Na2CO3 influence on DNA double helix stability: strong anion destabilizing effect

Addition of Na(2)CO(3) to almost salt-free DNA solution (5.10(-5)M EDTA, pH=5.7, T(m)=26.5 degrees C) elevates both pH and the DNA melting temperature (T(m)) if Na(2)CO(3) concentration is less than 0.004 M. For 0.004 M Na(2)CO(3), T(m)=58 degrees C is maximal and pH=10.56. Further increase in concentration gives rise to a monotonous decrease in T(m) to 37 degrees C for 1M Na(2)CO(3) (pH=10.57). Increase in pH is also not monotonous. The highest pH=10.87 is reached at 0.04 M Na(2)CO(3) (T(m)=48.3 degrees C). To reveal the cause of this DNA destabilization, which happens in a narrow pH interval (10.56/10.87) and a wide Na(2)CO(3) concentration interval (0.004/1M), a procedure has been developed for determining the separate influences on T(m) of Na(+), pH, and anions formed by Na(2)CO(3) (HCO(3)(-) and CO(3)(2-)). Comparison of influence of anions formed by Na(2)CO(3) on DNA stability with Cl(-) (anion inert to DNA stability), ClO(4)(-) (strong DNA destabilizing "chaotropic" anion) and OH(-) has been carried out. It has been shown that only Na(+) and pH influence T(m) in Na(2)CO(3) solution at concentrations lower than 0.001 M. However, the T(m) decrease with concentration for [Na(2)CO(3)]>/=0.004 M is only partly caused by high pH=10.7. Na(2)CO(3) anions also exert a strong destabilizing influence at these concentrations. For 0.1M Na(2)CO(3) (pH=10.84, [Na(+)]=0.2M, T(m)=42.7 degrees C), the anion destabilizing effect is higher 20 degrees C. For NaClO(4) (ClO(4)(-) is a strong "chaotropic" anion), an equal anion effect occurs at much higher concentrations approximately 3M. This means that Na(2)CO(3) gives rise to a much stronger anion effect than other salts. The effect is pH dependent. It decreases fivefold at neutral pH after addition of HCl to 0.1M Na(2)CO(3) as well as after addition of NaOH for pH greater than 11.2.     

Topological Comparison of Two Helix Destabilizing Proteins: Ribonuclease A and the Gene 5 DNA Binding Protein

Abstract

A topological comparison of the two helix destabilizing proteins, pancreatic ribonuclease A and the gene S DNA binding protein of bacteriophage fd has been completed utilizing the available high resolution tertiary structures of each protein. The results indicate these two proteins are structurally if not also evolutionarily related. Regions of closest topological equivalence occur between beta loops directly involved in nucleotide binding or are required for the maintenance of their respective oligonucleotide binding channels. In addition, there is a similar placement of critical amino acid side chains about the binding site. Further evidence for this structural relationship is obtained by comparison of structural data for the mode of complexation of polynucleotides to each protein. The results of topological comparison suggest the essential property shared by helix destabilizing proteins, whether specialized DNA binding proteins such as G5BP or proteins with other primary functional roles, like ribonuclease A, is the presence of an elongated oligonucleotide binding channel. Although ribonuclease A and G5BP are structurally related, it seems likely any protein with this structural feature will exhibit a helix destabilizing capacity. This conclusion is supported by the diversity of molecular characteristics shown by other proteins having this activity.     

Different Effects of Nonintercalative Antitumor Drugs on DNA Triple Helix Stability: SN-18071 Promotes Triple Helix Formation

Abstract

The interaction of the nonintercalating bisquaternary ammonium heterocyclic drugs SN- 18071 and SN-6999 with a DNA triple helix has been studied using thermal denaturation and CD spectroscopy. Our data show, that both minor groove binders can bind to the triple helix of poly(dA)-2poly(dT) under comparable ionic conditions, but they influence the stability of the triplex relative to the duplex structure of poly(dA)-poly(dT) in a different manner. SN- 18071, a ligand devoid of forming hydrogen bonds, can promote triplex formation and thermally stabilizes it up to 500 mM Na+ concentration. SN-6999 destabilizes the triplex to duplex equibilirium whereas it stabilizes the duplex. The binding constant of SN-18071 is found to be greater than that to the duplex. The stabilizing effect of SN-18071 is explained by electrostatic inetractions of three ligand molecules with the three grooves of the triple stranded structure. From the experiments it is concluded that SN-6999 binds to the triplex minor groove thereby destabilizing the triplex similar as previously reported for netropsin.     

