Binding of ligands to a one‐dimensional heterogeneous lattice. I. General model for the calculation of binding isotherms by a Monte Carlo approach

Sturm, Jürgen

doi:10.1002/bip.1981.360200409

Cited by 9 publications

(5 citation statements)

References 9 publications

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“…Their data show very low values for the apparent site size, which probably results from a considerable concentration of single-stranded regions in their material. Sturm (1981) found the same order of binding constants for the deoxypolynucleotides used in this study for another intercalator, tilorone, although the differences in exclusion values were not as pronounced. The specificity of binding seen for tilorone and daunomycin may be primarily governed by the conformation of the intercalation site of the polynucleotide, rather than specific interactions of the ligand with the different base pairs.…”

Section: Discussionsupporting

confidence: 65%

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Equilibrium studies on the interaction of daunomycin with deoxypolynucleotides

Chaires¹

1983

Biochemistry

122

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Fluorescence and absorbance methods were used to study the interaction of daunomycin with four deoxypolynucleotides. The binding may be described by the neighbor-exclusion model for binding ratios greater than 0.05, with intrinsic binding constants decreasing in the order poly[d(A-T)] X poly[d(A-T)] greater than poly[d(G-C)] X poly[d(G-C)] greater than poly(dG) X poly(dC) greater than poly(dA) X poly(dT). The exclusion parameter was found to be approximately 2 for the A-T-containing polynucleotides, 4 for the alternating G-C polymer, and nearly 10 for poly(dG) X poly(dC). Poly(dA) X poly(dT) showed positive cooperativity at low binding ratios. Thermal denaturation studies provided quantitative support for the measured binding parameters; the delta Tm values measured may be correlated primarily with the differences seen in the exclusion parameter. Sedimentation velocity experiments on daunomycin-deoxypolynucleotide complexes show an unusual nonlinear dependence of Sapp on the binding ratio for poly[d(A-T)] X poly[d(A-T)], poly[d(G-C)] X poly[d(G-C)], and poly(dA) X poly(dT), indicative of either a nonstandard conformational change accompanying intercalation or cooperative drug binding.

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Section: Discussionsupporting

confidence: 65%

“…Sedimentation guley & Falkenhaug, 1978), and echinomycin (Wakelin & Waring, 1976) binding to DNA. Information obtained from such studies may be used to calculate binding isotherms to heterogeneous DNA sequences (Sturm, 1981), providing insight into sequences particularly favorable to drug binding.…”

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confidence: 99%

Equilibrium studies on the interaction of daunomycin with deoxypolynucleotides

Chaires¹

1983

Biochemistry

122

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“…It is seen that even using a simple computer the algorithm affords to study lattices with, at least, a number of monomers N ∼ 20. As also seen from Figure 5, the total time needed for sampling of all configurational space grows nearly exponentially with N , hence, for longer sequences other algorithms, such as Monte‐Carlo,12 become more effective.…”

Section: Resultsmentioning

confidence: 88%

“…It is worth mentioning that similar approach to represent binding configuration of a biopolymer as a set of “0” and “1” is also used in Monte‐Carlo algorithms;12 however, in such approaches the scheme of generating is principally different from what is suggested in the present work, and based on intrinsically random, i.e. incomplete, sampling of all possible binding configurations.…”

Section: Resultsmentioning

confidence: 99%

“…Further introduction of nearest‐neighbor cooperative interactions between bound ligands requires explicit examination of the configurations containing pairs of interacting ligands, lowering the effectiveness of “forward‐backward” scheme in general case of complex interaction between the bound ligands. Explicit generating of binding configurations has long been used in Monte‐Carlo algorithm,12 however, as any other Monte‐Carlo‐based approach, it suffers from intrinsically random, i.e. incomplete, sampling of all possible binding configurations.…”

Section: Introductionmentioning

confidence: 99%

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A novel computational approach “BP-STOCH” to study ligand binding to finite lattice

et al. 2010

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We report a novel computational algorithm "BP-STOCH" to be used for studying single-type ligand binding with biopolymers of finite lengths, such as DNA oligonucleotides or oligopeptides. It is based on an idea to represent any type of ligand-biopolymer complex in a form of binary number, where "0" and "1" bits stand for vacant and engaged monomers of the biopolymer, respectively. Cycling over all binary numbers from the lowest 0 up to the highest 2(N) - 1 means a sequential generating of all possible configurations of vacant/engaged monomers, which, after proper filtering, results in a full set of possible types of complexes in solution between the ligand and the N-site lattice. The principal advantage of BP-STOCH algorithm is the possibility to incorporate into this cycle any conditions on computation of the concentrations and observed experimental parameters of the complexes in solution, and programmatic access to each monomer of the biopolymer within each binding site of every binding configuration. The latter is equivalent to unlimited extension of the basic reaction scheme and allows to use BP-STOCH algorithm as an alternative to conventional computational approaches.

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Binding of ligands to a one‐dimensional heterogeneous lattice. II. Intercalation of tilorone with DNA and polynucleotides

1981

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SynopsisThe interaction of tilorone with DNA and five synthetic polydeoxyribonucleotides [(I): poly[d(G-C)]; (IV): poly(dG).poly(dC); and (V): poly(dA)-poly(dT)] has been investigated. Binding isotherms for the homopolymers were obtained by microdialysis equilibria using ''CC-labeled tilorone and interpreted with different models: exclusion effect, associated or not associated with cooperativity, or variable exclusion. Affinity appears to be related more to local structure than to base composition and decreases in the following order: (I) > (11) > (111) > (IV) > (V). Intercalation in circular DNA was demonstrated by electrophoresis migration and electron microscopy, which yielded an average unwinding angle of 7 O per bound dye. The behavior observed in CD and UV spectroscopy shows a sequence similar to the affinities. Tilorone seems to be less intercalated in (IV) and not a t all in (V). The experimental binding isotherm of tilorone to DNA was well fitted on the basis of a model where DNA acts as a heterogeneous lattice built with the six different possible couples of adjacent base pairs, each potential site behaving as if it were in the corresponding homopolymer. The results are discussed in terms of specificity of alternating Pyr-Pur sequences and related to theoretical calculations on intercalation energies of DNA.

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Binding of ligands to a one‐dimensional heterogeneous lattice. I. General model for the calculation of binding isotherms by a Monte Carlo approach

Cited by 9 publications

References 9 publications

Equilibrium studies on the interaction of daunomycin with deoxypolynucleotides

Equilibrium studies on the interaction of daunomycin with deoxypolynucleotides

A novel computational approach “BP-STOCH” to study ligand binding to finite lattice

Binding of ligands to a one‐dimensional heterogeneous lattice. II. Intercalation of tilorone with DNA and polynucleotides

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