Inhibition of Vacuolar Ion Channels by Polyamines

In this work, direct effects of cytosolic polyamines on the two principle vacuolar ion channels were studied by means of patch-clamp technique. Fast and slow activating vacuolar channels were analyzed on membrane patches isolated from vacuoles of the red beet taproot. The potency of the fast and of the slow vacuolar channel blockage by polyamines decreased with a decrease of the polycation charge, spermine⁴⁺ > spermidine³⁺ > putrescine²⁺. In contrast to the inhibition of the fast vacuolar channel, the blockage of the slow vacuolar channel by polyamines displayed a pronounced voltage-dependence. Hence, in the presence of high concentration of polyamines the slow vacuolar channel was converted into a strong inward rectifier as evidenced by its unitary current-voltage characteristic. The blockage of the slow vacuolar channel by polyamines was relieved at a large depolarization, in line with the permeation of polyamines through this channel. The voltage-dependence of blockage was analyzed in terms of the conventional model, assuming a single binding site for polyamines within the channel pore. Taking advantage of a simple linear structure of naturally occurring polyamines, conclusions on a possible architecture of the slow vacuolar channel pore were drawn. The role of common polyamines in regulation of vacuolar ion transport was discussed. Received: 1 May 1998/Revised: 25 September 1998     

A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations

Four different molecular dynamics (MD) simulations have been performed for ordered DNA decamers, d(5′-ATGCAGTCAG)·d(5′-TGACTGCATC). The counterions were the two natural polyamines spermidine³⁺ (Spd³⁺) and putrescine²⁺ (Put²⁺), the synthetic polyamine diaminopropane²⁺ (DAP²⁺) and Na⁺. The simulation set-up corresponds to an infinite array of parallel DNA mimicking the state in oriented DNA fibers or crystals. This work describes general properties of polyamine and Na⁺ binding to DNA. Simulated diffusion coefficients show satisfactory agreement with experimental NMR diffusion data of comparable systems. The interaction of the polyamines with DNA is dynamic in character and the cations mostly form short-lived contacts with the electronegative binding sites of DNA. Polyamines, Na⁺ and water interact most frequently with the charged phosphate atoms with preference for association from the minor groove side with O1P over O2P. There is a strong anti-correlation in the cation binding to the electronegative groups of DNA, i.e. the presence of a cation near one of the DNA sites repels other cations from binding to this and to the other sites separated by <7.5 Å from each other. In contrast to the other polyamines, DAP²⁺ is able to form ‘bridges’ connecting neighboring phosphate groups along the DNA strand. A small fraction of DAP²⁺ and Put²⁺ can be found in the major grooves, while Spd³⁺ is absent there. The results of the MD simulations reveal principal differences in the polyamine–DNA interactions between the natural (Spd³⁺, Put²⁺ and spermine⁴⁺) and synthetic (DAP²⁺) polyamines.     

Effect of Glycine on DNA Structural Transitions Induced by Multivalent Cationic Compounds

Abstract

We have investigated the effect of glycine (an organic osmolyte) on several DNA transitions induced by Tb³⁺, spermidine³⁺ and spermine⁴⁺ addition, using light scattering, circular dichroism, UV spectroscopy and electric linear dichroism techniques.

DNA condensation and B-Z transition by the three compounds is perturbed by glycine: more Tb-¹⁺, spermidine³⁺ and spermine⁴⁺ must be added to obtain the same extent of condensation or Z-form as compared to the behaviour in the absence of this organic osmolyte. However, according to the light scattering experiments, glycine has also a structural effect on the DNA condensation that could be explained by an influence of the medium dielectric constant on the morphology of particles formed or on the rate of the condensation process.

Contrary to these transitions, the particular B-B'-ψ transition resulting from the addition of Tb³⁺ to a DNA solution is not observed in the presence of glycine. Since the chelation of Tb³⁺ by the phosphate group and the N-7 of guanine is presumably responsible for this transition, the glycine effect could probably be explained by a perturbation of this chelation by the change in solvent polarity and the chelating ability of the organic osmolyte.     

