The principal sequence feature responsible for intrinsic DNA curvature is generally assumed to be runs of adenines. However, according to the wedge model of DNA curvature, each dinucleotide step is associated with a characteristic deflection of the local helix axis. Thus, an important test of a more general view of sequence-dependent DNA curvature is whether sequence elements other than A-A cause the DNA axis to deflect. To address this question, we have applied the wedge model to a large body of experimental data. The axial path of DNA can be described at each step by three Eulerian angles: the helical twist, the deflection angle (wedge angle), and the direction of the deflection. Circularization and gel electrophoretic mobility data on 54 synthetic DNA fragments, both from other laboratories and from our own, were used to compare the theoretical predictions of the wedge model with experiment. By minimizing misfit between calculated and observed DNA curvature, we have found that the stacks AG/CT, CG/CG, GA/TC, and GC/GC, in addition to AA/TT, have large wedge values. We have also synthesized seven sequences without AA/TT elements but with these other wedges correctly phased to cause appreciable predicted curvature. All appear curved as demonstrated by anomalous gel mobilities. The full set of 16 roll and tilt wedge angles is estimated and, together with the known 10 helical twists, these allow prediction of the general sequence-dependent trajectory of the DNA axis.

The development of most unconventional oil and gas resources relies upon subsurface injection of very large volumes of fluids, which can induce earthquakes by activating slip on a nearby fault. During the last 5 years, accelerated oilfield fluid injection has led to a sharp increase in the rate of earthquakes in some parts of North America. In the central United States, most induced seismicity is linked to deep disposal of coproduced wastewater from oil and gas extraction. In contrast, in western Canada most recent cases of induced seismicity are highly correlated in time and space with hydraulic fracturing, during which fluids are injected under high pressure during well completion to induce localized fracturing of rock. Furthermore, it appears that the maximum-observed magnitude of events associated with hydraulic fracturing may exceed the predictions of an often-cited relationship between the volume of injected fluid and the maximum expected magnitude. These findings have far-reaching implications for assessment of inducedseismicity hazards.

We have obtained striking atomic force microscopy images of the intact A bacteriophage genome and of several A restriction fragments both in air and under water. The DNA is unstained and the images are stable under continuous scanning for up to 30 min. Measured contour lengths of fully imaged restriction fragments and intact A DNA are accurate to within a few percent. The key to this development is the use of a process for binding unmodified double-stranded DNA to chemically treated mica surfaces. This procedure leads to strong DNA attachment and yields high-quality images that are stable under repeated scanning, even with the sample submerged in water. This allows normal hydration conditions to be maintained during scanning and in addition leads to a general improvement of image quality. Both the lateral resolution and the contrast increase by a factor of -3 under water.Scanning probe microscopy, which currently includes scanning tunneling microscopy (STM) and atomic force microscopy (AFM), is a structural tool ofgreat potential importance to structural molecular biology. AFM can image thick insulators, whereas STM is limited to small molecules (1, 2). Resolution is limited by the size and geometry ofthe scanning tip (3), by the tendency of the tip to move the DNA (1, 4), and by deformation of the sample (5) and scanning probe (6). Bustamante et al. (7) have overcome the problem of holding DNA in place for AFM scanning with an ionic treatment of the mica surface that allows DNA to be imaged in air under ambient conditions. Hansma et al. (8) Chemical methods for holding DNA in place have been proposed by us (9) and others (10) and implemented in ambient conditions for STM imaging (11) and AFM imaging (12)(13)(14). Our method for chemically modifying mica substrates uses covalently bound 3-aminopropyltriethoxysilane (APTES) followed by methylation and hydrolysis (12)(13)(14). In preliminary scans in air, this method has enabled us to obtain high-quality images of linear and circular DNA (12). In the work reported here, we show that the method can be extended both to unstained DNA molecules as large as the intact A phage genome (48,502 bp) and to scanning DNA under water. DNA images obtained under water not only reflect normal hydration conditions but also show significantly improved lateral resolution over those obtained in air. It therefore appears possible to use AFM for direct conformational studies of nucleic acids and nucleoprotein complexes. MATERIALS AND METHODSThe procedure for mica modification is described in refs. 12-14. Briefly, freshly cleaved strips of mica were left in the APTES atmosphere created by a small pool of APTES in the bottom of a 2-liter glass desiccator left at ambient temperature for 2 h. The methylation procedure was the same as described in ref. 14. The amino groups of APTES are bound covalently to a freshly cleaved mica surface, endowing it with properties similar to an anion exchanger.Modified mica strips were immersed into DNA in Tris'HCl buffer (pH 7) (10 mM Tris.HCl/10-...

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Recent structural studies of the minimal core DNA-binding domain of p53 (p53DBD)