The Effect of Crystal Packing on Oligonucleotide Double Helix Structure

Abstract

Complexes formed between Actinomycin D (ActD) and the tetranucleotides d(AGCT)2 and d(CGCG)₂ were studied in detail by one and two-dimensional ¹H and ³¹P NMR. The ³¹P two dimensional chemical exchange experiment, at room temperature on saturated complexes (1:1), showed unambiguously that the asymmetrical phenoxazone ring binds to the unique GC site under the two possible orientations in the d(AGCT)₂ tetranucleotide but adopts a single orientation in the d(CGCG)₂ tetranucleotide. For the d(CGCG)₂: Act D saturated complex, complete assignments of all protons and phosphorus signals of the two-nucleotide strands, as well as of the two cyclic pentapeptide chains has allowed us to study in details the conformational features of the complex from NOE and coupling constants analysis. The tetranucleotide remains in a right-handed duplex, but the sugar puckers are modified for residues at the intercalation site. A uniform C_2′ endo pucker is observed for residues on the strand facing the quinoid side of the phenoxazone ring while a C_2′ endo-C_3′ endo equilibrium about 60% of C_2′ endo is proposed for the two residues on the strand facing the benzenoid side of the phenoxazone ring. In contrast to previous studies on ActD-DNA interactions, we have been able to measure the ³J phosphorus-proton coupling constants at the intercalation site but also adjacent to it, showing that ³¹P chemical shifts are not simply related to the backbone conformation. Molecular mechanics calculations, using empirical distances deduced from NOE effects as restrained distances during minimizations, led to a model differing mainly from those previously published by orientation of the N methyl groups of both N-Methyl-Valines.     

Na2CO3处理对黄瓜嫁接苗与自根苗耐盐性的影响

通过Na2CO3,胁迫对黄瓜嫁接苗和自根苗耐盐性差异的研究,揭示黄瓜幼苗的耐盐机制,为设施黄瓜生产提供理论依据。实验以孝感早瓠瓜为砧木,津春四号黄瓜为接穗,采用不同浓度Na2CO3,溶液对黄瓜嫁接苗和自根苗进行处理,研究其对黄瓜幼苗的生理胁迫效应。结果表明：在0—7000mg／L范围内,随着Na2CO3,处理浓度的增加,黄瓜嫁接苗和自根苗的株高、茎粗、叶面积、地上部鲜重、根鲜重、叶绿素和根系活力均下降,但嫁接苗受抑制的程度显著低于自根苗;脯氨酸、丙二醛和根冠比均呈上升趋势,且这三项指标均表现为嫁接苗显著高于自根苗;叶片SOD酶活性均呈先上升后下降趋势,均在Na2CO3,处理浓度为1000mg／L时达到最大值,且嫁接苗的活性显著高于自根苗。嫁接苗的耐盐性优于自根苗,Na2CO3胁迫条件下,嫁接苗和自根苗的生长条件盐浓度以不超过3000mg／L为宜。     

Melting of Cross-Linked DNA V. Cross-Linking Effect Caused by Local Stabilization of the Double Helix

Abstract

DNA interstrand cross-links are usually formed due to bidentate covalent or coordination binding of a cross-linking agent to nucleotides of different strands. However interstrand linkages can be also caused by any type of chemical modification that gives rise to a strong local stabilization of the double helix. These stabilized sites conserve their helical structure and prevent local and total strand separation at temperatures above the melting of ordinary AT and GC base pairs. This local stabilization makes DNA melting fully reversible and independent of strand concentration like ordinary covalent interstrand cross-links. The stabilization can be caused by all the types of chemical modifications (interstrand cross-links, intrastrand cross-links or monofunctional adducts) if they give rise to a strong enough local stabilization of the double helix. Our calculation demonstrates that an increase in stability by 25 to 30 kcal in the free energy of a single base pair of the double helix is sufficient for this “cross-linking effect” (i.e. conserving the helicity of this base pair and preventing strand separation after melting of ordinary base pairs). For the situation where there is more then one stabilized site in a DNA duplex (e.g., 1 stabilized site per 1000 bp), a lower stabilization per site is sufficient for the “cross-linking effect” (18–20 kcal). A substantial increase in DNA stability was found in various experimental studies for some metal-based anti-tumor compounds. These compounds may give rise to the effect described above. If ligand induced stabilization is distributed among several neighboring base pairs, a much lower minimum increase per stabilized base pair is sufficient to produce the cross-linking effect (1 bp- 24.4 kcal; 5 bp- 5.3 kcal; 10 bp- 2.9 kcal, 25 bp- 1.4 kcal; 50 bp- 1.0 kcal). The relatively weak non-covalent binding of histones or protamines that cover long regions of DNA (20–40 bp) can also cause this effect if the salt concentration of the solution is sufficiently low to cause strong local stabilization of the double helix. Stretches of GC pairs more than 25 bp in length inserted into poly(AT) DNA also exhibit properties of stabilizing interstrand cross-links.     