Molecular-Mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG)·d(CGCGAATTCGCG)

Molecular-mechanical simulations have been carried out on “mismatched base” analogs of the DNA double-helical structure d(CGCGAATTCGCG)₂, in which the base pairs CG at the 3 and 10 positions have been replaced by CA, AG, TC, and TG base pairs, as well as an insertion analog in which an extra adenine has been incorporated into one strand of the above structure between bases 3 and 4. The results of these simulations (calculated relative stabilities, structures, and nmr ring-current shifts) have been compared with calorimetric and nmr data. The calculated relative stabilities of the double-helical parent dodecamer and the various “wobble” base pairs qualitatively correlate with the experimental melting temperatures. The base-pairing structure for the GT wobble pair is in agreement with that previously determined from nmr experiments. For the GA base pair, the structure with both bases anti has a slightly more favorable energy from base pairing and stacking than a structure with non-Watson-Crick H-bonding with adenine syn, in agreement with nmr experiments. The CA wobble base is calculated to favor an adenine 6NH₂ …? cytosine N3 H-bond over cytosine 4NH₂ …? adenine N1, again, in agreement with nmr experiments. There is no definitive experimental data on the TC base pair, but the existence of (somewhat long and weak) H-bonds involving cytosine 4NH₂ …? thymine 4CO and cytosine N3 …? thymine HN3 seems reasonable. We find a structure in which the extra adenine base of the insertion analogs sits “inside” the double helix.     

Specifically alkylated DNA fragments. Synthesis and physical characterization of d[CGC(O6Me)GCG] and d[CGT(O6Me)GCG]

Two hexamer DNA fragments containing a carcinogenic modified base, O⁶-methyl guanine, have been synthesized by a solid-phase phosphotriester method, in which the unmodified guanine residues present were O⁶ protected with the 4-nitrophenylethyl group. These two alkylated oligonucleotides were found to have similar T_m's about 40° lower than the unmodified parent compund, d(CG)₃. Moreover, the presence of the (O⁶Me)G appears to inhibit the B→Z transition, as determined by CD spectroscopy.     

Studies of the B‐Z transition of DNA: The temperature dependence of the free‐energy difference,the composition of the counterion sheath in mixed salt,and the preparation of a sample of the 5′‐d[T‐(m5C‐G)12‐T] duplex in pure B‐DNA or Z‐DNA form

It is often envisioned that cations might coordinate at specific sites of nucleic acids and play an important structural role, for instance in the transition between B‐DNA and Z‐DNA. However, nucleic acid models explicitly devoid of specific sites may also exhibit features previously considered as evidence for specific binding. Such is the case of the “composite cylinder” (or CC) model which spreads out localized features of DNA structure and charge by cylindrical averaging, while sustaining the main difference between the B and Z structures, namely the better immersion of the B‐DNA phosphodiester charges in the solution. Here, we analyze the non‐electrostatic component of the free‐energy difference between B‐DNA and Z‐DNA. We also compute the composition of the counterion sheath in a wide range of mixed‐salt solutions and of temperatures: in contrast with the large difference of composition between the B‐DNA and Z‐DNA forms, the temperature dependence of sheath composition, previously unknown, is very weak. In order to validate the model, the mixed‐salt predictions should be compared to experiment. We design a procedure for future measurements of the sheath composition based on Anomalous Small‐Angle X‐ray Scattering and complemented by ³¹P NMR. With due consideration for the kinetics of the B‐Z transition and for the capacity of generating at will the B or Z form in a single sample, the 5′‐d[T‐(m⁵C‐G)₁₂‐T] 26‐mer emerges as a most suitable oligonucleotide for this study. Finally, the application of the finite element method to the resolution of the Poisson‐Boltzmann equation is described in detail. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 369–384, 2016.     

