The denaturation transition of DNA in mixed solvents

The helix-to-coil denaturation transition in DNA has been investigated in mixed solvents at high concentration using ultraviolet light absorption spectroscopy and small-angle neutron scattering. Two solvents have been used: water and ethylene glycol. The "melting" transition temperature was found to be 94 degrees C for 4% mass fraction DNA/d-water and 38 degrees C for 4% mass fraction DNA/d-ethylene glycol. The DNA melting transition temperature was found to vary linearly with the solvent fraction in the mixed solvents case. Deuterated solvents (d-water and d-ethylene glycol) were used to enhance the small-angle neutron scattering signal and 0.1M NaCl (or 0.0058 g/g mass fraction) salt concentration was added to screen charge interactions in all cases. DNA structural information was obtained by small-angle neutron scattering, including a correlation length characteristic of the inter-distance between the hydrogen-containing (desoxyribose sugar-amine base) groups. This correlation length was found to increase from 8.5 to 12.3 A across the melting transition. Ethylene glycol and water mixed solvents were found to mix randomly in the solvation region in the helix phase, but nonideal solvent mixing was found in the melted coil phase. In the coil phase, solvent mixtures are more effective solvating agents than either of the individual solvents. Once melted, DNA coils behave like swollen water-soluble synthetic polymer chains.     

Effect of aliphatic alcohols on the conformation of poly (l-ornithine hydrobromide) as studied by square-pulse and reversing-pulse electric birefringence

The electric birefringence and circular dichroism spectra of poly(l-ornithine hydrobromide) have been measured in ethanol/water, 2-propanol/water and tertiary butyl alcohol/water mixtures of various compositions. This charged polypeptide underwent a transition from the coil conformation to the helical conformation at high alcohol content in every case tested. Anomalous birefringence signals, indicative of a field-induced helix-to-coil transition. were observed at high electric fields only in the case of ethanol/water mixtures. The reversing-pulse electric birefringence of this polypeptide has been studied in ethanol/water mixtures and in neutral aqueous solution. Upon rapid reversal of the pulse field, no transient could be observed. This confirms that the electric-field orientation of poly(l-ornithine hydrobromide) results predominantly from the contribution of the counterion-induced dipole moment, regardless of its molecular conformations. It is very probable that the backbone permanent dipole moment of the helical conformation is largely suppressed by the counterion-induced dipole moment in the ionized form.     

Influence of isopropanol-water solvent mixtures on the conformation of poly-L-lysine

The helix–coil transition of poly-L -lysine (PLL) in water–isopropanol solvent mixtures has been investigated at room temperature by circular dichroism measurements. Within the range of 70%–80% isopropanol concentration (by volume), the polymer undergoes a sharp transition, characterized by the formation of a fully charged α-helical structure. On the basis of some experimental evidence the role of the organic component in solution appears more complicated than that of strengthening the intramolecular hydrogen bonds in the polymer. By analogy with the distribution of the components of alcohol–water mixtures in simple ionic systems, it is thought that only an high co-solvent concentration brings about an extensive and possible cooperative depletion of the clusters of firmly-bound water molecules in the domain of the polylelectrolyte, favoring the transition to the α-helical structure. On the other hand, CD spectral patterns show that the addition of NaCl in the alcohol-rich–water mixtures of charged poly-L -lysine gives rise to a transition from the α-helical to a β-structures conversion obeys a first-order rate law at all times, with a rate constant dependent on solvent composition and ionic strength. In these conditions, the rate of the process is close to that found for the thermally induced α–β transition. Higher polymer concentration and/or ionic strength cause a phase separation of β-PLL, suggesting that in this case interchain reactions (where hydrogen bonding should play the major role) predominate. Titration experiments on charged α-helical poly-L -lysine in 85% or 90% isopropanol mixtures confirm the occurrence of a conformational transition, which takes place within a degree of dissociation α of 0.2–0.75. The transition is accompanied by a visible turbidity, which increases as the titration proceeds. Implications of the solvent distribution around the macroion on the observed conformational phenomena are also discussed.     

