The Experts below are selected from a list of 1293 Experts worldwide ranked by ideXlab platform
Wilfred F Van Gunsteren - One of the best experts on this subject based on the ideXlab platform.
-
molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between Netropsin and dna
Journal of Physical Chemistry B, 2010Co-Authors: Jožica Dolenc, Sarah Gerster, Wilfred F Van GunsterenAbstract:With the aim to gain a better understanding of the various driving forces that govern sequence specific DNA minor groove binding, we performed a thermodynamic analysis of Netropsin binding to an AT-containing and to a set of six mixed AT/GC-containing binding sequences in the DNA minor groove. The relative binding free energies obtained using molecular dynamics simulations and free energy calculations show significant variations with the binding sequence. While the introduction of a GC base pair in the middle or close to the middle of the binding site is unfavorable for Netropsin binding, a GC base pair at the end of the binding site appears to have no negative influence on the binding. The results of the structural and energetic analyses of the Netropsin-DNA complexes reveal that the differences in the calculated binding affinities cannot be explained solely in terms of Netropsin-DNA hydrogen-bonding or interaction energies. In addition, solvation effects and entropic contributions to the relative binding free energy provide a more complete picture of the various factors determining binding. Analysis of the relative binding entropy indicates that its magnitude is highly sequence-dependent, with the ratio |TDeltaDeltaS|/|DeltaDeltaH| ranging from 0.07 for the AAAGA to 1.7 for the AAGAG binding sequence, respectively.
-
configurational entropy change of Netropsin and distamycin upon dna minor groove binding
Biophysical Journal, 2006Co-Authors: Jožica Dolenc, J Koller, Riccardo Baron, Chris Oostenbrink, Wilfred F Van GunsterenAbstract:Binding of a small molecule to a macromolecular target reduces its conformational freedom, resulting in a negative entropy change that opposes the binding. The goal of this study is to estimate the configurational entropy change of two minor-groove-binding ligands, Netropsin and distamycin, upon binding to the DNA duplex d(CGCGAAAAACGCG)·d(CGCGTTTTTCGCG). Configurational entropy upper bounds based on 10-ns molecular dynamics simulations of Netropsin and distamycin in solution and in complex with DNA in solution were estimated using the covariance matrix of atom-positional fluctuations. The results suggest that Netropsin and distamycin lose a significant amount of configurational entropy upon binding to the DNA minor groove. The estimated changes in configurational entropy for Netropsin and distamycin are −127 J K−1 mol−1 and −104 J K−1 mol−1, respectively. Estimates of the configurational entropy contributions of parts of the ligands are presented, showing that the loss of configurational entropy is comparatively more pronounced for the flexible tails than for the relatively rigid central body.
-
molecular dynamics simulations and free energy calculations of Netropsin and distamycin binding to an aaaaa dna binding site
Nucleic Acids Research, 2005Co-Authors: Jožica Dolenc, J Koller, Chris Oostenbrink, Wilfred F Van GunsterenAbstract:Molecular dynamics simulations have been performed on Netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of the ligands free in solution and when bound to DNA, the mobility and the hydrogen-bonding patterns of the ligands were studied, as well as their hydration. It is shown that even though distamycin is less hydrated than Netropsin, the loss of ligand-solvent interactions is very similar for both ligands. The relative mobilities of the ligands in their bound and free forms indicate a larger entropic penalty for distamycin when binding to the minor groove compared with Netropsin, partially explaining the lower binding affinity of the distamycin molecule. The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand-DNA binding.
Edwin A Lewis - One of the best experts on this subject based on the ideXlab platform.
-
role of water in Netropsin binding to an a2t2 hairpin dna site osmotic stress experiments
Journal of Physical Chemistry B, 2013Co-Authors: Joseph Ramos, Edwin A LewisAbstract:The formation of two different minor groove complexes between Netropsin and A2T2 DNA has been attributed to specific binding and hydration effects. In this study, we have examined the effect of added osmolyte (e.g., TEG or betaine) on the binding of Netropsin to a hairpin DNA, d(CGCGAATTCGCGTC-TCCGCGAATTCGCG)-3, having a single A2T2 binding site. Netropsin binding to this DNA construct is described by a two fractional site model with a saturation stoichiometry of 1:1. Free energy changes, ΔGi, for formation of both complex I and complex II decrease continuously as osmolyte is added (e.g., ΔG1 decreases by 1.3 kcal/mol and ΔG2 decreases by 0.8 kcal/mol in 4 m osmolyte vs buffer). The negative ΔCp values for formation of both complexes, I and II, are largely unaffected by the addition of osmolyte. Formation of complex I is accompanied by the acquisition of 31 water molecules vs 19 waters for complex II. The most significant difference between the two osmolytes is that betaine diminishes the fractional forma...
