Intrinsic bending of DNA molecules results from local structural polymorphism in regions of homopolymeric dA . dT which are at least 4 base pairs long; the A . T tracts must be repeated in phase with the helix screw. Bending, in the direction of base-pair tilt rather than roll, occurs at the junctions between the A . T tract and adjacent B-DNA, with a larger angle at the 3' than at the 5' end of the A tract.

Chemically synthesized duplex oligodeoxynucleotides having different average numbers of adenine tracts (A6) per helix turn were ligated into multimers and analyzed by electrophoresis on polyacrylamide gels. The magnitude of the anomaly in gel mobility is found to be a quadratic function of the curvature of the DNA molecule. Parameters that describe intrinsic DNA bending, expressed as the tilt and roll components of the helix-axis deflection at the junctions between the adenine tract and adjacent B-DNA, were adjusted to fit the measured relative curvature of regularly repeated DNA bending sequences known from other studies and synthesized for this study. The model developed here retains the predominance of bending in the direction of tilt at the junctions but incorporates an appreciable roll component at the 5' end of an adenine tract, opening the minor groove there. This feature is consistent with chemical "footprinting" experiments on molecules containing adenine tracts. The overall direction of bending is effectively toward the minor groove, viewed from the center of an A. or A6 tract. A possible underlying structure, which can also be described by a wedge bending model, is that derived from fiber diffraction studies of poly(dA)-poly(dT). However, alternative models for the adenine tract, such as propeller twisted DNA, cannot be eliminated, although they do not lead to the correct direction of bending. The results permit calculation of the helix-axis trajectory of natural DNA molecules containing adenine-tract bends.

We determined the magnitude of the bend induced in DNA by an adenine-thymine tract by measuring the rate of cyclization of DNA oligonucleotides containing phased A tracts. A series of linear multimers with 2-bp single-stranded ends, in which the (A.T)6 tracts are separated by CG2-3C sequences and are positioned 10 and 11 bp apart alternately, were prepared from 21 bp long synthetic duplexed deoxyoligonucleotides. The cyclization rates of the multimers (105-210 bp) and the bimolecular association rate of the 84 bp long multimer were measured in the presence of DNA ligase. From the rate constants of the cyclization and bimolecular association reactions, ring closure probabilities were obtained for the multimers. The systematically bent molecules were simulated by Monte Carlo methods, and the ring closure probabilities were calculated for a given set of junction bend angles. By comparing the calculated values of ring closure probabilities to experimental values and adjusting the junction bend angles to fit experimental values, the extent of bending at the junctions (or the extent of bending for an adenine tract) was determined. We conclude that an A6 tract bends the DNA helix by 17-21 degrees.

Calcineurin is a Ca(2+)-calmodulin-dependent serine/threonine protein phosphatase that has been implicated in various signaling pathways. Here we report the identification and characterization of calcineurin genes in Caenorhabditis elegans (cna-1 and cnb-1), which share high homology with Drosophila and mammalian calcineurin genes. C. elegans calcineurin binds calcium and functions as a heterodimeric protein phosphatase establishing its biochemical conservation in the nematode. Calcineurin is expressed in hypodermal seam cells, body-wall muscle, vulva muscle, neuronal cells, and in sperm and the spermatheca. cnb-1 mutants showed pleiotropic defects including lethargic movement and delayed egg-laying. Interestingly, these characteristic defects resembled phenotypes observed in gain-of-function mutants of unc-43/Ca(2+)-calmodulin-dependent protein kinase II (CaMKII) and goa-1/G(o)-protein alpha-subunit. Double mutants of cnb-1 and unc-43(gf) displayed an apparent synergistic severity of movement and egg-laying defects, suggesting that calcineurin may have an antagonistic role in CaMKII-regulated phosphorylation signaling pathways in C. elegans.

AAK-2 is one of two ␣ isoforms of the AMP-activated protein kinase in Caenorhabditis elegans and is involved in life span maintenance, stress responses, and germ cell cycle arrest upon dauer entry. We found that AAK-2 was phosphorylated at threonine 243 in response to paraquat treatment and that this phosphorylation depends on PAR-4, the C. elegans LKB1 homologue. Both aak-2 mutation and par-4 knockdown increased the sensitivity of C. elegans worms to paraquat, and the double deficiency did not further increase sensitivity, indicating that aak-2 and par-4 act in a linear pathway. Both mutations also slowed body bending during locomotion and failed to reduce head oscillation in response to anterior touch. Consistent with this abnormal motility and behavioral response, expression of the AAK-2::green fluorescent protein fusion protein was observed in the ventral cord, some neurons, body wall muscle, pharynx, vulva, somatic gonad, and excretory cell. Our study suggests that AMPK can influence the behavior of C. elegans worms in addition to its well known function in metabolic control.