting (17). Recently, it has become clear that certain eukaryotic gen- omes include sequences with a more extended anomalous character in which groups of An/Tn residues are present in a periodic and highly non-random manner over a range of *To whom correspondence should be addressed. Tel: +31 0 15 278 3219; Fax: +31 0 15 278 1202; Email: Nynke.Dekker@mb.tn.tudelft.nl Present address: Ralf Seidel, BioTechnological Center, University of Technology Dresden, Tatzberg 47-51, D-01307 Dresden, Germany 2006 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.