Conformation and interactions of the packaged double-stranded DNA genome of bacteriophage T7

Abstract

The structure of the packaged double‐stranded DNA genome of bacteriophage T7 was compared to that of unpackaged T7 DNA using digital difference Raman spectroscopy. Spectral data were obtained at 25°C from native T7 virus (100 mg/mL), empty T7 capsids (50 mg/mL), and purified T7 DNA (40 mg/mL) in buffer containing 200 mM NaCl, 10 mM MgCl2, and 10 mM Tris at pH 7.5. At these conditions, the local conformation of T7 DNA was not affected by packaging. Specifically, the local B‐form secondary structure of unpackaged T7 DNA, including furanose C2′‐endo pucker, anti glycosyl torsion, Watson‐Crick base pairing, and base stacking, were essentially fully (>98%) retained when the genome was condensed within the viral capsid. However, the average electrostatic environment of T7 DNA phosphates was altered dramatically by packaging as revealed by large perturbations in the Raman bands associated with localized vibrations of the DNA phosphate groups. The change in the phosphate environment was attributed to Mg2+ ions that were packaged with the genomic DNA, and the observed Raman perturbations of genomic DNA were equivalent to those generated by a 50–100‐fold increase in Mg2+ concentration in aqueous phosphodiester model compounds. The T7 data were qualitatively and quantitatively similar to those observed previously for packaged DNA of bacteriophage P22 and imply that genomic DNAs of T7 and P22 are both organized in a similar fashion within their respective capsids. The results show that the condensed genome does not contain kinks or folds that would disrupt the local B conformation by more than 2%. The present findings are discussed in relation to previously proposed models for condensation and organization of double‐stranded and single‐stranded viral DNA. © 1998 John Wiley & Sons, Inc. Biospectroscopy 4: S47–S56, 1998

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

“…164 Digital difference and H/D exchange methods provide convenient means of structurally interpreting the Raman spectral data on packaged viral DNAs. 23,165,166 These studies show that although the canonical B-form secondary structure of dsDNA is largely conserved with packaging, the H/D exchange dynamics of specific amino and imino groups of the bases are perturbed in the condensed state. Representative data obtained from studies of the Salmonella bacteriophage P22 are shown in Fig.…”

DNA structural transitions induced by divalent metal ions in aqueous solutions

“…However, no major departure from B-DNA conformation was observed before and after DNA condensation even though some local structural modifications were observed [34]. The structure of the packaged ds DNA genome of bacteriophage T7 was not affected by packaging as well [63]. DNA becomes more bent and more flexible in the presence of other condensing agents -spermine 4+ , spemidine 3+ and Co(NH 3 ) 6 3+ as well as substantial decrease in the persistent length of B-DNA have been observed in the presence of these multivalent cations [54,64].…”

Application of FTIR and Raman Spectroscopy to Characterisation of Bioactive Materials and Living Cells

“…Peak assignments for the MLE-12 Raman spectrum[31,[45][46][47][48][49] (Phe -phenylalanine, Tyr -tyrosine, A -adenine, C -cytosine, G -guanine, T -thymine)…”