-
complexity in the binding of minor groove agents Netropsin has two thermodynamically different dna binding modes at a single site
Nucleic Acids Research, 2011Co-Authors: Edwin A Lewis, Manoj Munde, Shuo Wang, Michael Rettig, Venkata R Machha, David W WilsonAbstract:Structural results with minor groove binding agents, such as Netropsin, have provided detailed, atomic level views of DNA molecular recognition. Solution studies, however, indicate that there is complexity in the binding of minor groove agents to a single site. Netropsin, for example, has two DNA binding enthalpies in isothermal titration calorimetry (ITC) experiments that indicate the compound simultaneously forms two thermodynamically different complexes at a single AATT site. Two proposals for the origin of this unusual observation have been developed: (i) two different bound species of Netropsin at single binding sites and (ii) a Netropsin induced DNA hairpin to duplex transition. To develop a better understanding of DNA recognition complexity, the two proposals have been tested with several DNAs and the methods of mass spectrometry (MS), polyacrylamide gel electrophoresis (PAGE) and nuclear magnetic resonance spectroscopy in addition to ITC. All of the methods with all of the DNAs investigated clearly shows that Netropsin forms two different complexes at AATT sites, and that the proposal for an induced hairpin to duplex transition in this system is incorrect.
-
break in the heat capacity change at 303 k for complex binding of Netropsin to aatt containing hairpin dna constructs
Biophysical Journal, 2007Co-Authors: Matthew W Freyer, David W Wilson, Robert Buscaglia, Joseph Ramos, Amy Hollingsworth, Meredith Blynn, Rachael Pratt, Edwin A LewisAbstract:Studies performed in our laboratory demonstrated the formation of two thermodynamically distinct complexes on binding of Netropsin to a number of hairpin-forming DNA sequences containing AATT-binding regions. These two complexes were proposed to differ only by a bridging water molecule between the drug and the DNA in the lower affinity complex. A temperature-dependent isothermal titration calorimetry (ITC)-binding study was performed using one of these constructs (a 20-mer hairpin of sequence 5'-CGAATTCGTCTCCGAATTCG) and Netropsin. This study demonstrated a break in the heat capacity change for the formation of the complex containing the bridging water molecule at approximately 303 K. In the plot of the binding enthalpy change versus temperature, the slope (DeltaCp) was -0.67 kcal mol-1 K-1 steeper after the break at 303 K. Because of the relatively low melting temperature of the 20-mer hairpin (341 K (68 degrees C)), the enthalpy change for complex formation might have included some energy of refolding of the partially denatured hairpin, giving the suggestion of a larger DeltaCp. Studies done on the binding of Netropsin to similar constructs, a 24-mer and a 28-mer, with added GC basepairs in the hairpin stem to increase thermal stability, exhibit the same nonlinearity in DeltaCp over the temperature range of from 275 to 333 K. The slopes (DeltaCp) were -0.69 and -0.64 kcal mol-1 K-1 steeper after 303 K for the 24-mer and 28-mer, respectively. This observation strengthens the argument regarding the presence of a bridging water molecule in the lower affinity Netropsin/DNA complex. The DeltaCp data seem to infer that because the break in the heat capacity change function for the lower affinity binding occurs at the isoequilibrium temperature for water, water may be included or trapped in the complex. The fact that this break does not occur in the heat capacity change function for formation of the higher affinity complex can similarly be taken as evidence that water is not included in the higher affinity complex.
