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PubMed1998

Pre-evaluation and system optimization of the Elecsys thyroid electrochemiluminescence immunoassays.

We present the results of a pre-evaluation of the thyroid function test free thyroxine, free triiodothyronine and third generation TSH using the Elecsys electrochemiluminescence immunoassay system. A collaborative field study between the development center of the manufacturer and a clinical chemistry laboratory addressed the reliability and comparability of the new Elecsys assays to established methods under clinical laboratory conditions using samples from routine in vitro thyroid testing. Preliminary (reference) formulations of the reagents and several electrochemiluminescent pilot models were used for assay measurements, either in the company's research center or in the clinical setting. The new thyroid assays were compared with the respective Enzymun-Test assays, performed on the ES300 automated immunoassay analyzer. A WHO standard was used for standardization of TSH, whereas an equilibrium dialysis method was applied for free triiodothyronine. The free thyroxine assay was standardized against the Enzymun-Test free thyroxine assay, which had previously been calibrated against equilibrium dialysis. The aim of this field study was to support the optimization of the technology used for Elecsys in an early stage of development and thereby prepare the ground for the adaptation of the immunoassays to the final Elecsys 2010 random access analyzer. A subsequent multicenter evaluation demonstrated that the requirements of routine thyroid testing in terms of reliability were fulfilled by the system.

Electrochemistry↗
PubMed1974

Further analysis of a simple prototypal muscle model near to and far from equilibrium.

The same prototypal model used in a previous paper to illustrate proper construction of a muscle model is modified here with the much more realistic choice e(Deltap) = 10(8) rather than e(Deltap) = 100, where e(Deltap) is the ratio of physiological ATP activity to equilibrium ATP activity. For steady isotonic contractions, the range 1 </= e(Delta) </= 10(4) can be approximated quite well by use of linear terms only in expansions of F (force) and J (ATP flux) in powers of e(Delta) - 1 and v (velocity). This will presumably also be true in most cases of much more complicated models. However, this region is of theoretical interest only (irreversible thermodynamics, etc.) because F and J are very small. In addition, numerical calculations of F and J were made in the region 10(4) </= e(Delta) </= 10(8). The optimal efficiency eta(*) is larger under physiological conditions (about 1%) than at equilibrium by a factor of 2.1 x 10(4). The rate of entropy production is discussed in this connection.

Adenosine Triphosphate↗
PubMed1982

Only the chemotactic subpopulation of human blood monocytes expresses receptors for the chemotactic peptide N-formylmethionyl-leucyl-phenylalanine.

Human peripheral blood monocytes comprise a subpopulation of 20 to 40% that is capable of responding to chemoattractants and a remaining subpopulation that cannot respond. We were able to obtain 99%-pure attractant-responsive monocytes by using a newly constructed separation chamber. The binding of the radioactive chemotactic peptide N-formylmethionyl-leucyl-[3H]phenylalanine to migrating and nonmigrating populations was then studied. The binding was saturable at room temperature in the presence of azide. Saturation occurred at 5 x 10(-8) M, and 50% of the maximal binding was obtained at 10(-8) M, the concentration that induced optimal chemotaxis. The nonmigrating monocytes did not bind the peptide under the same conditions, which shows that at least one reason for a nonresponsiveness to chemotaxin is apparently a lack of receptors. By Scatchard analysis we calculated an equilibrium dissociation constant ranging from 23 to 37 nM; the number of binding sites per cell ranged from 64,000 to 77,000. The binding was very rapid. Fifty percent of the optimal binding occurred at 3.5 min, and equilibrium was reached after 20 to 30 min. Chemotactic deactivation of the monocytes reduced the number of available binding sites by 60%.

Azides↗
PubMed1996

Calcium-mediated DNA adsorption to yeast cells and kinetics of cell transformation by electroporation.

