Flexibility of DNA in 2:1 drug-DNA complexes--simultaneous binding of two DAPI molecules to DNA.

Simultaneous binding of two DAPI molecules in the minor groove of (dA)15.(dT)15 B-DNA helix has been simulated by molecular mechanics calculations. The energy minimised structure shows some novel features in relation to binding of DAPI molecules as well as the flexibility of the grooves of DNA helices. The minor groove of the helix expands locally considerably (to 15 angstroms) to accommodate the two DAPI molecules and is achieved by positive propeller twisting of base pairs at the binding site concomitant with small variations in the local nucleotide stereochemistry. The expansion also brings forth simultaneously a contraction in the width of the major groove spread over to a few phosphates. These findings demonstrate another facet of the flexible stereochemistry of DNA helices in which the local features are significantly altered without being propagated beyond a few base pairs, and with the rest of the regions retaining the normal structure. Both the DAPI molecules are engaged in specific hydrogen bonds with the bases and non specific interactions with phosphates. Stacking interactions of DAPI molecules between themselves as well as with sugar-phosphate backbone contribute to the stability of the complex. The studies provide a stereochemical support to the experimental findings that under high drug-DNA ratio DAPI could bind in the 2:1 ratio.     

ATP Binding and Hydrolysis by Mcm2 Regulate DNA Binding by Mcm Complexes

The essential minichromosome maintenance (Mcm) proteins Mcm2 through Mcm7 likely comprise the replicative helicase in eukaryotes. In addition to Mcm2-7, other subcomplexes, including one comprising Mcm4, Mcm6, and Mcm7, unwind DNA. Using Mcm4/6/7 as a tool, we reveal a role for nucleotide binding by Saccharomyces cerevisiae Mcm2 in modulating DNA binding by Mcm complexes. Previous studies have shown that Mcm2 inhibits DNA unwinding by Mcm4/6/7. Here, we show that interaction of Mcm2 and Mcm4/6/7 is not sufficient for inhibition; rather, Mcm2 requires nucleotides for its regulatory role. An Mcm2 mutant that is defective for ATP hydrolysis (K549A), as well as ATP analogues, was used to show that ADP binding by Mcm2 is required to inhibit DNA binding and unwinding by Mcm4/6/7. This Mcm2-mediated regulation of Mcm4/6/7 is independent of Mcm3/5. Furthermore, the importance of ATP hydrolysis by Mcm2 to the regulation of the native complex was apparent from the altered DNA binding properties of Mcm2^KA-7. Moreover, together with the finding that Mcm2_K549A does not support yeast viability, these results indicate that the nucleotide-bound state of Mcm2 is critical in regulating the activities of Mcm4/6/7 and Mcm2-7 complexes.     

DNA-PHONA-PNA Chimeric Molecules: Contributions to Binding Against Complementary DNA

Abstract

The synthesis of a DNA-PHONA-PNA chimeric molecule using the Mmt protection strategy is described. The chimeric oligomer shows duplex binding properties that are comparable to PNA. Obviously, PHONA building blocks can be incorporated into PNAs without distortion of the PNA structure

     

Influence of Drug Binding on DNA Flexibility: A Normal Mode Analysis

Abstract

DNA-drug complexes are important because of their pharmacological interest but, in addition, they provide a useful model to study the essential aspects of DNA recognition processes. In order to investigate the influence of ligand binding on the dynamic properties of DNA we have carried out normal mode analysis for complexes with drugs of two types: a typical intercalator, 9-aminoacridine, and a typical groove binder, netropsin. Normal modes are analysed in terms of helicoidal parameter variations with special attention being paid to global deformations of the double helix. The results show that the influence of these two drugs is very different. Intercalation of 9-aminoacridine leads to an increase in the flexibility of the intercalated dinucleotide step, with notably larger vibrational amplitudes for both roll and twist parameters compared to free DNA. In contrast, the groove binding of netropsin induces a stiffening of the DNA segment which is in contact with the drug reflected by decreased vibrational amplitudes for backbone angles and inter base pair helicoidal parameters and an increase in vibrations for adjacent base pairs in terms of buckle and propeller twist.     

The Calcium-Dependent and Calcium-Independent Membrane Binding of Synaptotagmin 1: Two Modes of C2B Binding

The Ca²⁺-independent membrane interactions of the soluble C2 domains from synaptotagmin 1 (syt1) were characterized using a combination of site-directed spin labeling and vesicle sedimentation. The second C2 domain of syt1, C2B, binds to membranes containing phosphatidylserine and phosphatidylcholine in a Ca²⁺-independent manner with a lipid partition coefficient of approximately 3.0 × 10² M^− 1. A soluble fragment containing the first and second C2 domains of syt1, C2A and C2B, has a similar affinity, but C2A alone has no detectable affinity to phosphatidylcholine/phosphatidylserine bilayers in the absence of Ca²⁺. Although the Ca²⁺-independent membrane affinity of C2B is modest, it indicates that this domain will never be free in solution within the cell. Site-directed spin labeling was used to obtain bilayer depth restraints, and a simulated annealing routine was used to generate a model for the membrane docking of C2B in the absence of Ca²⁺. In this model, the polybasic strand of C2B forms the membrane binding surface for the domain; however, this face of C2B does not penetrate the bilayer but is localized within the aqueous double layer when C2B is bound. This double-layer location indicates that C2B interacts in a purely electrostatic manner with the bilayer interface. In the presence of Ca²⁺, the membrane affinity of C2B is increased approximately 20-fold, and the domain rotates so that the Ca²⁺-binding loops of C2B insert into the bilayer. This Ca²⁺-triggered conformational change may act as a switch to modulate the accessibility of the polybasic face of C2B and control interactions of syt1 with other components of the fusion machinery.     

DNA Recognition by Quinoline Antibiotics: Use of Base-Modified DNA Molecules to Investigate Determinants of Sequence-Specific Binding of Luzopeptin

Abstract

The luzopeptin antibiotics contain a cyclic decadepsipeptide to which are attached two quinoline chromophores that bisintercalate into DNA. Although they bind DNA less tightly than the structurally related quinoxaline antibiotics echinomycin and triostin A, the molecular basis of their interaction remains unclear. We have used the PCR in conjunction with novel nucleotides to create specifically modified DNA for footprinting experiments. In order to study the influence that removal, addition or relocation of the guanine 2-amino group, which normally identifies G. C base pairs from the minor groove, has on the interaction of luzopeptin antibiotics with DNA. The presence of a purine 2-amino group is not strictly required for binding of luzopeptin to DNA, but the exact location of this group can alter the position of preferred drug binding sites. It is, however, not the sole determinant of nucleotide sequence recognition in luzopeptin-DNA interaction. Nor can the selectivity of luzopeptin be attributed to the quinoline chromophores, suggesting that an analogue mode of DNA recognition may be operative. This is in contrast to the digital readout that seems to predominate with the quinoxaline antibiotics.     

Kinetic Aspects Of The Bioconversion Of 4-Chlorobenzoate To 4-Hydroxybenzoate By Alcaligenes Denitrificans Ntb-1 Immobilized In Carrageenan

Alcaligenes denitrificans NTB-1 converts 4-chlorobenzoate to 4-hydroxybenzoate by means of a hydrolytic dehalogenation. In the presence of oxygen the product is further metabolized by the cells. Although it has been shown that the dehalogenation does not require oxygen, no bioproduction of 4-hydroxybenzoate was achieved by whole cells when oxygen was absent. An energy-dependent active transport may explain this anomaly. Little activity was lost after immobilization of whole cells in carrageenan. Diffusion of oxygen within the carrageenan beads rapidly limited the rate of decolorization. This effect was magnified with increasing bead diameters and cell loadings. External transport of oxygen, on the other hand, did not decrease the reaction rate, except at extremely low oxygen concentrations. Maximal dehalogenation activity was observed at 35°C and at pH 8.0 and this was independent of whether free or immobilized cells were used. 4-Hydroxybenzoate significantly inhibited the rate of decolorization, while the chloride formed and the substrate 4-chlorobenzoate did not show inhibitory effects on decolorization. The yield of this bioconversion was mainly dependent on the oxygen concentration. In the case of free cells, 4-hydroxybenzoate was produced only at very low oxygen concentrations, while immobilized cells still produced 4-hydroybenzoate at air saturation as a result of oxygen diffusion limitation.     

Kinetic Aspects Of The Bioconversion Of 4-Chlorobenzoate To 4-Hydroxybenzoate By Alcaligenes Denitrificans Ntb-1 Immobilized In Carrageenan

Alcaligenes denitrificans NTB-1 converts 4-chlorobenzoate to 4-hydroxybenzoate by means of a hydrolytic dehalogenation. In the presence of oxygen the product is further metabolized by the cells. Although it has been shown that the dehalogenation does not require oxygen, no bioproduction of 4-hydroxybenzoate was achieved by whole cells when oxygen was absent. An energy-dependent active transport may explain this anomaly. Little activity was lost after immobilization of whole cells in carrageenan. Diffusion of oxygen within the carrageenan beads rapidly limited the rate of decolorization. This effect was magnified with increasing bead diameters and cell loadings. External transport of oxygen, on the other hand, did not decrease the reaction rate, except at extremely low oxygen concentrations. Maximal dehalogenation activity was observed at 35°C and at pH 8.0 and this was independent of whether free or immobilized cells were used. 4-Hydroxybenzoate significantly inhibited the rate of decolorization, while the chloride formed and the substrate 4-chlorobenzoate did not show inhibitory effects on decolorization. The yield of this bioconversion was mainly dependent on the oxygen concentration. In the case of free cells, 4-hydroxybenzoate was produced only at very low oxygen concentrations, while immobilized cells still produced 4-hydroybenzoate at air saturation as a result of oxygen diffusion limitation.     

Electron Microscopic and Physico-Chemical Studies of DNA Complexes with Synthetic Oligopeptides: Binding Specificity and DNA Compact Structures

Abstract

Binding to DNA of two synthetic peptides, Val-Thr-Thr-Val-Val-NH-NH-Dns and Thr-Val- Thr-Lys-Val-Gly-Thr-Lsy-Val-Gly-Thr-Val-Val-NH-NH-Dns (where Dns is a residue of 5- dimethylaminonaphthalene-l-sulfonic acid), has been studied by circular dichroism, electron microscopy and fluorescence methods. It has been found that these two peptides can self- associate in aqueous solution as follows from the fact that concentration-dependent changes are observed in the UV absorbance and fluorescence spectra. The two peptides can bind to DNA both in self-associated and monomeric forms. The pentapeptide in the β-associated form binds more strongly to poly(dG) · poly(dC) than to poly[d(A-C)] · poly[d(G-T)] and poly(dA) · poly(dT) whereas the tridecapeptide exhibits an opposite order of preferences binding more strongly to poly[d(A-C)] · poly[d(G-T)] and poly(dA) · poly(dT) than to poly(dG) · poly(dC).

Binding is a cooperative process which is accompanied by the DNA compaction at peptide/DNA base pair ratios greater than l. At the initial stage of the compaction process, the coalescence of DNA segments covered by bound peptide molecules leads to the formation of DNA loops stabilized by the interaction between peptide molecules bound to different DNA segments. Further increase in the peptide/DNA ratio leads to the formation of rod-like structures each consisting of two or more double-stranded DNA segments. The final stage of the compaction process involves folding of fibrillar macromolecular complexes into a globular structure containing only one DNA molecule.     

Visualising DNA: footprinting and 1-2D gels

The study of molecular recognition of DNA by natural and synthetic ligands has made enormous progress due in large part to the discovery and development of methods for separating DNA fragments by gel electrophoresis in one and two dimensions, and for characterizing DNA-ligand complexes by footprinting techniques.     

Histochemical Use Of Lead Tetra-Acetate I. Cleavage Of 1-2 Glycols

Lead tetra-acetate acts specifically to split the carbon-carbon single bond of the 1,2-glycol linkage to produce aldehyde radicals which may then be demonstrated by means of leucofuchsin, 2,4-dinitrophenlyhydrazine, or p-nitrophenylhydrazine. Routinely prepared slide sections from tissues fixed in 10% formalin are run down to 95% alcohol, rinsed in glacial acetic acid and then treated for 2 minutes in a saturated solution of lead tetra-acetate in glacial acetic acid with 5 g. of potassium acetate added for each 100 ml. of reagent. The sections are then washed in distilled water and placed in leucofuchsin for 10 minutes, or in a saturated 30% alcoholic solution of p-nitrophenylhydrazine for 5 minutes or 2,4-dini-trophenylhydrazine for 30 minutes. After staining, the sections are rinsed in 30% alcohol if the nitrophenylhydrazines were used, or in the standard dilute sulfite bath followed by running tap water for 5 minutes if leucofuchsin were used. Sections are routinely dehydrated, cleared, and covered. On examination, the sites of 1,2-glycol linkages will be stained violet by leucofuchsin or yellow by the nitrophenylhydrazines.     

Dynamics and Binding Modes of Free cdk2 and its Two Complexes with Inhibitors Studied by Computer Simulations

Abstract

This article presents a molecular dynamics (MD) study of the cdk2 enzyme and its two complexes with the inhibitors isopentenyladenine and roscovitine using the Cornell et al. force field from the AMBER software package. The results show that inserting an inhibitor into the enzyme active site does not considerably change enzyme structure but it seemingly changes the distribution of internal motions. The inhibitor causes differences in the domain motions in free cdk2 and in its complexes. It was found out that repulsion of roscovitine N9 substituent causes conformational change on Lys 33 side chain. Isopentenyladenine forms with Lys 33 side chain terminal amino group a hydrogen bond. It implies that the cavity, where N9 substituent of roscovitine is buried, can adopt larger substituent due to Lys 33 side chain flexibility. The composition of electrostatic and van der Waals interactions between the inhibitor and the enzyme were also calculated along both cdk2/inhibitor MD trajectories together with MM-PB/GBSA analysis. These results show that isopentenyladenine-like inhibitors could be more effective after modifications leading to an increase in their van der Waals contact with the enzyme. We suggest that a way leading to better inhibitors occupying isopentenyladenine binding mode could be: to keep N9 and N7 purine positions free, to keep 3,3-dimethylallylamino group at C6 position, and to add, e.g., benzylamino group at C2 position. The results support the idea that the isopentenyladenine binding mode can be used for cdk2 inhibitors design and that all possibilities to improve this binding mode were not uncovered yet.