Fluoroquinacrine binding to nucleic acids: Investigation of the 19F-nmr,optical, and fluorescence properties in the presence of DNA,poly(A), and tRNA

The interaction of fluoroquinacrine, 3-fluoro-7-chloro-9-(diethylamino-1-methylbutyl-amino)acridine, with poly(A), DNA, and tRNA has been investigated by monitoring changes in the ¹⁹F-nmr properties, the fluorescence, and the optical absorbance of the drug. The changes in the properties of fluoroquinacrine in the presence of nucleic acids are similar to those observed for quinacrine and suggest that the drugs bind in a similar fashion. The molecular dynamics of fluoroquinacrine bound to nucleic acids were determined by interpreting the data from a number of different nmr relaxation experiments with a two-correlation-time model. The two motions are the long-range bending motion of the drug-nucleic acid complex and the sliding of the drug between the base pairs. Both dipolar and chemical shift anisotropy contributions to the nmr relaxation parameters were taken into consideration. The binding of fluoroquinacrine to tRNA appears to be different from that observed for binding to DNA. Optical absorbance and ¹⁹F-nmr were also used to examine the helix-to-coil transitions of the drug–nucleic acid complexes. In the DNA complex, the ¹⁹F chemical shift changes parallel the absorption changes that occur during the transition. ¹⁹F-nmr and absorption show that the drug–tRNA complexes undergo a cooperative helix-to-coil transition, with the drug binding sites melting when the tRNA is 70% denatured.     

Electric birefringence of ionized polypeptides in solution and the effect of high electric fields on the helix-coil transition

Electric birefringence and circular dichroism measurements have been made on solutions of two po!y (L-lysine) homologs. The specific Kerr constant and the molar ellipticity at 222 nm of poly (L-alpha, gamma-diaminobutyric acid hydrochloride) in methanol/water mixtures underwent an abrupt change between 75 and 80 vol% methanol at 25 degrees C, corresponding to a solvent-induced helix-coil transition. On the helix side of the transition region, i.e., between 78 and 80 vol% methanol, anomalous birefringence transients indicative of field-induced helix-to-coil transition were observed at high fields. In the case of poly (L-ornithine hydrobromide) in methanol/water mixtures, a helix-coil transition was induced between 93 and 98 vol% methanol and anomalous birefringence transients were observed between 96 and 98 vol% methanol. The double logarithmic plots of the steady-state specific birefringence versus the square of field strength for various solvent compositions and polymer concentrations could be superimposed on one another by horizontal and vertical shifts, except for the range where anomalous birefringence transients were observed. This enabled us to estimate the threshold field strength.     

Enthalpy of helix-coil transition from heat of solutions. 3. Poly-N- -carbobenzoxy-L-ornithine and poly-N- -carbobenzoxy-L- , -aminobutyric acid

The helix-to-coil transition in dichloroethane–dichloroacetic acid (DCE–DCA) mixtures for poly-N-δ-carbobenzoxy-L -ornithine (PCBO) and for poly-N-γ-carbobenzoxy-L α,γ-aminobutyric acid (PCBBA) have been studied by ORD and the “heat of solution” method. The results provide strong evidence for the existence of a very specific side-chain/side-chain interaction in PCBBA, which is discussed on the basis of a detailed structural model. The main sources of enthalpy and entropy changes in helix-coil transitions of uncharged homopolypeptides in DCE–DCA mixtures are also discussed briefly.     

Kinetics of oxidation of ferrocene by tris-1,10-phenanthrolinecobalt(III) in t-butyl alcoholwater and acetonewater mixtures

Rate constants and activation parameters (ΔH^≠ and ΔS^≠)are reported for the oxidation of ferrocene by the tris-1,10-phenanthrolinecobalt(III) cation in t-butyl alcoholwater and in acetonewater solvent mixtures. Solvent effects on reactivity trends for these systems, for this same reaction in methanolwater mixtures, and for cobalt(II)-catalysed racemisation of Co(phen)_3³⁺ in t-butyl alcoholwater solvent mixtures are analysed into initial state and transition state contributions. The dependences of solubilities on solvent composition for ferrocene and for [Co(phen)₃](ClO₄)₃ in methanol, t-butyl alcohol, and acetonewater mixtures are also reported; these results are needed in order to establish solvent effects on the initial states of the reactions studied.     

Mechanochemical study of wet-spun lithium-DNA fibers

Uniform LiDNA fiber specimens of nearly 20 m length have been prepared with a wet-spinning method developed by the author. Samples immersed in the spinning bath (80% ethyl alcohol containing 0.4M LiCl) have been subjected to mechanochemical study involving stretching, relaxation, and contraction measurements. A special technique was developed to transfer the sample from the Teflon-coated cylinder used in spinning to the sample column of the mechanochemical apparatus without stretching or removing the sample from the spinning bath. Force–strain curves of samples consisting of two fiber bundles showed an initial region of low slope followed by a region of high slope and a second region of low slope up to rupture. Some thicker specimens showed an aging effect which abolished the initial low-slope region and was interpreted as indicative of crystallization. Force–strain curves of two-bundle samples showed a strong influence of temperature with a complete loss of tensile strength of the LiDNA fibers in the spinning bath at about 55°C. Furthermore, samples at zero strain exhibited a contractile force when subjected to temperatures above about 40°C; the contractile process was pronounced with samples kept above 48°C. On contraction these samples obtained a zero-force length 20–30% of the original. These data are taken as evidence for a helix-to-coil transition occurring in the DNA, the low melting temperature being caused by the chemical influence of the ambient aqueous alcohol–LiCl bath.     