-
binding of Netropsin to several dna constructs evidence for at least two different 1 1 complexes formed from an aatt containing ds dna construct and a single minor groove binding ligand
Biophysical Chemistry, 2007Co-Authors: Matthew W Freyer, Robert Buscaglia, Derek J Cashman, S Hyslop, W D Wilson, Jonathan B Chaires, Edwin A LewisAbstract:Abstract Isothermal titration calorimetry, ITC, has been used to determine the thermodynamics (Δ G , Δ H , and − T Δ S ) for binding Netropsin to a number of DNA constructs. The DNA constructs included: six different 20–22mer hairpin forming sequences and an 8-mer DNA forming a duplex dimer. All DNA constructs had a single –AT-rich Netropsin binding with one of the following sequences, (A 2 T 2 ) 2 , (ATAT) 2 , or (AAAA/TTTT). Binding energetics are less dependent on site sequence than on changes in the neighboring single stranded DNA (hairpin loop size and tail length). All of the 1:1 complexes exhibit an enthalpy change that is dependent on the fractional saturation of the binding site. Later binding ligands interact with a significantly more favorable enthalpy change (∂Δ H 1–2 from 2 to 6 kcal/mol) and a significantly less favorable entropy change (∂(− T Δ S 1–2 )) from − 4 to − 9 kcal/mol). The ITC data could only be fit within expected experimental error by use of a thermodynamic model that includes two independent binding processes with a combined stoichiometry of 1 mol of ligand per 1 mol of oligonucleotide. Based on the biophysical evidence reported here, including theoretical calculations for the energetics of “trapping” or structuring of a single water molecule and molecular docking computations, it is proposed that there are two modes by which flexible ligands can bind in the minor groove of duplex DNA. The higher affinity binding mode is for Netropsin to lay along the floor of the minor groove in a bent conformation and exclude all water from the groove. The slightly weaker binding mode is for the Netropsin molecule to have a slightly more linear conformation and for the required curvature to be the result of a water molecule that bridges between the floor of the minor groove and two of the amidino nitrogens located at one end of the bound Netropsin molecule.
Jožica Dolenc - One of the best experts on this subject based on the ideXlab platform.
-
molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between Netropsin and dna
Journal of Physical Chemistry B, 2010Co-Authors: Jožica Dolenc, Sarah Gerster, Wilfred F Van GunsterenAbstract:With the aim to gain a better understanding of the various driving forces that govern sequence specific DNA minor groove binding, we performed a thermodynamic analysis of Netropsin binding to an AT-containing and to a set of six mixed AT/GC-containing binding sequences in the DNA minor groove. The relative binding free energies obtained using molecular dynamics simulations and free energy calculations show significant variations with the binding sequence. While the introduction of a GC base pair in the middle or close to the middle of the binding site is unfavorable for Netropsin binding, a GC base pair at the end of the binding site appears to have no negative influence on the binding. The results of the structural and energetic analyses of the Netropsin-DNA complexes reveal that the differences in the calculated binding affinities cannot be explained solely in terms of Netropsin-DNA hydrogen-bonding or interaction energies. In addition, solvation effects and entropic contributions to the relative binding free energy provide a more complete picture of the various factors determining binding. Analysis of the relative binding entropy indicates that its magnitude is highly sequence-dependent, with the ratio |TDeltaDeltaS|/|DeltaDeltaH| ranging from 0.07 for the AAAGA to 1.7 for the AAGAG binding sequence, respectively.
-
configurational entropy change of Netropsin and distamycin upon dna minor groove binding
Biophysical Journal, 2006Co-Authors: Jožica Dolenc, J Koller, Riccardo Baron, Chris Oostenbrink, Wilfred F Van GunsterenAbstract:Binding of a small molecule to a macromolecular target reduces its conformational freedom, resulting in a negative entropy change that opposes the binding. The goal of this study is to estimate the configurational entropy change of two minor-groove-binding ligands, Netropsin and distamycin, upon binding to the DNA duplex d(CGCGAAAAACGCG)·d(CGCGTTTTTCGCG). Configurational entropy upper bounds based on 10-ns molecular dynamics simulations of Netropsin and distamycin in solution and in complex with DNA in solution were estimated using the covariance matrix of atom-positional fluctuations. The results suggest that Netropsin and distamycin lose a significant amount of configurational entropy upon binding to the DNA minor groove. The estimated changes in configurational entropy for Netropsin and distamycin are −127 J K−1 mol−1 and −104 J K−1 mol−1, respectively. Estimates of the configurational entropy contributions of parts of the ligands are presented, showing that the loss of configurational entropy is comparatively more pronounced for the flexible tails than for the relatively rigid central body.