An NMR self-diffusion study of the interactions between spermidine and oligonucleotides

Self-diffusion coefficients have been determined by pulsed field gradient nmr methods for spermidine in solutions of the oligonucleotides d(GC)₄ and d(GGAATTCC). The self-diffusion behavior of spermidine in solution of d(GC)₄ is very similar to that observed previously for methylspermidine (completely N-methylated spermidine). Moreover, the self-diffusion behaviors of spermidine in solutions of d(GC)₄ and d(GGAATTCC) are also quite similar, indicating that there is no significant influenceon on self-diffusion of oligonucleotide base composition. Furthermore, self-diffusion coefficients of the oligonucleotide d(GC)₈ show only a small dependence on oligonucleotide concentration, and no measurable dependence on sodium ion or magnesium ion concentration. © 1996 John Wiley & Sons, Inc.     

Ion competition and micrococcal nuclease digestion studies of spermidine-condensed calf thymus DNA: Evidence for torus organization by circumferential DNA wrapping

Spermidine-condensed calf thymus DNA structures have been studied by ion competition using a sedimentation assay and by micrococcal nuclease digestion. Competitor ions Mg²⁺, Ca²⁺ and putrescine²⁺ show specific ion effects; but all three appear to affect the DNA condensation-decondensation equilibrium caused by spermidine³⁺ in a qualitatively similar manner, suggesting the spermidine³⁺-DNA interaction is largely electrostatic. Our data show a hysteresis in condensation and decondensation transition directions. We interpret this in terms of a kinetic block in the condensation direction with decondensation representing the equilibrium state of the system. These results agree with results obtained from related systems using different measurement techniques. Micrococcal nuclease digestion of spermidine-condensed calf thymus DNA produces broad but discrete bands in gel electrophoresis experiments. At least two bands determined to be 760 ± 87 bp and 1355 ± 135 bp, possess the size ratio 1:1.8 ± 0.4 consistent with their forming the monomer and dimer fragments of an arithmetic band series. We rationalize this result in terms of a localized micrococcal nuclease cleavage model of circumferentially-wrapped DNA toruses proposed previously by Marx, K.A. and Reynolds, T.C. (Proc. Natl. Acad. Sci. (1982) 79, 6484–6488). The arithmetic series monomer band (760 ± 87 bp), corresponding to wrapping B̄ DNA once circumferentially about the torus, is in agreement with the electron microscopic measurements of hydrated calf thymus DNA torus circumferences presented by Marx, K.A. and Ruben, G.C. (Nucleic Acids Res. (1983) 11, 1839–1853).     

Involvement of polyamines,abscisic acid and anti-oxidative enzymes in adaptation of Blue Panicgrass (Panicum antidotale Retz.) to saline environments

A hydroponic experiment was conducted to assess the possible involvement of polyamines (PAs), abscisic acid (ABA) and anti-oxidative enzymes such as superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) in adaptation of six populations of Panicum antidotale Retz. to selection pressure (soil salinity) of a wide range of habitats. Plants of six populations were collected from six different habitats with ECe ranging from 3.39 to 19.23 dS m⁻¹ and pH from 7.65 to 5.86. Young tillers from 6-month-old plants were transplanted in plastic containers each containing 10 l of half strength Hoagland's nutrient solution alone or with 150 mol m⁻³ NaCl. After 42 days growth, contents of polyamines (Put, Spd and Spm) and ABA, and the activities of anti-oxidative enzymes (SOD, POD and CAT) of all populations generally increased under salt stress. The populations collected from highly saline habitats showed a greater accumulation of polyamines and ABA and the activities of anti-oxidative enzymes as compared to those from mild or non-saline habitats. Moreover, Spm/Spd and Put/(Spd + Spm) ratios generally increased under salt stress. However, the populations from highly saline environments had significantly higher Spm/Spd and Put/(Spd + Spm) ratios as compared to those from mild or non-saline environments. Similarly, the populations adapted to high salinity accumulated less Na⁺ and Cl⁻ in culm and leaves, and showed less decrease in leaf K⁺ and Ca²⁺ under salinity stress. Higher activities of anti-oxidative enzymes and accumulation of polyamines and ABA, and increased Spm/Spd and Put/(Spm + Spd) ratios were found to be highly correlated with the degree of adaptability of Panicum to saline environment.     

