DNA coiled coils

Abstract

We report the coiled-coil structure of DNA, which is generated by the dodecanucleotide d(ATATATATATAT). The structure has been determined by single-crystal x-ray crystallography. The molecules form duplexes with single-stranded overhangs, which associate with neighbor molecules and give rise to infinite double helices in a coiled-coil conformation, with staggered nicks in both strands. The coiled coils have six dodecamer duplexes per turn. Despite the presence of nicks, the structure is very rigid. Statistical disorder is present, which gives rise to continuous scattering along the layer lines. This observation can be interpreted by the classical theory of coiled coils developed for proteins, which we apply here to a DNA structure. A clear splitting of the original layer lines of the DNA double helix is detected. The structure we have found adds a previously unrecognized element to the architectures that can be built from DNA oligonucleotides. Any duplex with complementary single-strand overhangs should be expected to give rise to regular coiled-coil structures.oligonucleotides ͉ x-ray crystallography

Structure of the DNA Coiled Coil Formed by d(CGATATATATAT)

“…[2] The presence of continuous diffraction indicates screw disorder, with parallel orientation of the diffracting entities. Slight variations in the crystallization conditions resulted in crystals that show little screw disorder and Bragg spots that extend for up to 3 .…”

“…The crystals were practically isomorphous to those previously described. [2] We determined the 3.1 X-ray structure and found that this dodecamer forms a continuous coiled coil with Hoogsteen base pairs between A and T.…”

“…We recently described the structure of the coiled coil formed by duplex d(ATATATATATAT). [2] Due to the presence of sticky ends it forms a continuous double helix. However diffraction data could only be obtained with a limited resolution of 5 ; this is probably due to a combination of factors: high solvent content, screw disorder, and possible multiple alignments.…”

“…[1,2] As part of our studies on these sequences, we have determined the molecular structure of the coiled coil obtained from duplex d(CGATATATATAT) by single-crystal X-ray diffraction. We recently described the structure of the coiled coil formed by duplex d(ATATATATATAT).…”

Low level epifluorescent detection of nanoparticles and DNA on dielectrophoretic microarrays

“…If the DNA molecules assume a minimum spherical volume, the 48 kbp and 300 bp fragments will have particle diameters of 57.25 nm and 11.6 nm, respectively [42].…”