Detailed kinetic data suggest that the direct transfer of plasmid DNA (YEp 351, 5.6 kbp, supercoiled, Mr approximately 3.5 x 10(6)) by membrane electroporation of yeast cells (Saccharomyces cerevisiae, strain AH 215) is mainly due to electrodiffusive processes. The rate-limiting step for the cell transformation, however, is a bimolecular DNA-binding interaction in the cell interior. Both the adsorption of DNA, directly measured with [32P]dCTP DNA, and the number of transformants are collinearly enhanced with increasing total concentrations [Dt] and [Cat] of DNA and of calcium, respectively. At [Cat] = 1 mM, the half-saturation or equilibrium constant is KD = 15 +/- 1 nM at 293 K (20 degrees C). The optimal transformation frequency is TFopt = 4.1 +/- 0.4 X 10(-5) if a single exponential pulse of initial field strength E0 = 4 kV cm-1 and decay time constant tauE = 45 ms is applied at [Dt] = 2.7 nM and 10(8) cells in 0.1 ml. The dependence of TF on [Cat] yields the equilibrium constants KCazero = 1.8 +/- 0.2 mM (in the absence of DNA) and K'Ca (at 2.7 nM DNA), comparable with and derived from electrophoresis data. In yeast cells, too, the appearance of a DNA molecule in its whole length in the cell interior is clearly an after-field event. At Eo = 4.0 kV cm-1 and T = 293 K, the flow coefficient of DNA through the porous membrane patches is Kto = 7.0 +/- 0.7 x 10(3)S-1 and the electrodiffusion of DNA is approximately 10 times more effective than simple diffusion: D/D0 approximately 10.3. The mean radius of these pores is rp = 0.39 +/- 0.05 nm, and the mean number of pores per cell (of size ø approximately 5.5 microns) is Np = 2.2 +/- 0.2 x 10(4). The maximal membrane area that is involved in the electrodiffusive penetration of adsorbed DNA into the outer surface of the electroporated cell membrane patches is only 0.023% of the total cell surface. The surface penetration is followed either by additional electrodiffusive or by passive (after-field) diffusive translocation of the inserted DNA into the cell interior. For practical purposes of optimal transformation efficiency, 1 mM calcium is necessary for sufficient DNA binding and the relatively long pulse duration of 20-40 ms is required to achieve efficient electrodiffusive transport across the cell wall and into the outer surface of electroporated cell membrane patches.

Adsorption↗
PubMedDate not supplied

Codon equilibrium I: Testing for homogeneous equilibrium.

We present theoretical considerations that suggest that synonymous-codon usage might be expected to be close to an equilibrium distribution given a very homogeneous process of silent substitution. By homogeneous we mean that substitution depends only on the two bases involved, so that 12 base-substitution rates completely describe the silent substitution process. We have developed a method of statistically testing for such homogeneous equilibrium and applied it to reported data on the codon usages of different classes of organisms. Weakly expressed bacterial sequences and both mammalian and nonmammalian eukaryotic sequences deviate significantly from a random pattern of codon usage, in the direction of homogeneous equilibrium. On the other hand, highly expressed bacterial sequences do not exhibit homogeneous equilibrium, which may be correlated with recent experimental results showing that they are optimized to accept the most abundant tRNAs. To examine the effect of amino acid replacements on the homogeneous model of silent substitution, we divided the amino acids with degenerate codes into two classes, those with high mutabilities and those with low, and performed the same analysis on bacterial and eukaryotic data sets. The codon sets of the highly mutable class of amino acids are not further from homogeneous equilibrium than are the codon sets of the class with low mutabilities. We also found for the eukaryotic data that these independent classes of codon sets show very similar equilibrium patterns. The various results suggest a high level of uniformity in the process of silent fixation in the different synonymous-codon sets, especially in eukaryotes.

Amino Acid Sequence↗
PubMed1996

Pharmacological characterization of inositol-1,4,5,-trisphosphate binding to membranes from retina and retinal cultures.