-
an ab initio qm mm study of the conformational stability of complexes formed by Netropsin and dna the importance of van der waals interactions and hydrogen bonding
Journal of Molecular Structure-theochem, 2005Co-Authors: Jožica Dolenc, Urban Borstnik, Milan Hodoscek, J Koller, Dusanka JanežicAbstract:Abstract The conformational stability of three different conformations of Netropsin with DNA have been studied by ab initio QM/MM calculations and the interactions between the Netropsin conformers and DNA have been inspected in detail. The importance of hydrogen bonding and van der Waals contacts to the Netropsin–DNA complex stability was investigated with calculations in explicit solvent. Several aspects of the Netropsin binding characteristics are discussed in terms of structural and energetic differences among the modeled complexes. It was found that van der Waals interactions are at least as important as hydrogen bonding in determining the conformational stability of the resulting complexes.
-
molecular dynamics simulations and free energy calculations of Netropsin and distamycin binding to an aaaaa dna binding site
Nucleic Acids Research, 2005Co-Authors: Jožica Dolenc, J Koller, Chris Oostenbrink, Wilfred F Van GunsterenAbstract:Molecular dynamics simulations have been performed on Netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of the ligands free in solution and when bound to DNA, the mobility and the hydrogen-bonding patterns of the ligands were studied, as well as their hydration. It is shown that even though distamycin is less hydrated than Netropsin, the loss of ligand-solvent interactions is very similar for both ligands. The relative mobilities of the ligands in their bound and free forms indicate a larger entropic penalty for distamycin when binding to the minor groove compared with Netropsin, partially explaining the lower binding affinity of the distamycin molecule. The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand-DNA binding.
Kenneth J. Breslauer - One of the best experts on this subject based on the ideXlab platform.
-
influence of drug binding on dna hydration acoustic and densimetric characterizations of Netropsin binding to the poly dadt poly dadt and poly da poly dt duplexes and the poly dt poly da poly dt triplex at 25 degrees c
Biochemistry, 1994Co-Authors: Tigran V Chalikian, G E Plum, Armen Sarvazyan, Kenneth J. BreslauerAbstract:We use high-precision acoustic and densimetric techniques to determine, at 25 degrees C, the changes in volume, delta V, and adiabatic compressibility, delta Ks, that accompany the binding of Netropsin to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes, as well as to the poly(dT).poly(dA).poly(dT) triplex. We find that Netropsin binding to the heteropolymeric poly(dAdT).poly(dAdT) duplex is accompanied by negative changes in volume, delta V, and small positive changes in compressibility, delta Ks. By contrast, Netropsin binding to the homopolymeric poly(dA).poly(dT) duplex is accompanied by large positive changes in both volume, delta V, and compressibility, delta Ks. Furthermore, Netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes changes in both volume and compressibility that are nearly twice as large as those observed when Netropsin binds to the poly(dA).poly(dT) duplex. We interpret these macroscopic data in terms of binding-induced microscopic changes in the hydration of the DNA structures and the drug. Specifically, we find that Netropsin binding induces the release of approximately 22 waters from the hydration shell of the poly(dAdT).poly(dAdT) heteropolymeric duplex, approximately 40 waters from the hydration shell of the poly(dA).poly(dT) homopolymeric duplex, and about 53 waters from the hydration shell of the poly(dA).poly(dT), induces the release of 18 more water molecules than Netropsin binding to the heteropolymeric duplex, poly(dAdT).poly(dAdT). On the basis of apparent molar volume, phi V, and apparent molar adiabatic compressibility, phi Ks, values for the initial drug-free and final drug-bound states of the two all-AT duplexes, we propose that the larger dehydration of the poly(dA).poly(dT) duplex reflects, in part, the formation of a less hydrated poly(dA).poly(dT)-Netropsin complex compared with the corresponding poly(dAdT).poly(dAdT)-Netropsin complex. In conjunction with our previously published entropy data [Marky, L. A., & Breslauer, K. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4359-4363], we calculate that each water of hydration released to the bulk solvent by ligand binding contributes 1.6 cal K-1 mol-1 to the entropy of binding. This value corresponds to the average difference between the partial molar entropy of water in the bulk state and water in the hydration shells of the two all-AT duplexes. When Netropsin binds to the poly(dT).poly(dA).poly(dT) triplex, the changes in both volume and compressibility suggest that the binding event induces more dehydration of the triplex than of the duplex state. Specifically, we calculate that Netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes the release of 13 more waters than Netropsin binding to the poly(dA).poly(dT) duplex.(ABSTRACT TRUNCATED AT 400 WORDS)
