The structure of a pseudo intercalated complex between actinomycin and the DNA binding sequence d(GpC)

Takusagawa, Fusao; Dabrow, Michael; Neidle, Stephen; Berman, Helen M.

doi:10.1038/296466a0

Cited by 113 publications

(61 citation statements)

References 28 publications

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“…Housing of G (purine) and Cy (pyrimidine) into the adjacent large cavities allows location of these N-bases at such distances of one another that the lengths of the H-bonds between them (nm, 0.287, 0.295, and 0.288) almost coincide with those calculated earlier in (White et al 1978) (nm, 0.293, 0.296, and0.293) andin (Yčas 1969) (nm, 0.284, 0.292, and0.284) on the basis of X-ray measurements of crystallized DNA double helixes. Housing of G and DDR radicals into the adjacent large and small cavities, respectively, allows their arrangement within these cavities with no structural destruction at a distance of 0.148 nm ; this distance correlates well with the G-DDR chemical bond length (0.151 nm) calculated from the X-ray study of crystallized DNA double helixes (Takusagawa et al 1982). Meanwhile, housing of two purine N-bases into the gashydrate adjacent large cavities leads to a significant tension of the structure and to its partial destruction.…”

Section: Observations and Simulations Counting In Favor Of The Loh-thmentioning

confidence: 69%

Life Origination Hydrate Theory (LOH-Theory) and the Explanation of the Biological Diversification

Ostrovskii

Kadyshevich

2014

J Mol Evol

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The Life Origination Hydrate Theory (LOH-Theory) considers the life origination process as a sequence of thermodynamically caused regular and inevitable chemical transformations regulated by universal physical and chemical laws. The LOH-Theory bears on a number of experimental, thermodynamic, observation, and simulation researches. N-bases, riboses, nucleosides, and nucleotides and DNAs and RNAs are formed repeatedly within structural cavities of localizations of underground and underseabed honeycomb CH4-hydrate deposits from CH4 and nitrate and phosphate ions that diffused into the hydrate structures; proto-cells and their agglomerates originated from these DNAs and from the same minerals in the semi-liquid soup after liquation of the hydrate structures. Each localization gave rise to a multitude of different DNAs and living organisms. The species diversity is caused by the spatial and temporal repeatability of the processes of living matter origination under similar but not identical conditions, multiplicity of the DNA forms in each living matter origination event, variations in the parameters of the native medium, intraspecific variations, and interspecific variations. The contribution of the last to the species diversity is, likely, significant for prokaryotes and those eukaryotes that are only at low steps of their biological organization; however, in the light of the LOH-Theory, of available long-term paleontological investigations, and of studies of reproduction of proliferous organisms, we conclude that, in toto, the contribution of interspecific variations to the species diversity was earlier overestimated by some researchers. The reason of this overestimation is that origination of scores of «spores» of different organisms in any one event and multiple reproductions of such events in time and Earth's space were not taken into consideration.

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Section: Observations and Simulations Counting In Favor Of The Loh-thmentioning

confidence: 69%

Life Origination Hydrate Theory (LOH-Theory) and the Explanation of the Biological Diversification

Ostrovskii

Kadyshevich

2014

J Mol Evol

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“…Some of the structures are specifically labeled as unusual in the Nucleic Acid Database (Berman et al, 1992), while others have been identified on the basis of unusual features in selected helical structures. The examples span the gamut from free and drug- bound dinucleoside monophosphates (Seeman et al, 197 1;Rubin et al, 1972;Neidle et al, 1978;Takusagawa et al, 1982) to longer chains with hairpin loops and/or singlestranded unpaired bases (Robertus et d., 1974;Chattopadhyaya et al, 1988;Joshua-Tor et al, 1992). The modeling points to a potential new role for the unusual backbone conformations observed experimentally, while the correspondence between predicted and solved structures provides an added measure of confidence in the computational approach.…”

Section: Resultsmentioning

confidence: 95%

Computer Models of DNA Four-Way Junctions

Srinivasan

Olson²

1994

Biochemistry

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A modeling scheme that combines a constrained backbone generating algorithm with simple hard-sphere packing calculations is offered to build the four-stranded structures of DNA found in Holliday junctions. Two standard B-DNA duplexes are oriented side by side with helix axes at different relative inclinations and then systematically rotated and translated to identify closely spaced contact-free states. Attempts are subsequently made to introduce a low-energy sugar-phosphate linkage that serves as the site of strand exchange between the two duplexes. The chemical connection is sought using an algorithm which identifies the possible arrangements of the intervening backbone torsions between arbitrarily positioned bases. The goal is to identify the multiple conformational solutions associated with a particular arrangement of neighboring DNA helices in the four-way junction rather than a single optimum structure. The methodology is general, in terms of accommodating four-way junctions with arms of variable conformation and chain length and of dimensions much greater than treated heretofore. The only deformation in the four-way structures relative to B-DNA occurs at the site of backbone exchange, with base stacking and Watson-Crick pairing completely preserved in all models. The arrangements of neighboring bases at these sites resemble the unusual conformational steps found in a number of small molecule nucleic acid crystal structures. An interesting outcome of the calculations is the formation of sterically acceptable four-arm Holliday junctions over a wide range of angles at the cross. The potential mobility of the Holliday junctions is inferred from visualization and energetic analysis of the various models. Long-range electrostatic energies based on different currently available treatments of the dielectric constant are used to estimate the conformational preferences and flexibility of the four-stranded structures. The various dielectric schemes, however, are not in complete agreement on the likely conformational variability of the four-way junctions. The structures suggest a possible mechanism for branch migration and detail a pathway linking the antiparallel uncrossed Holliday structure inferred from solution measurements and the parallel cross-packed helical arrangements observed in single-crystal X-ray studies.

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“…Solution studies are consistent with intercalation as a mode of binding and reveal a preference for guanine-pyrimidine sequences (1,(5)(6)(7)(8)(9). Crystallographic studies have provided some insight into the nature of the specific guanine-actinomycin interaction (10,11).…”

mentioning

confidence: 70%

Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II).

Dyke¹,

Hertzberg²,

Dervan³

1982

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

326

143

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We report a direct technique for determining the binding sites of small molecules on naturally occurring heterogeneous DNA. Methidiumpropyl-EDTAFe(II) [MPE-Fe(II)] cleaves double helical DNA with low sequence specificity. Using a combination of MPE-Fe(H) cleavage of drug-protected DNA fragments and Maxam-Gilbert gel methods of sequence analysis, we have determined the preferred binding sites on a Rsa I-EcoRI restriction fragment from pBR322 for the intercalator actinomycin D and the minor groove binders netropsin and distamycin A. Netropsin and distamycin A gave identical DNA cleavage-inhibition patterns and bound preferentially to A+T-rich regions with a minimal protected site offour base pairs. We were able to observe the effect ofincreasing concentration on site selection by netropsin and distamycin A. Actinomycin D afforded a completely different cleavage-inhibition pattern, with 4-to 16-base-pair-long protected regions centered around one or more G-C base pairs.

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The structure of a pseudo intercalated complex between actinomycin and the DNA binding sequence d(GpC)

Cited by 113 publications

References 28 publications

Life Origination Hydrate Theory (LOH-Theory) and the Explanation of the Biological Diversification

Life Origination Hydrate Theory (LOH-Theory) and the Explanation of the Biological Diversification

Computer Models of DNA Four-Way Junctions

Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II).

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