Light and excitatory amino acids (EAA) stimulate the phosphoinositide cycle in the vertebrate retina. The regulation of Ca2+ release from intracellular stores by inositol-1,4, 5-trisphosphate (IP3) involves an interaction of this compound with specific receptors. By means of [3H]IP3-specific binding, we studied the kinetic and pharmacological properties of IP3 receptors in the chick retina as well as in primary cultures of neurons and glia from this tissue. The equilibrium time for the binding reaction was 15 min and was optimal at alkaline pH (8.3). IP3 receptor displayed high affinity (K(B) approximately 40 nM) and selectivity for D-IP3, compared to D-IP4 > L-IP3 > D-IP2 > D-IP1. These characteristics were the same in subcellular fractions from outer (P1) and thinner (P2) plexiform layers, binding sites being more abundant in P2 (2.65 pmol/mg protein). IP3 receptors were present in both neuronal and glial cultures, but were concentrated in neuronal cultures. Binding was not affected by ryanodine, or caffeine, related to calcium-induced calcium release (CICR) channels, nor by the endoplasmic reticulum Ca2+ ATPase inhibitor thapsigargin, while heparin affectively inhibited IP3 binding. GSSG and thimerosal increased the affinity of [3H]IP3 binding from IC50 approximately 80 nM to IC50 approximately 40 nM; this effect was reversed by DTT. Binding in zero Ca2+ was decreased by low concentrations of Ca2+ (350 nM). These results suggest that actions of IP3 in the retina are regulated by physiological changes in intracellular pH and Ca2+ concentrations, as well as by the oxidation state of the receptor. Additionally, the presence of IP3 receptors in Müller glia opens the possibility of IP3 participation in nonsynaptic signalling through Ca2+ waves in glial cells.

Analysis of Variance↗
PubMed1998

Temperature titration: a new approach to the thermodynamics of oxygen binding to hemoglobin.

A cell was constructed in order to study hemoglobin's reaction with gaseous ligands. The temperature of the hemoglobin sample is systematically altered within a given temperature range (275-310 degrees K), while the percentage of oxygen in the equilibrating gas is kept constant. The equilibration time of the sample at each temperature step depends on sample concentration, ligand affinity, and absolute temperature; in most cases, the equilibration time is on the order of minutes. The construction of the optical compartment allows the experimenter to vary the optical pathlength using specially designed spacers, thus making it possible to study hemoglobin-ligand interactions over a wide range of protein concentrations (0.1-200 mg/ml). Optical glass is used in the construction of the cuvette in order to optimize its optical stability over a long period of time. At equilibrium the absorption spectrum of the sample is collected and decomposed into the relative contributions of oxy-Hb, deoxy-Hb, and ferric-Hb, thus revealing the fraction of oxyhemoglobin as well as any baseline drifts and protein degradation. Temperature steps of 1 degree K are already sufficient to change the absorption spectra in a significant way. This type of setup is also advantageous in that the experimenter can change the sample at any point (temperature) without having to restart the entire experiment. This makes it possible to study the oxygen binding characteristics of unstable hemoglobins. Analyses of the binding curves obtained with this technique immediately yield the overall oxygen binding constants beta i together with the respective standard enthalpies delta H(i).

Hemoglobins↗
PubMed1990

Sodium-dependent D-aspartate 'binding' is not a measure of presynaptic neuronal uptake sites in an autoradiographic assay.