Torsional and Bending Rigidity of the Double Helix from Data on Small DNA Rings

Abstract

We have calculated the variance of equilibrium distribution of a circular wormlike polymer chain over the writhing number, ?(Wr)²?, as a function of the number of Kuhn statistical segments, n, For large n these data splice well with our earlier results obtained for a circular freely jointed polymer chain. Assuming that ?(ΔLk)²? = ?(ΔTw)²? + ?(Wr)²? we have compared our results with experimental data on the chain length dependence of the ?(ΔLk) ²? value recently obtained by Horowitz and Wang for small DNA rings. This comparison has shown an excellent agreement between theory and experiment and yielded a reliable estimate of the torsional and bending rigidity parameters. Namely, the torsional rigidity constant is C = 3.0·10^?19 erg cm, and the bending rigidity as expressed in terms of the DNA persistence length is a = 500 A. The obtained value of C agrees well with earlier estimates by Shore and Baldwin as well as by Horowitz and Wang whereas the a value is in accord with the data of Hagerman. We have found the data of Shore and Baldwin on the chain length dependence of the ?(ΔLk) ²? value to be entirely inconsistent with our theoretical results.     

Effects of NaCl and Na2CO3 stresses on photosynthetic ability of Chlamydomonas reinhardtii

Chloride and carbonate salts are the main salts causing salinization and widely exist in aquatic environment, so algae may suffer from salinization stress for high water evaporation. In this study, in order to investigate and compare the toxic effects of the two salts on algal photosynthesis, we used NaCl and Na₂CO₃ to stress Chlamydomonas reinhardtii. Under the two salt stresses, the content of O ₂ ^?· and H₂O₂ in the cells was increased significantly, and it was much higher in Na₂CO₃ treatment than in NaCl treatment at the same Na⁺ concentration. The absorbance spectra and 4^th derivative spectra of photosynthetic pigments were declined under 300 mM NaCl and 25 mM Na₂CO₃ stresses, and remarkably changed under 50 mM and 100 mM Na₂CO₃ stresses. When the cells stressed by the two salts, the maximum quantum yield (Fv/Fm), electron transport rate (ETR) and photochemical quenching (qP) were reduced markedly, but the nonphotochemical dissipation (NPQ) was increased markedly. At the same Na⁺ concentration, Na₂CO₃ stress had stronger toxic effects on photosynthetic ability than NaCl stress.     

Na2Zn3(CO3)4.3H2O: a potentially useful compound for zinc supplementation.

The infrared and Raman spectra of the title compound were recorded and are briefly discussed on the basis of its structural characteristics. Its thermal behaviour was investigated by means of TG and DTA measurements. Several dissolution tests were also performed. The results support the potential usefulness of this double carbonate as a useful compound for Zn(II) supplementation.     

Left-Handed Intercalated DNA Double Helix: Rendezvous of Ethidium and Actinomycin D in the Z-Helical Conformation Space

Abstract

It is now very well recognized that the DNA double helix is conformationally pluralistic and that this flexibility is derived from internal motions due to backbone torsions. But what is less apparent is that such internal motions can occur in a correlated fashion and express themselves in a wide variety of structural motifs and phenomena. For example, flexibility inherent in the DNA molecule can lead to a family of Z-DNA, LZ1 and LZ2 being the two extremes and correlated internal motion can cause LZ1?LZ2 transition. More interestingly, such motions manifest themselves as breathing modes on the DNA lattice resulting in the sequence specific intercalation sites. Following a detailed stereochemical analyses we observed that the intercalation site for ethidium is located at the dCpdG sequence of the intercalated LZ1 helix (LZ1*) while that for actinomycin D is located at the dGpdC sequence of the intercalated LZ2 helix (LZ2*). From the stereochemistry of the drug binding we make experimentally testable predictions which are in fact supported by a few recent experimental studies. These studies also show that a left-handed intercalated B-DNA model is a viable intermediate in the Z to B transition which can hold the drug with binding energy comparable to that of the intercalated right-handed B-DNA.     