Raman studies of the helix-to-coil transition in poly-L-glutamic acid and poly-L-ornithine

The conformational transitions in water and in the solid state of poly-L -glutamic acid (PGA) and poly-L -ornithine (PO) have been studied by Raman spectroscopy. The Raman spectra of PGA, PO, and the monomer, dimer, and trimer of PGA in aqueous solutions and solid state are presented. The Raman spectral changes of PGA and PO were followed through the helix-to-coil transition induced by p^H, temperature, and solvent composition. A hyperchromic shift in the intensity of the amide III line accompanying the helix-to-coil transition was observed. This hyperchromic intensity shift occurs abruptly as a function of p^H but more slowly with heat denaturation of the alpha helix indicating that the Raman spectrum is sensitive to the transition mechanism. The high-temperature coil and the charged coil may have different conformations as evidenced by different amide III frequencies but similar intensities in these two conformations.     

Structural stability of DNA in nonaqueous solvents

One of the defining physicochemical features of DNA in aqueous solution is its ability to maintain a double-helical structure and for this structure to undergo a cooperative, heat-induced denaturation (melting). Herein we show that a 21-mer synthetic DNA can form and maintain such a duplex structure not only in water but even in 99% glycerol; moreover, this double-helical structure reversibly and cooperatively melts in that solvent, with a T(m) value of some 30 degrees lower than in water. Two much larger, natural DNAs, from calf thymus and salmon testes, exhibit similar behavior in glycerol. All three DNAs can also sustain a double-helical structure in 99% ethylene glycol, although its thermostability (as reflected by the melting temperature) is some 20 degrees lower than in glycerol. In contrast, no duplex structure of any of the DNAs was detected in 99% formamide, methanol, or DMSO. This solvent trend resembles that previously observed in studies of protein structure and folding and underscores the importance of hydrophobic interactions in both protein and DNA structure and stability. Our findings suggest that water may not be unique as a suitable medium not only for protein structure but also for that of nucleic acids.     

Role of the heat capacity change in understanding and modeling melting thermodynamics of complementary duplexes containing standard and nucleobase-modified LNA

Melting thermodynamic data obtained by differential scanning calorimetry (DSC) are reported for 43 duplexed oligonucleotides containing one or more locked nucleic acid (LNA) substitutions. The measured heat capacity change (ΔC(p)) for the helix-to-coil transition is used to compute the changes in enthalpy and entropy for melting of an LNA-bearing duplex at the T(m) of its corresponding isosequential unmodified DNA duplex to allow rigorous thermodynamic analysis of the stability enhancements provided by LNA substitutions. Contrary to previous studies, our analysis shows that the origin of the improved stability is almost exclusively a net reduction (ΔΔS° < 0) in the entropy gain accompanying the helix-to-coil transition, with the magnitude of the reduction dependent on the type of nucleobase and its base pairing properties. This knowledge and our average measured value for ΔC(p) of 42 ± 11 cal mol(-1) K(-1) bp(-1) are then used to derive a new model that accurately predicts melting thermodynamics and the increased melting temperature (ΔT(m)) of heteroduplexes formed between an unmodified DNA strand and a complementary strand containing any number and configuration of standard LNA nucleotides A, T, C, and G. This single-base thermodynamic (SBT) model requires only four entropy-related parameters in addition to ΔC(p). Finally, DSC data for 20 duplexes containing the nucleobase-modified LNAs 2-aminoadenine (D) and 2-thiothymine (H) are reported and used to determine SBT model parameters for D and H. The data and model suggest that along with the greater stability enhancement provided by D and H bases relative to their corresponding A and T analogues, the unique pseudocomplementary properties of D-H base pairs may make their use appealing for in vitro and in vivo applications.     