The binding of D-[3H]aspartate to sections of rat brain was examined in an autoradiographic assay. Binding was entirely dependent on the presence of sodium ions, but not chloride ions, and was optimal at 2 degrees C. D-Aspartate bound rapidly, reached equilibrium within 20 min and remained stable for 45 min. The rate of dissociation was relatively rapid with a t1/2 of 56 s, but was not as fast as anticipated, perhaps because of some sequestration of ligand. Binding had a Kd of 6.8 +/- 1.2 microM and a Bmax of 49.4 +/- 8.6 pmol/mg protein. The high Bmax value may further indicate some sequestration of D-aspartate. L-Glutamate, unlabeled D-aspartate, and D,L-threo-hydroxyaspartate, a potent inhibitor of synaptosomal uptake, each competed for D-[3H]aspartate binding with IC50s of 7.0 +/- 4.3 microM, 5.4 +/- 1.5 microM, and 2.5 +/- 1.0 microM, respectively. N-methyl-D-aspartate (NMDA), quisqualate, and kainate had no affinity for this site. The regional distribution of D-aspartate binding sites was unique and did not conform to the distribution of neuronal uptake sites described by others. Striatal D-aspartate binding was unaffected by unilateral decortication or striatal quinolinic acid lesions. In contrast, binding to NMDA, quisqualate, and kainate receptors was reduced by 80-90% by quinolinate lesions of the striatum. The results of D-aspartate binding after lesions strongly suggest that this site is not associated with either lesioned glutamatergic afferents or intrinsic neurons of the striatum; it may be associated with glia.

Animals↗
PubMed1983

Specific binding of [3H]+/- 2-amino-7-phosphono heptanoic acid to rat brain membranes in vitro.

The specific binding of [3H]+/- 2-amino-7-phosphono heptanoic acid (3H-APH), a potent N-methyl-D-aspartate (NMDA) antagonist, to extensively washed, previously frozen crude mitochondrial fractions of rat brain is described. Binding was optimal at physiological pH and temperature and, in Triscitrate buffer, attained equilibrium within 60 minutes. Scatchard analysis of the equilibrium data for forebrain revealed a single, non-interacting population of binding sites (BMapp = 15 picomoles/mg protein; KDapp = 3.6 uM; Hill coefficient = 0.92, r = 0.99; N = 5). Specific binding of the ligand was readily reversible by unlabeled APH and was absent in peripheral tissues including heart, lung, kidney, liver, spleen and striate muscle and in heat treated brain sonicates. An 8-fold variation in the amount of ligand bound to brain membranes prepared from different regions was observed with binding being greatest in the hippocampal formation and least in the midbrain. Kainic acid, NMDA and aspartic acid exhibited negligible affinity for the [3H]-APH site; in contrast, quisqualic acid, ibotenic acid, glutamatic acid, homocysteic acid and 2-amino-4-phosphono butyric acid were moderately potent displacers. The results indicate that [3H]-APH labels a quisqualate preferring site in vitro. Unlike the receptor labeled by [3H]-glutamate however, [3H]-APH binding was attenuated in the presence of chloride ions suggesting that this ligand may label a subpopulation of excitatory amino acid receptors.

2-Amino-5-phosphonovalerate↗
PubMed1989

Semisynthetic hemoglobin A: reconstitution of functional tetramer from semisynthetic alpha-globin.

The optimal conditions for the semisynthesis of alpha-globin through Staphylococcus aureus V8 protease condensation of a synthetic fragment (alpha 1-30) with the complementary apo fragment (alpha 31-141) in the presence of structure-inducing organic cosolvents and the reconstitution of the functional tetramer from semisynthetic alpha-globin have been investigated. The protease-catalyzed ligation of the complementary apo fragments alpha 1-30 and alpha 31-141 proceeds with very high selectivity at pH 6.0 and 4 degrees C in the presence of 1-propanol as the organic cosolvent. A 30% 1-propanol solution was optimal for the semisynthetic reaction, and the synthetic reaction attained an equilibrium (approximately 50%) in 72 h. The synthetic reaction proceeds smoothly over a wide pH range (pH 5-8). Besides, the semisynthetic system is flexible, and it also proceeded well if trifluoroethanol or 2-propanol was used instead of 1-propanol. However, glycerol, a versatile organic cosolvent used in all other proteosynthetic reactions reported in the literature, was not very efficient as an organic cosolvent in the present synthetic reaction. The semisynthetic alpha-globin prepared with 1-propanol as the organic cosolvent has been reconstituted into HbA. The semisynthetic HbA was then purified by CM-cellulose chromatography. The semisynthetic HbA is indistinguishable from native HbA, in terms of its structural and functional properties. The semisynthetic approach provides the flexibility in protein engineering studies for the incorporation of spectroscopic labels (13C- and/or 15N-labeled amino acids), noncoded amino acids, or unnatural bond functionalities, which at present is not possible with genetic approaches.