Z → B transition in poly[d(G-m5C)2] induced by interaction with 4′,6-diamidino-2-phenylindole

The Z form of poly[d(G-m⁵C)₂], in presence of Mg²⁺ ion, is found to be transformed into B form upon interaction with 4′,6-diamidino-2-phenylindole (DAPI). The Z → B transformation is complete at a mixing ratio of about 0.07 DAPI per DNA base pairs, i.e., each DAPI molecule may be related to the conversion of 6–7 base pairs. An interaction between DAPI and poly[d(G-m⁵C)₂] in its Z form at low drug: DNA ratios is suggested from optical dichroism and time-resolved luminescence anisotropy results. The spectroscopic behaviour of DAPI indicates that the Z conformation of DNA does not provide normal binding sites for DAPI, such as groove or intercalation sites, but that the initial association may be of external nature. © 1993 John Wiley & Sons, Inc.     

A novel Z-structure for poly d(GC).poly d(GC)

A novel zig-zag (Z) structure is proposed for poly d(GC).poly d(GC). The proposed model closely resembles the crystal structure of d(CG)₃.     

Laser Photofootprinting of d(C)·d(G)·d(G) Intramolecular Triplex

Abstract

Supercoiling-induced structural transition of the d(C₂₄GC₂₁,) · d(G₂₁CG₂₄) sequence in plasmid DNA in the presence of Mg²⁺ at neutral pH results in alterations of efficiencies of not only single-quantum (pyrimidine[6–4]pyrimidone adducts) but also two-quantum (alkalisensitive lesions of dG residues) photomodifications of nucleoside residues within this sequence. The generation of both types of photoreactions was achieved by the application of high-intensity laser UV radiation (intensity ～ 10¹¹ W/m², pulse duration ～ 10^?8 s, λ= 266 nm) for irradiation of a plasmid DNA The modification extent sufficient for analysis of photoreaction efficiency distributions along both strands of the insert (photofootprinting) was obtained by the action of a single nanosecond pulse of laser UV radiation. The pattern of a laser photofootprinting is consistent with the d(C) · d(G) · d(G) triplex formation in the presence of Mg²⁺ within the insert and shows some details of this triplex structure.     

High Efficiency Photocatalytic Water Splitting Using 2D α‐Fe2O3/g‐C3N4 Z‐Scheme Catalysts

Photocatalysis is the most promising method for achieving artificial photosynthesis, but a bottleneck is encountered in finding materials that could efficiently promote the water splitting reaction. The nontoxicity, low cost, and versatility of photocatalysts make them especially attractive for this application. This study demonstrates that small amounts of α‐Fe₂O₃ nanosheets can actively promote exfoliation of g‐C₃N₄, producing 2D hybrid that exhibits tight interfaces and an all‐solid‐state Z‐scheme junction. These nanostructured hybrids present a high H₂ evolution rate >3 × 10⁴ µmol g^‐1 h^‐1 and external quantum efficiency of 44.35% at λ = 420 nm, the highest value so far reported among the family of g‐C₃N₄ photocatalysts. Besides effectively suppressing the recombination of electron–hole pairs, this Z‐scheme junction also exhibits activity toward overall water splitting without any sacrificial donor. The proposed synthetic route for controlled production of 2D g‐C₃N₄‐based structures provides a scalable alternative toward the development of highly efficient and active photocatalysts.     