Enthalpy of helix-coil transitions from heats of solution. II. Poly-epsilon-carbobenzoxy-L-lysine and copolymers with L-phenylalanine

The heal of solution of Poly-ε-carbobenzoxy-L -lysine and of a series of its copolymers with phenylalanine was measured as a function of solvent composition. The enthalpy change of the helix-to-coil transition was estimated for the various cases. The previous findings that side chains do not greatly affect the transition enthalpy is confirmed also in cases having much larger differences in helix stability.     

Structural organization of double-stranded RNA from killer yeasts Saccharomyces cerevisiae by the thermal denaturation method

The thermal denaturation method for studying the structural organization of double-stranded RNA (dsRNA) from virus-like particles of killer yeasts Saccharomyces cerevisiae was used. High resolution derivative denaturation profiles of total dsRNA and its L- and M-types were obtained. Comparative analysis of these data with those on phage DNA denaturation demonstrated that the processes of denaturation of dsRNA and phage DNA were identical in quality. Increase of thermostability, interval of thermal denaturation and width of local helix-to-coil transitions in dsRNA as compared with phage DNA are caused by the differences of corresponding thermodynamic parameters. Derivative denaturation profiles of L- and M-types of yeasts dsRNA were shown to have certain identical local transitions. Low melting transition, consisting of three local thermalites, is due to the denaturation of AU-rich region (about 200 n.b.p.) in M-dsRNA.     

Interactions of two cytotoxic organotin(IV) compounds with calf thymus DNA

The reactions with DNA of two antitumor active organotin(IV) compounds, the dimer of bis[(di-n-butyl 3,6-dioxaheptanoato)tin] (C(52)H(108)Sn(4)O(1) x 2H(2)O), compound 1, and tri-n-butyltin 3,6,9-trioxodecanoate (C(19)H(40)SnO(5) x 1/2H(2)O), compound 2, were analysed by circular dichroism, DNA melting experiments and gel mobility shift assays. It is found that both complexes modify only slightly the B-type circular dichroism spectroscopy (CD) spectrum of calf thymus DNA. On the other hand, both complexes were found to affect significantly the parameters of the thermally induced helix-to-coil transition. Addition of 1 or 2 to calf thymus DNA samples does not favor DNA renaturation after melting ruling out formation of interstrand crosslinks. Moreover, the effects of both compounds on plasmid DNA gel mobility were investigated. From the analysis of the present results it is inferred that both organotin(IV) compounds do interact with DNA, probably at the level of the phosphate groups.     

Moistening Liquid-Dependent De-aggregation of Microcrystalline Cellulose and Its Impact on Pellet Formation by Extrusion–Spheronization

The wet-state particle size of microcrystalline cellulose (MCC) dispersed in different moistening liquids was characterized to elucidate the effect of moistening liquid type on the extent of MCC particle de-aggregation. Cohesive strength of moistened MCC masses was also assessed and pellet production by extrusion–spheronization attempted. MCC dispersed in alcohol or water–alcohol mixtures with higher alcohol proportions generally had larger particle sizes. Moistened mass cohesive strength decreased and poorer quality pellets were obtained when water–alcohol mixtures with higher alcohol proportions were used as the moistening liquid. MCC comprise aggregates of small sub-units held together by hydrogen bonds. As MCC particle de-aggregation involves hydrogen bond breaking, moistening liquids with lower polarity, such as water–alcohol mixtures with higher alcohol proportions, induced lesser de-aggregation and yielded MCC with larger particle sizes. When such water–alcohol mixtures were employed during extrusion–spheronization with MCC, the larger particle size of MCC and lower surface tension of the moistening liquid gave rise to moistened masses with lower cohesive strength. During pelletization, agglomerate growth by coalescence and closer packing of components by particle rearrangement would be limited. Thus, weaker, less spherical pellets with smaller size and wider size distribution were produced.     

Physical properties of insect cuticular hydrocarbons: Model mixtures and lipid interactions

Cuticular lipids include a diverse array of hydrophobic molecules that play an important role in the water economy of terrestrial arthropods. Their waterproofing abilities are believed to depend largely on their physical properties, but little is known about interactions between different surface lipids to determine the phase behavior of the total lipid mixture. I examined the biophysical properties of binary hydrocarbon mixtures, as a model for interactions between different epicuticular lipids of insects. The midpoint of the solid/liquid phase transition (T_m) for mixtures of n-alkanes differing in chain length equaled the weighted average of the T_ms of the component lipids. This was also true for n-alkane-methylalkane mixtures. However, alkane-alkene mixtures melted at temperatures up to 17°C above the temperature predicted from the weighted average of component lipid T_m values. Hydrocarbon mixtures did not exhibit biphasic melting transitions indicative of independent phase behavior of the component lipids. Instead, melting occurred continuously, over a broader temperature range than pure hydrocarbons.     

