Conformational changes in deoxyribonucleic acid during transcription

Wachsman, William; Anthony, Donald D.

doi:10.1021/bi00567a006

Cited by 12 publications

(5 citation statements)

References 22 publications

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“…Double stranded, fiber DNA is found in two major configurations: A‐helix and B‐helix [19]. Based on the CD analysis by Wachsman and Anthony [20], it has been thought that A‐helix exists in cells only during the transcription process. It is reasonable to assume, however, that within a generally B‐helical molecule, localized regions of A‐helix may exist as a consequence of the nucleotide composition of specific stretches of DNA [4,21,22].…”

Section: Resultsmentioning

confidence: 99%

Structural bistability of repetitive DNA elements featuring CA/TG dinucleotide steps and mode of evolution of satellite DNA

Kato

1999

European Journal of Biochemistry

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Satellite DNA sequences are known to be important components required for the construction of centromeres and are common to all higher eukaryotes. Nevertheless, their nucleotide sequences vary significantly, even in evolutionarily related species. In order to elucidate how the nucleotide sequences define the conformational character of centromeric satellite DNA, an evolutionary path toward repetitive units has been hypothesized. In that context, the DNA conformation of fish satellite DNA was evaluated in two ways: the organization of subrepeats and sequence characteristics were compared, and the differences in stacking energies between A-helix and B-helix and the sequence-dependent bendability of the helices were evaluated. Our findings suggest that the monomeric units making up currently observed repetitive sequences have evolved through stepwise amplification of shorter, ancestral sequences by increasing the length of the units. In addition, we suggest that potentially key sequences required for DNA amplification comprise highly flexible structures. Thus flexibility of the DNA structure may be a primary prerequisite for DNA amplification.

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Section: Resultsmentioning

confidence: 99%

Structural bistability of repetitive DNA elements featuring CA/TG dinucleotide steps and mode of evolution of satellite DNA

Kato

1999

European Journal of Biochemistry

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“…The ability of a polynucleotide to function as a template could depend on the rate at which the RNA polymerase is able to induce local conformational conversion to a suitable form. There is already evidence that localized unwinding (Reisbig et al, 1979) and other conformational changes (Wachsman & Anthony, 1980) occur at this site, and as we have indicated in this paper, at high RNA polymerase concentrations CD changes occur which are in line with partial reconversion of Z to B. It is possible that the ease of local conversion from Z to B or to another duplex conformation, or unwinding directly from Z, could limit the degree of inhibition, but we have as yet no evidence to support such possibilities.…”

Section: Discussionmentioning

confidence: 99%

Effect of template conversion from the B to the Z conformation on RNA polymerase activity

Butzow¹,

Shin²,

Eichhorn³

1984

Biochemistry

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Transition from the right-handed B to the left-handed Z conformation of DNA was studied by circular dichroism in parallel with the ability of the DNA to support RNA synthesis with Escherichia coli RNA polymerase. Since the B to Z transition is generally induced by a chemical agent, a definitive demonstration that a change in activity is due to the conformational change, and not to the agent itself or to other factors, requires the clear-cut correlation of template activity and conformation under a variety of conditions that result in conformational change. Such correlation was achieved by following the [Co(NH3)6]3+-induced transition of poly(dG-dC) X poly(dG-dC) and poly(dG-dm5C) X poly(dG-dm5C) and the Mg2+-induced transition of poly(dG-dm5C) X poly(dG-dm5C). In addition, conditions were chosen to minimize possible aggregation. In each of these three systems, the B to Z conformational transition was accompanied by a substantial decrease in transcription activity. While the conversion from B to Z of poly(dG-dm5C) X poly(dG-dm5C) is induced by a 25-fold lower concentration of [Co(NH3)6]3+ than that required for the conversion of unmethylated polymer, in both cases the RNA polymerase activity is decreased at the same cation concentration as that producing the conformational transition. Neither [Co(NH3)6]3+ nor Mg2+ inhibits RNA synthesis with control templates that are not converted to Z under the same conditions, such as poly(dA-dT) X poly(dA-dT) or calf thymus DNA with [Co(NH3)6]3+ or poly(dG-dC) X poly(dG-dC) with Mg2+.(ABSTRACT TRUNCATED AT 250 WORDS)

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“…The role of DNA structure in gene regulation has been stressed repeatedly (e.g., Wells et al, 1980;Jovin, 1976 (Wachsman and Anthony, 1980, and …”

Section: Discussionmentioning

confidence: 99%

Z* DNA, the left-handed helical form of poly[d(G-C)] in MgCl2-ethanol, is biologically active.

Sande¹,

Jovin²

1982

The EMBO Journal

164

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The interconversion between the right (R) and left (L) helical forms of poly [d(G-C)] occurs at low concentrations of MgCI2 and EtOH, acting together in a highly synergistic manner. established by X-ray crystallography (Wang et al., 1979;Drew et al., 1980). However, L DNA formed in Mg2+-EtOH (which we designate as Z* DNA) has unique properties: a) it can be sedimented readily out of solution at low speed, indicative of condensation and intermolecular aggregation; b) it supports the binding of several intercalating (ethidium bromide, actinomycin D) and non-intercalating (mithramycin) drugs, although these interact preferentially with the R (i.e., B) form of DNA; and c) it functions as a template for Escherichia coli RNA polymerase. B and Z* DNAs can be generated under idential ionic conditions and compared in a number of biochemical systems. Our results suggest that left-handed DNA may form under physiological conditions and serve a biological function.

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Conformational changes in deoxyribonucleic acid during transcription

Cited by 12 publications

References 22 publications

Structural bistability of repetitive DNA elements featuring CA/TG dinucleotide steps and mode of evolution of satellite DNA

Structural bistability of repetitive DNA elements featuring CA/TG dinucleotide steps and mode of evolution of satellite DNA

Effect of template conversion from the B to the Z conformation on RNA polymerase activity

Z* DNA, the left-handed helical form of poly[d(G-C)] in MgCl2-ethanol, is biologically active.

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