Temperature Dependence of the DNA Double Helix at the Nanoscale: Structure,Elasticity, and Fluctuations

Biological organisms exist over a broad temperature range of −15°C to +120°C, where many molecular processes involving DNA depend on the nanoscale properties of the double helix. Here, we present results of extensive molecular dynamics simulations of DNA oligomers at different temperatures. We show that internal basepair conformations are strongly temperature-dependent, particularly in the stretch and opening degrees of freedom whose harmonic fluctuations can be considered the initial steps of the DNA melting pathway. The basepair step elasticity contains a weaker, but detectable, entropic contribution in the roll, tilt, and rise degrees of freedom. To extend the validity of our results to the temperature interval beyond the standard melting transition relevant to extremophiles, we estimate the effects of superhelical stress on the stability of the basepair steps, as computed from the Benham model. We predict that although the average twist decreases with temperature in vitro, the stabilizing external torque in vivo results in an increase of ∼1°/bp (or a superhelical density of Δσ ?  + 0.03) in the interval 0–100°C. In the final step, we show that the experimentally observed apparent bending persistence length of torsionally unconstrained DNA can be calculated from a hybrid model that accounts for the softening of the double helix and the presence of transient denaturation bubbles. Although the latter dominate the behavior close to the melting transition, the inclusion of helix softening is important around standard physiological temperatures.     

Temperature Dependence of the DNA Double Helix at the Nanoscale: Structure,Elasticity, and Fluctuations

Biological organisms exist over a broad temperature range of −15°C to +120°C, where many molecular processes involving DNA depend on the nanoscale properties of the double helix. Here, we present results of extensive molecular dynamics simulations of DNA oligomers at different temperatures. We show that internal basepair conformations are strongly temperature-dependent, particularly in the stretch and opening degrees of freedom whose harmonic fluctuations can be considered the initial steps of the DNA melting pathway. The basepair step elasticity contains a weaker, but detectable, entropic contribution in the roll, tilt, and rise degrees of freedom. To extend the validity of our results to the temperature interval beyond the standard melting transition relevant to extremophiles, we estimate the effects of superhelical stress on the stability of the basepair steps, as computed from the Benham model. We predict that although the average twist decreases with temperature in vitro, the stabilizing external torque in vivo results in an increase of ∼1°/bp (or a superhelical density of Δσ?+0.03$\text{Δ}\sigma ?+0.03$) in the interval 0–100°C. In the final step, we show that the experimentally observed apparent bending persistence length of torsionally unconstrained DNA can be calculated from a hybrid model that accounts for the softening of the double helix and the presence of transient denaturation bubbles. Although the latter dominate the behavior close to the melting transition, the inclusion of helix softening is important around standard physiological temperatures.     

Na2CO3胁迫对星星草叶肉细胞超微结构的影响

利用透射电镜技术对Na2CO3胁迫下星星草叶肉细胞超微结构进行了观察。结果表明：未胁迫的叶肉细胞排列疏松,各种细胞器结构完整,叶绿体含少量淀粉粒和脂质球。轻度盐胁迫（2g/L,4g／LNa2CO3）对叶肉细胞超微结构影响较小。中度盐胁迫（6g／L,8g／L Na2CO3）引起叶肉细胞超微结构的变化,叶绿体类囊体肿胀,基粒紊乱,不含淀粉粒,脂质球数量增加,叶绿体由原来的梭形或椭球形变成圆球状;部分线粒体嵴消失,出现晶体结构;中央大液泡破裂;核逐渐降解。高度盐胁迫（10g／L,12g／LNa2CO3）下,叶绿体片层结构消失,脂质球数量增加,体积变大,被大量的膜片层所包围,叶绿体内、外膜消失,叶肉细胞中看不到叶绿体的存在;膜片层包围线粒体;叶肉细胞中可见大量的泡状结构和膜片层,叶肉细胞死亡。上述结果表明,细胞器特别是叶绿体膜结构的破坏与盐胁迫叶肉细胞最终死亡密切相关。     

Influence of CO2 on Stomatal Numbers

From nine different plant species grown at 1500 cm³ m^-3 CO₂ five responded with a significant increase in stomatal numbers per mm² as compared with plants grown under normal air conditions. Within a collection of twelve french bean cultivars remarkable cultivar differences with regard to the CO₂ enhancement effect on stomatal numbers was found.     