Human tropoelastin sequence: Dynamics of polypeptide coded by exon 6 in solution

Calorimetric studies were performed on exon 6 in powdered form and in solution [water and 2,2,2‐trifluoroethanol (TFE), a structure‐inducing solvent or cosolvent]. Dynamic dielectric spectroscopy (DDS) analyses were realized in water and 20% TFE. The major role of solvent–peptide organization is evidenced with these techniques. Calorimetric measurements reveal the structural water organization around the polypeptide as well as the presence of hydrophobic interactions in TFE solution. Dielectric measurements showed for exon 6/water a decrease of relaxations times of bulk solvent implying a faster dynamics with a slight increase of the activation entropy, suggesting that exon 6 probably creates disorder within the solvent. For TFE/water mixtures, an influence of exon 6 on its environment was seen with a relaxation associated with the exon 6/solvent interactions reinforced by storage of 72 h. Finally, exon 6/solvent interactions were clearly observed with additionof TFE. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 943–952, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

DNA melting temperatures and renaturation rates in concentrated alkylammonium salt solutions

DNA melting temperatures and renaturation rates have been determined for Me₂Et₂NBr and a series of RMe₃NBr and REt₃NBr solvents where R is a linear hydrocarbon chain. The point of independence of DNA melting temperature on base composition has been investigated for each solvent system. Renaturation rates are compared with those found in other concentrated salt solutions. Solvent mixtures which accelerate DNA renaturation have also been investigated.     

Effect of low-molecular amines on DNA conformation and stability of the double helix]

Interaction of low-molecular amines (cystamine, cysteamine, cystaphose, asparagine, beta-alanine) with DNA was studied. The amines change the positive circular dichroism (CD) band of DNA as well as temperature and range width of melting. Effect of amines on DNA depends on ionic strength of the solvent, concentration and structure of the ligand. Monamines cause destabilization of DNA double helix followed by stabilization as ligand concentration increases. At concentrations stabilizing the double helix DNA conformation undergoes transition from the B- to C-form. The results obtained enable to relate the stabilizing effect of low-molecular amines and conformational B leads to C-transition to the non-specific interaction of ligand amino groups with DNA phosphates, and the destabilizing effect of monoamines of low concentrations to their interaction with bases, mainly in the denaturated sites of DNA. It is proposed that a stronger effectiveness of amines as compared to monovalent metals in the conformational shift of DNA towards the C-form is due to the additional effect of disturbance of hydrophobic interactions in DNA double helix.     

Human platelet P-235, a talin-like actin binding protein, binds selectively to mixed lipid bilayers

The interaction of platelet talin (P-235) with mixtures of dimyristoylphosphatidylcholine (DMPC), dimyristoylphosphatidylglycerol (DMPG) and dimyristoylphosphatidylserine (DMPS) as well as with pure lipids was studied in reconstituted lipid bilayers. Incorporation of platelet talin into vesicles was achieved by self-assembly during cycles of freeze-thawing of co-dispersions containing vesicles and the purified protein. The yield of protein incorporation as a function of lipid composition was determined by measuring the protein/lipid ratio using protein assay, phosphate determination and gel electrophoresis in parallel. Protein-lipid interactions are monitored by high sensitive differential scanning calorimetry (DSC) measuring (i) the shifts of transition states delta Ts* and delta Tl*, where Ts represents the solidus line, the onset of lipid chain melting, and Tl the liquidus line, the endpoint of chain melting, and (ii) the heats of transition. Cytoplasmic talin differs from a membrane bound form by its ability and mode of lipid interaction. The latter partially penetrates into the hydrophobic region of the bilayer, which renders a low incorporation rate even into neutral lipids. This interaction is greatly enhanced in the presence of charged lipids: a marked shift of Tl occurs due to a selective electrostatic interaction of the protein with the membrane surface. Evidence for a selective binding is also provided by Fourier transform infrared spectroscopy (FTIR). Right-side-out oriented platelet talin can be cleaved by proteinases, which truncate the extrinsic electrostatic binding domain but not the hydrophobic. In addition, reconstituted platelet talin, like in vivo, can be cleaved by thrombin. The interaction of cytoplasmic platelet talin with lipid bilayers is purely electrostatic. Our data suggest that protein reconstitution by freeze-thawing is an equilibrium process and that the protein distribution between the membrane and water is determined by the Nernst distribution law. Consequently, the work of protein transfer from water into the bilayer can be measured as a function of charged lipids.