-
drug binding to higher ordered dna structures Netropsin complexation with a nucleic acid triple helix
Proceedings of the National Academy of Sciences of the United States of America, 1992Co-Authors: Youngwhan Park, Kenneth J. BreslauerAbstract:We have used a combination of spectroscopic and calorimetric techniques to characterize how Netropsin, a ligand that binds in the minor groove of DNA, influences the properties of a DNA triple helix. Specifically, our data allow us to reach the following conclusions: (i) Netropsin binds to the triplex without displacing the major-groove-bound third strand; (ii) Netropsin binding to the triplex exhibits a lower saturation binding density (7.0 base triplets per Netropsin bound) than Netropsin binding to the corresponding duplex (5.5 base pairs per Netropsin bound); (iii) the Netropsin-free and the Netropsin-bound triplexes each melt in two well-resolved transitions, initial conversion of the triplex to the duplex state followed by duplex melting to the component single-stranded states; (iv) Netropsin remains bound to DNA as the triplex melts to the duplex state; (v) Netropsin binding thermally destabilizes the triplex in equilibrium with duplex equilibrium dramatically, while thermally stabilizing the duplex to single-strand equilibrium; (vi) Netropsin binding to the triplex is enthalpically 4 times more favorable (more exothermic) than Netropsin binding to the corresponding duplex; (vii) Netropsin binding to the triplex decreases the cooperativity of the triplex----duplex melting event. These results demonstrate that occupancy of the minor groove of a triplex by a ligand such as Netropsin can exert a profound impact on the properties of the host triplex, particularly with regard to the equilibrium in which the third strand is expelled from the major groove. Thus, our results reveal considerable major groove/minor groove crosstalk. Such knowledge may prove of practical importance by providing an approach for modulating the affinity and specificity of major-groove-binding third strands in triplex-forming protocols designed to target specific duplex domains. Fundamentally, our results provide insights into the crosstalk that can result when ligands bind to the two major receptor sites of duplex DNA--namely, the major and minor grooves.
S L Grokhovsky - One of the best experts on this subject based on the ideXlab platform.
-
inhibition of herpes simplex virus helicase ul9 by Netropsin derivatives and antiviral activities of bis Netropsins
Biophysics, 2012Co-Authors: N P Bazhulina, A N Surovaya, Y G Gursky, V L Andronova, V S Arkhipova, M V Golovkin, A M Nikitin, G A Galegov, S L Grokhovsky, G V GurskyAbstract:Data obtained show that antiviral activities of bis-linked Netropsin derivatives are targeted by specific complexes formed by helicase UL9 of herpes simplex virus type 1 with viral DNA replication origins, represented by two OriS sites and one OriL site. According to the results of footprinting studies bis-Netropsins get bound selectively to an A+T-cluster which separates interaction sites I and II for helicase UL9 in OriS. Upon binding to DNA bis-Netropsins stabilize a structure of the A+T-cluster and inhibit thermal fluctuation-induced opening of AT- base pairs which is needed for local unwinding of DNA by helicase UL9. Kinetics of ATP-dependent DNA unwinding in the presence and absence of Pt-bis-Netropsin are studied by measuring the efficiency of Forster resonance energy transfer (FRET) between the fluorescent probes attached covalently to 3?- and 5?-ends of the oligonucleotides in the minimal OriS duplex. Pt-bis-Netropsin and related molecules inhibit unwinding of OriS duplex by helicase UL9. Pt-bis-Netropsin is also able to reduce the rate of unwinding of the AT- rich hairpin formed by the upper strand in the minimal OriS duplex. The antiviral activities and toxicity of bis-linked Netropsin derivatives are studied in cell cultured experiments and experiments with animals infected by herpes virus.