Circular Dichroism↗
PubMed1997

Conformational investigation of alpha,beta-dehydropeptides. VIII. N-acetyl-alpha,beta-dehydroamino acid N'-methylamides: conformation and electron density perturbation from infrared and theoretical studies.

The Fourier transform infrared spectra are analyzed in the regions of Vs(N-H), amide I, amide II and Vs(C alpha = C beta) bands for a series of Ac-delta Xaa-NHMe, where delta Xaa = delta Ala, (Z)-delta Abu, (Z)-delta Leu, (Z)-delta Phe and delta Val, to determine the predominant solution conformation of these alpha,beta-dehydropeptide-related molecules and the electron distribution perturbation in their amide bonds. The measurements were performed in dichloromethane (DCM). To confirm and rationalize the assignments, the spectra of the respective series of saturated Ac-Xaa-NHMe, recorded in DCM, and the spectra of these two series of unsaturated and saturated compounds, recorded in acetonitrile, were examined. To help interpret the spectroscopic results, the equilibrium geometrical parameters for some selected amides were used. These were optimized with ab initio methods in the 6-31G** basis set. Each of the dehydroamides studied adopted a C5 structure, which in Ac-delta Ala-NHMe is fully extended and accompanied by the strong C5 hydrogen bond. Interaction with the C alpha = C beta bond lessened the amidic resonance within each of the flanking amide groups. The N-terminal C = O bond was noticeably shorter, both amide bonds were longer than the corresponding bonds in the saturated entities and the N-terminal amide system was distorted. Ac-delta Ala-NHMe constituted an exception. Its C-terminal amide bond was shorter than the standard one and both amide systems were prototypically planar.

Amides↗
PubMed1987

Regulation of nitrogenase activity by oxygen in Azospirillum brasilense and Azospirillum lipoferum.

The nitrogenase activity of the microaerophilic bacteria Azospirillum brasilense and A. lipoferum was completely inhibited by 2.0 kPa of oxygen (approximately 0.02 atm of O2) in equilibrium with the solution. The activity could be partially recovered at optimal oxygen concentrations of 0.2 kPa. In contrast to the NH4+ switch off, no covalent modification of the nitrogenase reductase (Fe protein) was involved, as demonstrated by Western-blotting and 32P-labeling experiments. However, the inhibition of the nitrogenase activity under anaerobic conditions was correlated with covalent modification of the Fe protein. In contrast to the NH4+ switch off, no increase in the cellular glutamine pool and no modification of the glutamine synthetase occurred under anaerobic switch-off conditions. Therefore, a redox signal, independent of the nitrogen control of the cell, may trigger the covalent modification of the nitrogenase reductase of A. brasilense and A. lipoferum.

Amino Acids↗
PubMed1988

Approach to stationary two-dimensional pattern: influence of focusing time and immobiline/carrier ampholytes concentrations.

