Peculiarities of the secondary structure of phage DNA in situ

Tikchonenko, T.I.; Добров, Е. Н.; Velikodvorskaya, G. A.; Kisseleva, Natalia

doi:10.1016/s0022-2836(66)80076-1

Cited by 50 publications

(10 citation statements)

References 15 publications

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“…Experimental evidence suggests that the DNA inside the phage head is in a partially denatured conformation (22), an observation which supports the model discussed. As a whole, it is likely that the acidic peptides are involved in the DNApackaging process; of course, we do not, by any means, exclude the additional envolvement of basic, DNA binding, peptides.…”

Section: Discussionsupporting

confidence: 77%

Characterization of DNA condensates induced by poly(ethylene oxide) and polylysine.

Laemmli¹

1975

Proc. Natl. Acad. Sci. U.S.A.

339

162

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High-molecular-weight DNA is known to collapse into very compact particles in a salt solution containing polymers like poly(etaylene oxide) [(EO)] or polyacrylate. The biological relevance of this phenomenon is suggested by our recent finding that high concentrations of the highly acidic internal pe tides found in the mature T4 bacteriophage head, as well as poly(glutamic acid) and poly(aspartic acid), can collapse DNA in a similar manner.The structure of DNAs collapsed by various methods has been studied with electron microscope. We find (EO There is now good evidence that the DNA of several bacteriophages (including T4 and lambda), is packaged into an empty, preformed head (1, 2). A preformed, empty capsid likewise appears to be a precursor of mature polio, adeno-, and herpes viruses (3).What is the mechanism by which the DNA is pulled into a preformed head? We have enumerated several possibilities elsewhere in some detail (4). The three most obvious are (a) DNA could be collapsed by titration with a basic peptide, (b) DNA binding sites could be formed sequentially inside the head to "reel in" the DNA (5); or, (c) DNA could be collapsed by a repulsive interaction between acidic peptides and the DNA (4). We have recently shown that the DNA packaging event in phage T4 appears to occur coordinately with the cleavage of protein P22 (6). This protein is the major component of the internal core seen in the empty precursor particles (7,8) and is cleaved to small fragments (5). One of these fragments is the so-called internal peptide II (9). This peptide II and another VII (probably derived from a different precursor protein) are highly acidic (10, 11), and we have shown that high concentrations of these internal peptides, as well as poly(aspartic acid) and poly(glutamic acid) can collapse DNA (4), suggesting that the internal peptides are involved in the DNA packaging event according to possibility (c) above.The idea that DNA might be collapsed by a repulsive interaction into a highly ordered structure originated with the Abbreviation: (EO)n, poly(ethylene oxide). studies of Lerman and his collaborators (12, 13). They demonstrated that in a salt solution containing a sufficient concentration of a simple polymer, high-molecular-weight DNA undergoes a cooperative structural transition which results in a very compact configuration. (The salt is required for charge neutralization of the DNA.) Circular dichroism, x-ray, and birefringence studies were used to show that collapsed DNA adopts a highly ordered and compact conformation (12)(13)(14). In this paper we examine in additional detail the structure of DNA collapsed by repulsive polymer interaction and compare it with the different structure of DNA collapsed by titration with polylysine.MATERIAL AND METHODS Enzyme Studies. Endonuclease from Neurospora crassa (EC 3.1.4.21) (15) was purchased from Boehringer (no. 15280). This enzyme, supplied as a suspension in ammonium sulfate, was centrifuged at 8000 X g for 10 min prior to use and resuspended in a buffer conta...

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Section: Discussionsupporting

confidence: 77%

Characterization of DNA condensates induced by poly(ethylene oxide) and polylysine.

Laemmli¹

1975

Proc. Natl. Acad. Sci. U.S.A.

339

162

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“…The shape and position of the maximum in the near UV CD spectrum of PVA virions (Fig. 4) were similar to those of other helical plant viruses [8], but the intensity of this spectrum (Δε∼3 units) was exceptionally low. Such intensity (and the position of the maximum) are similar to those of thermally denatured isolated single-stranded RNA [14], [15].…”

Section: Resultssupporting

confidence: 71%

“…True absorption (E) spectra of light-scattering suspensions were calculated by the extrapolation method [8] using different computer programs [9], [10]. The spectral region of 320−338 nm was used for extrapolation.…”

Section: Methodsmentioning

confidence: 99%

Partially Disordered Structure in Intravirus Coat Protein of Potyvirus Potato Virus A

et al. 2013

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Potyviruses represent the most biologically successful group of plant viruses, but to our knowledge, this work is the first detailed study of physicochemical characteristics of potyvirus virions. We measured the UV absorption, far and near UV circular dichroism spectra, intrinsic fluorescence spectra, and differential scanning calorimetry (DSC) melting curves of intact particles of a potato virus A (PVA). PVA virions proved to have a peculiar combination of physicochemical properties. The intravirus coat protein (CP) subunits were shown to contain an unusually high fraction of disordered structures, whereas PVA virions had an almost normal thermal stability. Upon heating from 20°C to 55°C, the fraction of disordered structures in the intravirus CP further increased, while PVA virions remained intact at up to 55°C, after which their disruption (and DSC melting) started. We suggest that the structure of PVA virions below 55°C is stabilized by interactions between the remaining structured segments of intravirus CP. It is not improbable that the biological efficiency of PVA relies on the disordered structure of intravirus CP.

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“…Directly measured and scattering-corrected spectra are shown. Light-scattering correction was performed with extrapolation procedure as described in Tikchonenko et al 1966 [41].…”

Section: Resultsmentioning

confidence: 99%

Structural Lability of Barley Stripe Mosaic Virus Virions

et al. 2013

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Virions of Barley stripe mosaic virus (BSMV) were neglected for more than thirty years after their basic properties were determined. In this paper, the physicochemical characteristics of BSMV virions and virion-derived viral capsid protein (CP) were analyzed, namely, the absorption and intrinsic fluorescence spectra, circular dichroism spectra, differential scanning calorimetry curves, and size distributions by dynamic laser light scattering. The structural properties of BSMV virions proved to be intermediate between those of Tobacco mosaic virus (TMV), a well-characterized virus with rigid rod-shaped virions, and flexuous filamentous plant viruses. The BSMV virions were found to be considerably more labile than expected from their rod-like morphology and a distant sequence relation of the BSMV and TMV CPs. The circular dichroism spectra of BSMV CP subunits incorporated into the virions, but not subunits of free CP, demonstrated a significant proportion of beta-structure elements, which were proposed to be localized mostly in the protein regions exposed on the virion outer surface. These beta-structure elements likely formed during virion assembly can comprise the N- and C-terminal protein regions unstructured in the non-virion CP and can mediate inter-subunit interactions. Based on computer-assisted structure modeling, a model for BSMV CP subunit structural fold compliant with the available experimental data was proposed.

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Peculiarities of the secondary structure of phage DNA in situ

Cited by 50 publications

References 15 publications

Characterization of DNA condensates induced by poly(ethylene oxide) and polylysine.

Characterization of DNA condensates induced by poly(ethylene oxide) and polylysine.

Partially Disordered Structure in Intravirus Coat Protein of Potyvirus Potato Virus A

Structural Lability of Barley Stripe Mosaic Virus Virions

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