-
binding of bis linked Netropsin derivatives in the parallel stranded hairpin form to dna
Journal of Biomolecular Structure & Dynamics, 2001Co-Authors: A N Surovaya, Ch. Zimmer, A M Nikitin, S L Grokhovsky, G Burckhardt, Eckhard Birchhirschfeld, Hartmut Fritzsche, G V GurskyAbstract:Cis-diammine Pt(II)- bridged bis-Netropsin and oligomethylene-bridged bis-Netropsin in which two monomers are linked in a tail-to-tail manner bind to the DNA oligomer with the sequence 5'-CCTATATCC-3' in a parallel-stranded hairpin form with a stoichiometry 1:1. The difference circular dichroism (CD) spectra characteristic of binding of these ligands in the hairpin form are similar. They differ from CD patterns obtained for binding to the same duplex of another bis-Netropsin in which two Netropsin moieties were linked in a head-to-tail manner. This reflects the fact that tail-to-tail and head-to-tail bis-Netropsins use parallel and antiparallel side-by-side motifs, respectively, for binding to DNA in the hairpin forms. The binding affinity of cis-diammine Pt(II)-bridged bis-Netropsin in the hairpin form to DNA oligomers with nucleotide sequences 5'-CCTATATCC-3' (I), 5'-CCTTAATCC-3' (II), 5'-CCTTATTCC-3' (III), 5'-CCTTTTTCC-3' (IV) and 5'-CCAATTTCC-3' (V) decreases in the order I = II > III > IV > V . The binding of oligomethylene-bridged bis-Netropsin in the hairpin form follows a similar hierarchy. An opposite order of sequence preferences is observed for partially bonded monodentate binding mode of the synthetic ligand.
-
dna sequence recognition by bis linked Netropsin and distamycin derivatives
FEBS Letters, 1998Co-Authors: Ch. Zimmer, A N Surovaya, S L Grokhovsky, G Burckhardt, V F Pismensky, B K Chernov, G V GurskyAbstract:We studied the interaction of cis-diammine Pt(II)- bridged bis-Netropsin, cis-diammine Pt(II)-bridged bis-distamy- cin and oligomethylene-bridged bis-Netropsin with synthetic DNA fragments containing pseudosymmetrical AT-rich nucleo- tide sequences and compared it with the interaction of the parent compounds Netropsin and distamycin A. For fragments contain- ing multiple blocks of (A/T)4 and (T/A)4 separated by zero, one, two and three GC-base pairs, DNase I footprinting and CD spectroscopy studies reveal that 5P-TTTTAAAA-3P is the strongest affinity binding site for cis-diammine Pt(II)-bridged bis-Netropsin and bis-distamycin. They both bind less strongly to a DNA region containing the sequence 5P-AAAATTTT-3P. Netropsin, distamycin A and oligomethylene-bridged bis-netrop- sin exhibit far less sequence discrimination. z 1998 Federation of European Biochemical Societies.
-
human dna topoisomerase i activity is affected by bis Netropsin s binding to dna minor groove
Iubmb Life, 1998Co-Authors: Alyona Sukhanova, S L Grokhovsky, A L Zhuze, David I Roper, Igor B BronsteinAbstract:SUMMARY Bis-Netropsins (bis-Nts) are known to be efficient inhibitors of human DNA topoisomerase (topo) I with a higher antitumor activity than Netropsin. New sequence-specific derivatives of bis-Nts were used for modulation of topo I-mediated DNA cleavage with and without camptothecin (CPT). Relation between the bis-Nts binding sites and topo I cleavage sites has been analyzed with the plasmid DNA constructs generated by insertion of synthetic oligonucleotides containing various topo I-cleavage and bis-Nt-binding sites. These constructs offer an opportunity to study minor groove binders effects on the topo I reaction on DNA. Three major effects: (i) bis-Nt - mediated disappearance of some of the topo I cleavage sites; (ii) enhancement of some other sites, and, (iii) generation of new cleavage sites, have been found and analyzed. These effects demonstrate that bis-Nts drastically change the topo Imediated DNA cleavage.
-
mono di and trimeric binding of a bis Netropsin to dna
FEBS Letters, 1995Co-Authors: A S Zasedatelev, G V Gursky, A M Nikitin, S L Grokhovsky, A L Zhuze, V B Borodulin, D V Salmanova, Richard H ShaferAbstract:An unusual 3:1 stoichiometry for complex formation between an elongated bis-Netropsin compound and its binding site on DNA has been observed. Circular dichroism measurements distinguish two types of complexes formed between this bisNetropsin and poly[d(A-T)] · poly[d(A-T)]. The first type is characterized by a 1:1 saturating ratio of bound molecules per ten base pairs. Formation of the second type results from the cooperative binding of two additional bis-Netropsin molecules to the first type of complex. In contrast to these results observed for binding to the alternating polynucleotide, only the 1:1 type of complex is formed when this ligand binds to the homopolymer poly(dA) · poly(dT).