Horizontal two-dimensional (2-D) electrophoresis with immobilized pH gradients (IPG) in the first dimension for buffer soluble proteins and for complex proteins solubilized in the presence of Nonidet P-40 (Görg et al., Electrophoresis 1987, 8, 45-51), has been extended to analyze basic proteins of yeast cells focused under non-equilibrium and equilibrium conditions. Transient state isoelectric focusing (IEF) in IPG gels revealed sample smearing and background staining, displaying horizontal streaks in the resultant 2-D patterns. Inclusion of 0.5% carrier ampholytes (CA) to the IPG gel (IPG-CA), resulted in the formation of many sharp protein bands after transient state IEF with resultant distinct spots in the 2-D patterns; however, resolution was poor and the gel contained heavy background staining. With prolonged focusing time, background staining disappeared and there was less difference in the final steady state IEF patterns obtained with IPG and IPG-CA. Reduction of the Immobiline concentration to one third the manufacturer's recommended amount did not improve IEF resolution with respect to streaking and background staining under either transient state or equilibrium conditions. In general, spot intensities were less on 2-D gels using diluted IPG gels than with "standard" IPG gels. Optimization of 2-D electrophoresis with IPGs in the first dimension was strongly related to IEF conditions. The use of IPG gels focused to equilibrium should not only improve inter-gel reproducibility and resolution but also the quality of the final 2-D patterns with respect to background staining and horizontal streaking.

Ampholyte Mixtures↗
PubMed1978

Glucose-6-phosphate dehydrogenase of Anabaena sp. Kinetic and molecular properties.

The kinetic and molecular properties of cyanobacterial glucose-6-phosphate dehydrogenase, partly purified from Anabaena sp. ATCC 27893, show that it undergoes relatively slow, reversible transitions between different aggregation states which differ in catalytic activity. Sucrose gradient centrifugation and polyacrylamide gel electrophoresis reveal three pincipal forms, with approximate molecular weights of 120 000 (M1), 240 000 (M2) and 345 000 (M3). The relative catalytic activities are: M1 less than M2 less than M3. In concentrated solutions of the enzyme, the equilibrium favors the more active, oligomeric forms. Dilution in the absence of effectors shifts the equilibrium in favor of the M1 form, with a marked diminution of catalytic activity. This transition is prevented by a substrate, glucose-6-phosphate, and also by glutamine. The other substrate, nicotinamide adenine dinucleotide phosphate (NADP+), and (in crude cell-free extracts) ribulose-1,5-diphosphate are negative effectors, which tend to maintain the enzyme in the M1 form. The equilibrium state between different forms of the enzyme is also strongly dependent on hydrogen ion concentration. Although the optimal pH for catalytic activity is 7.4, dissociation to the hypoactive M1 form is favored at pH values above 7; a pH of 6.5 is optimal for maintenance of the enzyme in the active state. Reduced nicotamide adenine dinucleotide phosphate (NADPH) and adenosine 5'-triphosphate (ATP), inhibit catalytic activity, but do not significantly affect the equilibrium state. The relevance of these findings to the regulation of enzyme activity in vivo is discussed.

Adenosine Triphosphate↗
PubMed1990

The role of oligomerization in regulation of maize phosphoenolpyruvate carboxylase activity. Influence of Mg-PEP and malate on the oligomeric equilibrium of PEP carboxylase.

A purification procedure which yields a near homogenous preparation of phosphoenolpyruvate (PEP) carboxylase from the leaves of Zea mays is reported. The enzyme had a final specific activity of 33.3 micromoles per minute per milligram protein. Size exclusion high performance liquid chromatography and dynamic laser-light scattering spectroscopy showed that PEP carboxylase exists in an equilibrium of aggregates. Enzyme predominantly in the dimeric configuration is less active (when assayed at sub-optimal Mg-PEP concentrations, less than 0.4 millimolar) than when in its tetrameric arrangement. The difference in activity diminishes and disappears as the concentration of the substrate Mg-PEP increases. The substrate drives the equilibrium toward the tetramer, while malate, an inhibitor of PEP carboxylase, shifts the equilibrium toward the dimer. It thus appears that the quaternary structure (oligomeric state) of maize PEP carboxylase can be regulated by the naturally occurring effector molecules Mg-PEP and malate which in turn can control the enzyme's activity.

Chromatography, High Pressure Liquid↗
PubMed1994

Optimal control of antagonistic muscle stiffness during voluntary movements.

