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

Abstract

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)

Raman, polarized Raman and ultraviolet resonance Raman spectroscopy of nucleic acids and their complexes

“…Because filamentous viruses are not amenable to study by high-resolution structural methods, Raman spectroscopy has long been recognized as a convenient structural alternative for both the protein and DNA constituents. 157,158 In the well-studied filamentous phages fd, Pf1, Pf3 and PH75, Raman markers of the deoxynucleosides indicate, respectively, C3 0 -endo/anti (665 cm 1 ), 158,159 C2 0 -endo/anti (682 cm 1 ), 158,160 C3 0 -endo/anti (663 cm 1 ) 158,161 and C2 0 -endo/anti (679 cm 1 ) 162 conformations. In a related application, interactions of packaged ssDNA genomes of fd and Pf1 with metal ions have also been probed by Raman methods.…”

Raman spectroscopic study on the conformation of a peptide fragment representing the DNA‐binding domain of filamentous virus Pf3 coat protein

“…Positive and negative peaks around 1450 cm -~ may be due to band shifts of Trp ring modes and/or C-H bending modes of aliphatic side chains. The 1320 cm -~ peak is ascribed to a conformation-sensitive guanine ring mode, which appears strong at 1318 cm -t in the C3'endo/anti conformation [18,19]. This conformation is found for guanine residues in the genome of the Pf3 virion [19].…”

“…The 1320 cm -~ peak is ascribed to a conformation-sensitive guanine ring mode, which appears strong at 1318 cm -t in the C3'endo/anti conformation [18,19]. This conformation is found for guanine residues in the genome of the Pf3 virion [19]. A positive peak at 1481 cm -~ is also ascribed to changes in frequency and intensity of a guanine Raman band at 1486 cm -l. Since strong hydrogen bonding at guanine N7 is known to decrease the frequency of this band [18], the N7 sites of some guanine bases may be hydrogen-bonded with strong proton donors, possibly with the Lys NH~-or Arc C(NH2)., + groups of CP9.…”

“…A positive peak at 1481 cm -~ is also ascribed to changes in frequency and intensity of a guanine Raman band at 1486 cm -l. Since strong hydrogen bonding at guanine N7 is known to decrease the frequency of this band [18], the N7 sites of some guanine bases may be hydrogen-bonded with strong proton donors, possibly with the Lys NH~-or Arc C(NH2)., + groups of CP9. The appearance of a positive peak at 1398 cm -t is analogous to an intensity increase at 1402 cm -I accompanied by a conformationai transition from C2"endo/anti to C3"endo/anti of thymine [20,21], the latter conformation being found in the Pf3 virion [19]. Fig.…”

Magic angle spinning NMR of viruses

“…Interestingly, they observed no evidence of structural inhomogeneity. Downfield-shifted C3′ and C5′ 13 C peaks of DNA suggest the nucleic acid is in a C2′-endo or C3′-exo sugar pucker conformation, in contrast to previous studies [233, 234]. Subsequent work probed interactions between the protein capsid and nucleic acid [64].…”