No abstract

The circular dichroism (CD) spectrum of tumor necrosis factor-alpha has been measured into the vacuum UV to 168 nm. Analysis of the CD for secondary structure is in good agreement with X-ray diffraction results, but the analysis is somewhat unstable. Adding the CD of this protein together with its X-ray determined secondary structure to the basis set should improve subsequent analyses of CD spectra for other all-beta proteins.

Flow linear dichroism measurements extended into the vacuum uv region yield inclinations for the base normal from the helix axis of 21 degrees for dA and 40 degrees for dT in the X-form of poly(dAdT).poly(dAdT). These inclination angles are similar to the B form of the synthetic polymer, but the axes around which the bases incline are different. Hydrogen-bonded base pairs are consistent with the geometry for the standard B, C, D, and Z forms of natural DNA, but will not fit into the A form. Fourier transform ir spectra indicate that the X form has sugar pucker and phosphate geometry similar to B-form DNA, and supports the dinucleotide repeat with two kinds of phosphates seen in earlier work, in analogy to Z-form DNA. Clearly, X-form DNA has a unique geometry.

SYNOPSISThe Z-form of poly(dG-m5dC)~poly(dG-m5dC) in 85% ethanol/MOPS and the Z-form poly ( rG-rC ) . poly ( rG-rC) in 4.8 M NaClO,, 20% ethanol are studied by flow linear dichroism. Simultaneous analysis of the isotropic absorption and linear dichroism data yields the angle of inclination of the base normal relative to the helix axis, and the orientation of the axis around which the bases incline. For the Z-form of poly(dGm5dC) .poly(dG-m5dC) the inclination angles are 31.3" for guanine, and 27.9" for cytosine; for the Z-form of poly(rG-rC).poly(rG-rC) they are 25.0" for guanine, and 23.3" for cytosine. The inclination angles for the Z-form DNA are similar to those for the Zform, and the angles for Z-form RNA are somewhat smaller. The axes of inclination for guanine and cytosine are similar in all three left-handed forms. 0 1995 John Wiley & Sons, Inc.