NaCl和Na2CO3对盐地碱蓬胁迫效应的比较

在相同的Na 浓度(如100 mmol/L)下,NaCl处理促进碱蓬植株干重增加,提高根系活力,而Na2CO3处理导致植株干重减少,根系活力降低;与NaCl胁迫相比,Na2CO3胁迫下叶片内Na 含量上升和K 含量下降幅度更大,叶肉细胞质Na 含量和叶内脯氨酸含量增加幅度更大,而V-H -ATPase(液泡膜H -ATPase)和V-H -PPase (液泡膜H -PPase)增加幅度较少;与NaCl胁迫不同,Na2CO3胁迫下SOD(超氧化物歧化酶)活性不是增加,而是降低,与此相一致,MDA(丙二醛)含量大幅度增加.上述结果表明,碱蓬对Na2CO3胁迫的抗性低于对NaCl的抗性,这可能与Na2CO3胁迫引起的Na 、K 离子严重失衡、活性氧清除能力降低有关.     

Effect of angiotensin-II on renal Na/H exchanger-NHE3 and NHE2

The purpose of the present study was to determine the effect of angiotensin II (A-II) on membrane expression of Na⁺/H⁺ exchange isoforms NHE3 and NHE2 in the rat renal cortex. A-II (500 ng/kg per min) was chronically infused into the Sprague-Dawley rats by miniosmotic pump for 7 days. Arterial pressure and circulating plasma A-II level were significantly increased in A-II rats as compared to control rats. pH-dependent uptake of ²²Na⁺ study in the presence of 50 μM HOE-694 revealed that Na⁺ uptake mediated by NHE3 was increased ∼88% in the brush border membrane from renal cortex of A-II-treated rats. Western blotting showed that A-II increased NHE3 immunoreactive protein levels in the brush border membrane of the proximal tubules by 31%. Northern blotting revealed that A-II increased NHE3 mRNA abundance in the renal cortex by 42%. A-II treatment did not alter brush border NHE2 protein abundance in the renal proximal tubules. In conclusion, chronic A-II treatment increases NHE3-mediated Na⁺ uptake by stimulating NHE3 mRNA and protein content.     

The Effect of Methylation of the 6 Oxygen of Guanine on the Structure and Stability of Double Helical DNA

Abstract

The effect of methylation of the 0–6 position of guanine in short segments of double helical DNA has been investigated by molecular mechanical simulations on the sequences d(CGCGCG)₂, d(CGC+AFs-OMG+AF0-CG)₂, d(CGT+AFs-OMG+AF0-CG)₂, d(CGC+AFs-OMC+AF0-CG/(CGCGCG), d(CGC+AFs-OMG+AF0-CG/d(CGTGCG), d(CGCGAATTCGCG)₂ and d(CGCGAATTC+AFs-OMG+AF0-CG)₂. Guanines methylated at the 0–6 position are found to form hydrogen bonds of roughly equal strength to cytosine and thymine. The optimum structure of these modified base pairs are not dramatically different from normal GC pairs, but both involve some bifurcation of the proton donors of cytosine (4NH₂) or thymine (3NH) between the guanine N3 and O6 groups.     

Influence of elevated CO2 and O3 on Betula pendula Roth crown structure

Elevated CO(2) and ozone effects were studied singly and in combination on the crown structure of two Betula pendula clones. Measurements were made at the end of the second fumigation period in an open-top-chamber experiment with 9-year-old trees. Shoot ramification (number of long and short daughter shoots), shoot length, and number of metamers, leaves and buds were measured at four positions in every tree. As a result of increased temperature, trees in chambers had longer shoots and more frequent shoot ramification than control trees not enclosed in chambers. Ozone treatment decreased shoot ramification significantly. Additionally, ozone treatment resulted in an increased number of metamers in one clone. There was no statistically significant interaction between ozone effect and crown position; however, there was a slight tendency for the lower crown to be more affected by ozone. Elevated CO(2) caused a significant increase in the number of long-shoot metamers. Therefore, 2x ambient CO(2) concentration partly ameliorated the negative effect of ozone because the increased number of leaves per shoot counteracted the decreased branching. Although the main effects of elevated ozone and CO(2) were similar in the two clones, slight, statistically insignificant, differences appeared in their responses when interactions with crown position were considered.