DNA packing in the filamentous viruses fd, Xf, Pf1 and Pf3.

Spectral data for filamentous viruses in the presence and absence of Ag+, together with other parameters, indicate that the DNA structures in two of the viruses, fd and Xf, are similar to each other but that these differ from two quite unusual and different DNA structures in Pf1 and Pf3.     

Silver and mercury probing of deoxyribonucleic acid structures in the filamentous viruses fd, If1, IKe, Xf, Pf1, and Pf3

Ag+ binding and Hg2+ binding to both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) have been examined in some detail, and the results have been applied to study the structures of circular ssDNA in several filamentous viruses. It has been known for some time that Ag+ and Hg2+ bind to the bases of DNA producing characteristic large changes in absorbance and circular dichroism (CD) spectra, as well as changes in sedimentation rates. In the case of Ag+, it is known that there are three modes of binding to isolated dsDNA, referred to as types I, II, and III. Type III binding, by definition, occurs when Ag+ binds to Ag-dsDNA complexes having sites for binding types I and II extensively occupied, if not saturated. It produces CD spectra, assigned in this study, and absorbance spectra that are isosbestic with those of the Ag-dsDNA complexes present prior to its onset. In phosphate buffers binding is restricted to types I and II, whereas in borate buffers weaker type III binding can occur. Characteristics of types I, II, and III were observed for the DNAs in fd, If1, IKe, and Xf, but not for those in Pf1 and Pf3. Similarly, many of the spectral changes seen when Hg2+ binds to isolated double-stranded DNA are mimicked by Hg2+ binding to the DNAs within fd, IKe, If1, and Xf, but not for those in Pf1 and Pf3. The Ag+ and Hg2+ results indicate the presence of right-handed DNA helices in fd, If1, IKe, and Xf, with the two antiparallel strands of the covalently closed single-stranded DNAs having the bases directed toward the virion axes. For Pf1 and Pf3, Ag+ and Hg2+ binding cause large absorbance changes but only small CD changes. The very different results for Pf1 and Pf3 are consistent with the presence of inverted DNA structures (I-DNA) with the bases directed away from the structure axes, but the two structures differ from one another. Sedimentation velocity changes with Ag+ and Hg2+ binding strongly suggest structural linkages between the DNA and the surrounding protein sheath in each of the viruses.     

A CD determination of the alpha-helix contents of the coat proteins of four filamentous bacteriophages: fd, IKe, Pf1, and Pf3

The CD spectra of four filamentous bacteriophages--fd, IKe, Pf1, and Pf3--were analyzed to determine the alpha-helix contents of their major coat proteins. Measured spectra included the 192-nm band so that analyses could be carried out over the full wavelength range of the reference spectra for protein secondary structures available (a) from globular proteins [J.T. Yang, C.S.C. Wu, and H.M. Martinez (1986) Methods in Enzymology 130, 208-269] and (b) from poly(L-lysine) [N. Greenfield and G.D. Fasman (1960) Biochemistry 8, 4108-4116]. Extended analyses were also performed with the addition of the spectrum of a model beta-turn to the Greenfield and Fasman reference set, with the spectrum of a short alpha-helix in the Yang et al. reference set, and with an estimate of the spectrum of Trp added to both reference sets. The reference set based on the simple poly(L-lysine) polypeptide, plus a spectrum of a model beta-turn or of Trp, gave reasonably good fits to the measured spectra for all four phages and yielded the largest percentages of alpha-helix. The class I phages--fd and IKe--had large percentages of alpha-helix of 98 +/- 2 and 97 +/- 5%, respectively, while the two class II phages--Pf1 and Pf3--had similar but smaller alpha-helix contents of 83 +/- 6 and 84 +/- 2, respectively. While these alpha-helix contents were within the ranges previously reported from CD spectra of these phages in solution, they were more precise, and they indicated that the coat proteins of the intact phages have CD spectra that are probably modeled better by the reference spectra of polypeptides than by those of globular proteins.     

Sugar pucker and phosphodiester conformations in viral genomes of filamentous bacteriophages: fd, If1, IKe, Pf1, Xf, and Pf3

The laser Raman spectra of filamentous viruses contain discrete bands which are assignable to molecular vibrations of the encapsidated, single-stranded DNA genomes and which are informative of their molecular conformations. Discrimination between Raman bands of the DNA and those of the coat proteins is facilitated by analysis of viruses containing deuterium-labeled amino acids. Specific DNA vibrational assignments are based upon previous studies of A-, B-, and Z-DNA oligonucleotide crystals of known structure [Thomas, G.J., Jr., & Wang, A.H.-J. (1988) in Nucleic Acids and Molecular Biology (Eckstein, F., & Lilley, D.M.J., Eds.) Vol. 2, Springer-Verlag, Berlin]. The present results show that canonical DNA structures are absent from six filamentous viruses: fd, If1, IKe, Pfl, Xf, and Pf3. The DNAs in three viruses of symmetry class I (fd, If1, IKe) contain very similar nucleoside sugar puckers and glycosyl torsions, deduced to be C3'-endo/anti. However, nucleoside conformations are not the same among the three class II viruses examined: Pf1 and Xf DNAs contain similar conformers, deduced to be C2'-endo/anti, whereas Pf3 DNA exhibits bands usually associated with C3'-endo/anti conformers. Conformation-sensitive Raman bands of the DNA 3'-C-O-P-O-C-5' groups show that in all class I viruses and in Pf1 the ssDNA backbones do not contain regularly ordered phosphodiester group geometries, like those found in ordered single- and double-stranded nucleic acids.(ABSTRACT TRUNCATED AT 250 WORDS)