DNA binding and cleavage activity of [Ru(NH3)4(diimine)]Cl2 complexes

The interaction of a series of mixed ligand complexes of the type [Ru(NH₃)₄(diimine)]Cl₂, where diimine=2,2^′-bipyridine (bipy), 1,10-phenanthroline (phen), 5,6-dimethyl-1,10-phenanthroline (5,6-dmp), 4,7-dimethyl-1,10-phenanthroline (4,7-dmp), 2,9-dimethyl-1,10-phenanthroline (2,9-dmp), 3,4,7,8-tetra-methyl-1,10-phenanthroline (Me₄phen), with calf thymus DNA has been studied using absorption, emission and circular dichroic spectral measurements and viscometry and electrochemical techniques. On interaction with DNA the complexes show hypochromism and red-shift in their MLCT band suggesting that the complexes bind to DNA. The magnitude of the binding constant (K_b) obtained from absorption spectral titration varies depending upon the nature of the diimine ligand: Me₄phen > 5,6-dmp > 4,7-dmp > phen suggesting the use of diimine ‘face’ of the octahedral complexes in binding to DNA. The interaction of phen complex possibly involves phen ring partially inserted into the DNA base pairs. In contrast, the methyl-substituted phen complexes would involve hydrophobic interaction of the phen ring in the grooves of DNA, which is supported by hydrogen bonding interactions of the ammonia ligands with the intrastrand nucleobases. Also the shape and size of the phen ligand as modified by the methyl substituents determine the DNA binding site sizes (0.12-0.45 base pairs). The relative emission intensities (I/I₀) of the DNA-bound complexes parallel the variation in K_b values. Almost all the metal complexes exhibit induced CD bands on binding to B DNA, with the 4,7-dmp and Me₄phen complexes inducing certain structural modifications on the biopolymer. DNA melting curves obtained in the presence of metal complexes reveal a monophasic melting of the DNA strands, the Me₄phen complex exhibiting a slightly enhanced tendency to stabilize the double-stranded DNA. There were slight to appreciable changes in the relative viscosities of DNA, which are consistent with enhanced hydrophobic interaction of the methyl-substituted phen rings. Upon interaction with CT DNA, the Me₄phen, 4,7-dmp and 5,6-dmp complexes, in contrast to bipy, phen and 2,9-dmp complexes, show a decrease in anodic peak current in their cyclic voltammograms suggesting that they exhibit enhanced DNA binding. DNA cleavage experiments show that all the complexes induce cleavage of pBR322 plasmid DNA, the Me₄phen and 5,6-dmp complexes being remarkably more efficient than other complexes.     

Infrared Spectral Studies of the Non Regularly Alternating Purine-Pyrimidine Hexamers d(m5CGGCM5CG), d(CBr8GGCCBr8G) and d(CGCGGC)

Abstract

The oligonucleotides d(m⁵CGGCm⁵CG), d(CBr⁸GGCCBr⁸G) and d(CGCGGC) have been prepared and studied by infrared spectroscopy. The three sequences contain two GC pairs which are out of purine-pyrimidine alternation with the rest of the sequence. From the IR data of the dlm⁵CGGCm^CG) hexamer, it is shown that all of the dG residues adopt a syn conformation. The marker IR bands for the C3′ endo syn conformation are at 1410, 1354, 1320 and 925 cm^?1 whereas those for the C2′ endo and conformation at 1420, 1374 and 890 cm^?1 are clearly absent. This result implies that the two adjacent guanines of the d(m⁵CGGCm⁵CG) sequence are in syn conformation. It is suggested that duplex formation occurs in d(CGCGGC) films and that all of the guanines are in syn conformation. In contrast, the central non-brominated guanine of the dlCBr⁸GGCCBr⁸G) hexamer is found in ami conformation, as expected in a Z type structure of the non-alternating region.     