This paper presents a study on the control of antagonist muscle stiffness during single-joint arm movements by optimal control theory with a minimal effort criterion. A hierarchical model is developed based on the physiology of the neuromuscular control system and the equilibrium point hypothesis. For point-to-point movements, the model provides predictions on (1) movement trajectory, (2) equilibrium trajectory, (3) muscle control inputs, and (4) antagonist muscle stiffness, as well as other variables. We compared these model predictions to the behavior observed in normal human subjects. The optimal movements capture the major invariant characteristics of voluntary movements, such as a sigmoidal movement trajectory with a bell-shaped velocity profile, an 'N'-shaped equilibrium trajectory, a triphasic burst pattern of muscle control inputs, and a dynamically modulated joint stiffness. The joint stiffness is found to increase in the middle of the movement as a consequence of the triphasic muscle activities. We have also investigated the effects of changes in model parameters on movement control. We found that the movement kinematics and muscle control inputs are strongly influenced by the upper bound of the descending excitation signal that activates motoneuron pools in the spinal cord. Furthermore, a class of movements with scaled velocity profiles can be achieved by tuning the amplitude and duration of this excitation signal. These model predictions agree with a wide body of experimental data obtained from normal human subjects. The results suggest that the control of fast arm movements involves explicit planning for both the equilibrium trajectory and joint stiffness, and that the minimal effort criterion best characterizes the objective of movement planning and control.

Arm↗
PubMed1996

Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides.

A new method of DNA sequencing by hybridization using a microchip containing a set of immobilized oligonucleotides is being developed. A theoretical analysis is presented of the kinetics of DNA hybridization with deoxynucleotide molecules chemically tethered in a polyacrylamide gel layer. The analysis has shown that long-term evolution of the spatial distribution and of the amount of DNA bound in a hybridization cell is governed by "retarded diffusion," i.e., diffusion of the DNA interrupted by repeated association and dissociation with immobile oligonucleotide molecules. Retarded diffusion determines the characteristic time of establishing a final equilibrium state in a cell, i.e., the state with the maximum quantity and a uniform distribution of bound DNA. In the case of cells with the most stable, perfect duplexes, the characteristic time of retarded diffusion (which is proportional to the equilibrium binding constant and to the concentration of binding sites) can be longer than the duration of the real hybridization procedure. This conclusion is indirectly confirmed by the observation of nonuniform fluorescence of labeled DNA in perfect-match hybridization cells (brighter at the edges). For optimal discrimination of perfect duplexes from duplexes with mismatches the hybridization process should be brought to equilibrium under low-temperature nonsaturation conditions for all cells. The kinetic differences between perfect and nonperfect duplexes in the gel allow further improvement in the discrimination through additional washing at low temperature after hybridization.

DNA↗
PubMed1998

Hydration and conformational equilibria of simple hydrophobic and amphiphilic solutes.

We consider whether the continuum model of hydration optimized to reproduce vacuum-to-water transfer free energies simultaneously describes the hydration free energy contributions to conformational equilibria of the same solutes in water. To this end, transfer and conformational free energies of idealized hydrophobic and amphiphilic solutes in water are calculated from explicit water simulations and compared to continuum model predictions. As benchmark hydrophobic solutes, we examine the hydration of linear alkanes from methane through hexane. Amphiphilic solutes were created by adding a charge of +/-1e to a terminal methyl group of butane. We find that phenomenological continuum parameters fit to transfer free energies are significantly different from those fit to conformational free energies of our model solutes. This difference is attributed to continuum model parameters that depend on solute conformation in water, and leads to effective values for the free energy/surface area coefficient and Born radii that best describe conformational equilibrium. In light of these results, we believe that continuum models of hydration optimized to fit transfer free energies do not accurately capture the balance between hydrophobic and electrostatic contributions that determines the solute conformational state in aqueous solution.

Alkanes↗