Hydrodynamic behavior and molecular weight of homogeneous and of polydisperse native DNA

Reinert, K.E.; Triebel, Hans; Strassburger, John

doi:10.1016/0005-2787(72)90280-8

Cited by 12 publications

(4 citation statements)

References 32 publications

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“…Viscosity measurements were performed as previously described (12,22,23). The intrinsic viscosity ffllwas approximated by lnlirele/c and used for the estimation of the DNA molecular weights (23)(24)(25). The interpretation of relative viscosity 2m66 Nucleic Acids Research changesAy = AfJ/ rC; in terms of changes of the persistence length and contour length was based on a first order approximation (12,23,34).…”

Section: Methodsmentioning

confidence: 99%

Specific interactions of distamycin A and its analogs with (A-T) rich and (G-C) rich duplex regions of DNA and deoxypolynucleotides

Luck¹,

Zimmer²,

Reinert³

et al. 1977

Nucl Acids Res

106

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The specific interaction of distamycin A and analogs with DNA's and synthetic deoxypolynucleotide duplexes were studied in detail by means of circular dichroism and the data were analyzed together with viscosity results of several natural DNA's. At low ligand to nucleotide ratio the previously reported specific binding to (A-T) pairs of DNA is verified by a highly favoured interaction with (A-T)-enriched segments of distamycins containing four and five methylpyrrole carboxamide units. At higher distamycin concentration a second specific binding to (G-C) pairs most probably through hydrogen bonding is established. Viscometric results suggest a distamycin-induced local bending of the helix and could support the idea of a preferential alignment of the ligand molecule along only one strand in the groove which differs from the netropsin interaction mechanism. The possibility of an overlapping binding of the oligopeptides in the small groove is discussed.

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Section: Methodsmentioning

confidence: 99%

Specific interactions of distamycin A and its analogs with (A-T) rich and (G-C) rich duplex regions of DNA and deoxypolynucleotides

Luck¹,

Zimmer²,

Reinert³

et al. 1977

Nucl Acids Res

106

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“…Very early on, viscometric studies 38,39,49,69 of rather long DNA chains recorded that the linearity of log-log plots was broken around the value of M % (3 6 1) 3 10…”

Section: Break Pointmentioning

confidence: 98%

The intrinsic viscosity of linear DNA

2011

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We measured the intrinsic viscosity of very small synthetic DNA molecules, of 20-395 base pairs, and incorporated them in a nearly complete picture for the whole span of molecular weights reported in the literature to date. A major transition is observed at M approximately 2 × 10(6) . It is found that in the range of approximately 7 × 10(3) ≤ M ≤ 2 × 10(6) , the intrinsic viscosity scales as [η] approximately M(1.05) , suggesting that short DNA chains are not as rigid as generally thought. The corresponding scaling for the range of 2 × 10(6) ≤ M ≤ 8 × 10(10) is [η] approximately M(0.69) . A comparison of our results with existing equations, for much narrower data distributions, is made, and the agreement is very satisfactory considering the huge range of data analyzed here. Experimental concerns such as the effect of ionic strength, polydispersity, temperature, and shear rate are discussed in detail. Some issues concerning the Huggins coefficient, polymer chain stiffness, and the relationship between the Mark-Houwink constants K, α are also presented; it is found that log K = 1.156 - 6.19α.

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“…also Table I). all(Mr) had been derived experimentally (15,16), and Ka(Mr) was taken from such worm-like chain theories which are in best accord with experimental data [in particular with the dependence on molar mass of the characteristic Mandelkem-Flory parameter ~ (16,15) ]. In doing so we restrict to theories neglecting the excluded volume effect and restrict to experiments with DNA of corresponding low molar mass (17).…”

Section: Changes Of Dna Conformation and Viscositymentioning

confidence: 94%

“…dlog[T]]/dlogM. For semirigid DNA molecules in the transition range between very short and almost rigid rods ( ~; 1.8) and Gau~ian coils ( ~ =0.5), and continuously drops with rising Mr [above Mr=0.2Xl0 6 (5,15)]. The required values of Ka and (a'l + 1), as also those of Qaa' QLL and QaL' are plotted in paper (5) physiological salt conditions as a function ofMr (cf.…”

Section: Changes Of Dna Conformation and Viscositymentioning

confidence: 99%

DNA-Helix Bending, Stiffening and Elongation on Ligand Binding; Analysis for Serveral DNA-Drug Systems, General Viscometric DNA Response and Stereochemical Implications

Reinert¹

1991

Journal of Biomolecular Structure and Dynamics

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For several DNA-ligand systems the DNA helix bending, stiffening and elongation behaviour is treated quantitatively. The experimental basis are viscosity data from literature as a function of r, the ratio of drug molecules bound per DNA monomer unit. If the relative viscosity changes delta y1(r) and delta yh(r) for DNA of low and high molar mass, respectively, are known, the relative changes of contour length, delta L/L degrees, and of persistence length, delta a/a degrees, can be evaluated as a function of r, as repeatedly demonstrated. For random sequence-independent interactions, helix-bending is reflected by a helix-typical increment of delta a/a degrees (r), being zero at r = 0 and also at DNA saturation by bound ligand molecules [Reinert, Biophysical Chemistry 13, 1-14 (1981)]. This characteristic DNA behaviour often enables us to separate the bending and the stiffening increment of delta a/a degrees. The theoretical treatment of this problem (Schütz and Reinert, J. Biomolec. Struct. & Dynam. 9, 315-329, 1991) now permits a more detailed study of the ligand-induced DNA bending. The ligand-DNA systems treated here concern the following drugs (in parentheses DNA bending angle at low r-values): proflavin (8 degrees), daunomycin (11 degrees), aclacinomycin A (9.7 degrees, on cooperative interaction), actinomycin D (16 degrees), mitomycin C (16 degrees), a double intercalating bisphenantridine (12 degrees), 9-deacetyl-daunomycin (8 degrees) and 9-epi-deacetyl-daunomycin (12-18 degrees). We also demonstrate that the consideration of the DNA flexibility and its change on interaction of short DNA molecules with intercalating drugs delivers helix elongation values in better accord with the theoretical value. In the Appendix, a catalogue of simulated delta y(r)-dependences is given for both short and long DNA molecules. It systematically describes the DNA viscosity response upon typical DNA stiffening, elongation, and helix-bending effects.

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Hydrodynamic behavior and molecular weight of homogeneous and of polydisperse native DNA

Cited by 12 publications

References 32 publications

Specific interactions of distamycin A and its analogs with (A-T) rich and (G-C) rich duplex regions of DNA and deoxypolynucleotides

Specific interactions of distamycin A and its analogs with (A-T) rich and (G-C) rich duplex regions of DNA and deoxypolynucleotides

The intrinsic viscosity of linear DNA

DNA-Helix Bending, Stiffening and Elongation on Ligand Binding; Analysis for Serveral DNA-Drug Systems, General Viscometric DNA Response and Stereochemical Implications

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