DNA frayed wires: Differential polymerization of d(AnGm) oligonucleotides

Oligodeoxyribonucleotides with terminal runs of contiguous guanines, d(A_nG_m), spontaneously associate into high molecular weight complexes that resolve on polyacrylamide gels as a regular ladder pattern of bands with low mobility. The aggregates, which we call frayed wires, arise from the interaction between the guanine residues of the oligonucleotides; the adenine tracts are single stranded and can take part in Watson–Crick interactions. Oligonucleotides, with different arm‐to‐stem ratios and total length, readily associate in the presence of Mg²⁺ to form aggregates consisting of an integer number of strands. The type of the observed aggregates is determined by the length of the guanine run. Oligonucleotides with six guanines form four‐ and eight‐stranded complexes; there is no further polymerization. An increase in the number of guanine residues to 10 and 15 leads to polymerization resulting in a ladder pattern of up to 9 bands and an intense signal at the top of the gel. The relative population of any given species in a frayed wire sample is governed by the guanine stem length and is not affected to any substantial extent by arms up to 40 bases long. The type and concentration of the cation in the solution affect the degree of aggregation, with Na⁺ and K⁺ promoting the formation of complexes comprised of 2–4 strands and Mg²⁺ being the most effective in facilitating polymerization. The electrophoretic behavior of frayed wires was analyzed in the framework of the Ogston theory. The free mobility of frayed wires in the solution is close to the values reported for single‐stranded DNA, indicating the equivalence of the charge density of the two conformations. The retardation coefficients for frayed wires arising from a single kind of parent strand increase with the introduction of each additional strand. There is no correlation between the retardation coefficient and the type of parent strand; rather, the magnitude of the retardation coefficient is determined by the total molecular weight of the complex. The values of the retardation coefficients are consistently higher than those for double‐stranded DNA and they display much stronger dependence on the total molecular weight. Presumably, the distinct structural and dynamic characteristics of the two conformations account for their different electrophoretic behavior. © 1999 John Wiley & Sons, Inc. Biopoly 49: 287–295, 1999     

N-2-acetylaminofluorene modification of poly(dG-m5dC)·poly(dG-m5dC) induces the Z-DNA conformation

Poly(dG-m⁵dC)·poly(dG-m⁵dC) was modified by treatment with N-acetoxy-N-2-acetylaminofluorene (N-Aco-AAF) and its conformation examined by circular dichroism (CD) and susceptibility to S₁ nuclease digestion. A sample with a modification level of 10% shows a CD spectrum characteristic of the Z form and is resistant to digestion by S₁ nuclease. The relative reactivity of several polymers with N-Aco-AAF was shown to follow the order of ease of formation of Z DNA: poly(dG-m⁵dC)·poly(dG-m⁵dC) > poly(dG-dC)·poly(dG-dC) > poly(dG)·poly(dC). This suggests that AAF reacts more readily with Z DNA than B DNA.     

Tetraamine‐modified octreotide and octreotate: labeling with 99mTc and preclinical comparison in AR4‐2J cells and AR4‐2J tumor‐bearing mice

Two somatostatin analogues, [^99mTc]Demotide and [^99mTc]Demotate 4, were compared with [^99mTc]Demotate 1, a previously reported somatostatin receptor subtype 2 (sst₂) targeting tracer. Conjugates were prepared by coupling an open‐chain tetraamine chelator to D ‐Phe¹ of [Tyr³]‐octreotide or [Tyr³]‐octreotate, respectively, via a p‐benzylaminodiglycolic acid spacer adopting solid‐phase peptide synthesis techniques. Peptide conjugates were collected in a highly pure form after chromatographic purification. Eventually, [^99mTc]Demotide and [^99mTc]Demotate 4 were obtained in ～1 Ci/µmol specific activity and >96% purity after labeling under alkaline conditions. Demotide and Demotate 4 exhibited similar high binding affinities for the sst₂ expressed in AR4‐2J cells with IC₅₀ values 0.16 and 0.10 nM, respectively. The (radio)metallated analogues [^99mTc]Demotide and [^99mTc]Demotate 4 showed equally high affinities to the sst₂ during saturation binding assays in AR4‐2J cell membranes (K_ds 0.08 and 0.07 nM, respectively). During incubation at 37 °C with AR4‐2J cells, the radiopeptides internalized effectively via a receptor‐mediated process, with [^99mTc]Demotate 4 exhibiting a faster internalization rate than [^99mTc]Demotide. After injection in athymic mice bearing sst₂‐expressing AR4‐2J tumors, the radiotracers showed high and specific uptake in the tumor (>25%ID/g at 1 h) and in the sst₂–positive organs. However, both [^99mTc]Demotide and [^99mTc]Demotate 4 showed unfavorably higher background activity, especially in the abdomen, in comparison to [^99mTc]Demotate 1 and are, therefore, less suited than [^99mTc]Demotate 1 for sst₂‐targeted tumor imaging in man. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd.