Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy

A revision (C35r) to the CHARMM ether force field is shown to reproduce experimentally observed conformational populations of dimethoxyethane. Molecular dynamics simulations of 9, 18, 27, and 36-mers of polyethylene oxide (PEO) and 27-mers of polyethylene glycol (PEG) in water based on C35r yield a persistence length λ = 3.7 Å, in quantitative agreement with experimentally obtained values of 3.7 Å for PEO and 3.8 Å for PEG; agreement with experimental values for hydrodynamic radii of comparably sized PEG is also excellent. The exponent υ relating the radius of gyration and molecular weight of PEO from the simulations equals 0.515 ± 0.023, consistent with experimental observations that low molecular weight PEG behaves as an ideal chain. The shape anisotropy of hydrated PEO is 2.59:1.44:1.00. The dimension of the middle length for each of the polymers nearly equals the hydrodynamic radius R_h obtained from diffusion measurements in solution. This explains the correspondence of R_h and R_p, the pore radius of membrane channels: a polymer such as PEG diffuses with its long axis parallel to the membrane channel, and passes through the channel without substantial distortion.     

Association of hydrophobically-modified poly(ethylene glycol) with fusogenic liposomes

We present results on using cooperative interactions to shield liposomes by incorporating multiple hydrophobic anchoring sites on polyethylene glycol (PEG) polymers. The hydrophobically-modified PEGs (HMPEGs) are comb-graft polymers with strictly alternating monodisperse PEG blocks (M_w=6, 12, or 35 kDa) bonded to C18 stearylamide hydrophobes. Cooperativity is varied by changing the degree of oligomerization at a constant ratio of PEG to stearylamide. Fusogenic liposomes prepared from N-C12-DOPE:DOPC 7:3 (mol:mol) were equilibrated with HMPEGs. Affinity for polymer association to liposomes increases with the degree of oligomerization; equilibrium constants (given as surface coverage per equilibrium concentration of free polymer) for 6 kDa PEG increased from 6.1±0.8 (mg/m²)/(mg/ml) for 2.5 loops to 78.1±12.2 (mg/m²)/(mg/ml) for 13 loops. In contrast, the equilibrium constant for distearoylphosphatidylethanolamine-poly(ethylene glycol) (DSPE-PEG5k) was 0.4±0.1 (mg/m²)/(mg/ml).The multi-loop HMPEGs demonstrate higher levels of protection from complement binding than DSPE-PEG5k. Greater protection does not correlate with binding strength alone. The best shielding was by HMPEG6k-DP3 (with three 6 kDa PEG loops), suggesting that PEG chains with adequate surface mobility provide optimal protection from complement opsonization. Complement binding at 30 min and 12 h demonstrates that protection by multi-looped PEGs is constant whereas DSPE-PEG5k initially protects but presumably partitions off of the surface at longer times.     

Electrophoresis of periodontal pathogens in poly(ethyleneoxide) solutions with uncoated capillary

Periodontitis is a prevalent inflammatory disease caused by different species of anaerobic bacteria such as Porphyromonas gingivalis (P.g), Treponema denticola (T.d), and Tannerella forsythia (T.f). We compared the separation result of DNA ladders in hydroxyethyl cellulose, poly(ethyleneoxide) (PEO), and polyethylene glycol and analyzed the effect of polymer concentration, electric field, and temperature of the background electrolyte on the separation performance. Results demonstrated that there was a linear relationship (R = 0.942) for 100 to 700 bp of DNA and its migration time. Finally, the polymerase chain reaction products of P.g, T.d, and T.f were successfully identified within 8.5 min in 0.5% PEO with uncoated capillary.     

A Guide to Establishing Water Potential of Aqueous Two-Phase Solutions (Polyethylene Glycol plus Dextran) by Amendment with Mannitol

A practical guide to calculating the mannitol (MAN) amendment required to achieve the desired water potential (Ψ) of polyethylene glycol/dextran (PEG/DEX) aqueous two-phase systems for protoplast purification is presented. The empirically generated equation Ψ = 305[PEG′]²[MAN] + 0.74[PEG′][MAN]T − 103[PEG′][MAN] + 5.6[PEG′]²T − 623[PEG′]² − 0.25[PEG′]T + 12.7[PEG′] − 0.078[MAN]T − 22.75[MAN]accurately predicts experimental Ψ (in bars). [PEG′] indicates the presence of DEX where [DEX] = [PEG]/(0.6−0.4[PEG]). The equation is applicable for these ranges: [PEG′] from 0.047 to 0.13 gram per gram H₂O; [MAN] from 0 to 0.7 molal; T from 4.5 to 40°C. Actual Ψ should differ from derived Ψ by no more than 8% for the least negative values to 4% for the most negative values. The Ψ for solutions of MAN, of PEG, and of DEX were also determined. Equations to fit data for each were generated. Analyses indicated a significant synergistic effect on Ψ when MAN is added to PEG/DEX and, at certain concentrations, between PEG and DEX.     

Poly(ethyleneoxide) for high resolution and high-speed separation of DNA by capillary electrophoresis

Capillary electrophoresis (CE) with polyacrylamide gels has already been demonstrated to allow single-base resolution of single-stranded DNA. However, linear polyacrylamide is not an ideal matrix because of a high viscosity and difficulties in preparing the polymer with well defined pore sizes. Alternatively, poly(ethyleneoxide) (PEO) with a large range of molecular masses from 300 000 to 8 000 000 is available commercially. In addition, it is easy to prepare homogeneous solutions to provide highly reproducible separation performance with sufficient resolution. Single-base resolution of double-stranded DNA between 123 and 124 base pairs can be achieved by the use of homogeneous matrices prepared from PEO (2.5% M_r 8 000 000), and even better resolution is achieved by using mixed polymer matrices. With further work, it should be possible to change the fractions and the total amounts of polymers to achieve even higher resolution for different samples with different size ranges of fragments. Another advantage of mixed polymer matrices is that relatively high resolution can be obtained while maintaining a relatively low viscosity compared to linear polyacrylamide with identical contents of formamide and urea, which makes it easier to fill these matrices into small capillaries.     

The osmotic potential of polyethylene glycol 6000

Osmotic potential (ψ_s) of aqueous solutions of polyethylene glycol 6000 (PEG-6000) was curvilinearly related to concentration. At given concentrations, ψ_s increased linearly with temperature. The effects of concentration and temperature on ψ_s of PEG-6000 solutions differ from those for most salts and sugars and apparently are related to structural changes in the PEG polymer. Measurements of ψ_s with thermocouple psychrometers are more negative than those with a vapor pressure osmometer, with the psychrometer probably giving the more nearly correct ψ_s for bulk solutions. An empirical equation permits calculation of ψ_s from known concentrations of PEG-6000 over a temperature range of 15 to 35 C. Viscometery and gravimetric analysis are convenient methods by which the concentrations of PEG-6000 solutions may be measured.     

Water Relations of Growing Maize Coleoptiles : Comparison between Mannitol and Polyethylene Glycol 6000 as External Osmotica for Adjusting Turgor Pressure

Water relations of growing segments of maize (Zea mays L.) coleoptiles were investigated with osmotic methods using either mannitol (MAN) or polyethylene glycol 6000 (PEG) as external osmotica. Segments were incubated in MAN or PEG solutions at 0 to - 15 bar water potential (Ψ_o) and the effects were compared on elongation growth, osmotic shrinkage, cell sap osmolality (OC), and osmotic pressure (π_i). The nonpenetrating osmoticum PEG affects π_i in agreement with Boyle-Mariotte's law, i.e. the segments behave in principle as ideal osmometers. There is no osmotic adjustment in the Ψ_o range permitting growth (0 to −5 bar) nor in the Ψ_o range inducing osmotic shrinkage (−5 to −10 bar). Promoting growth by auxin (IAA) has no effect on the osmotic behavior of the tissue toward PEG. In contrast to PEG, MAN produces an apparent increase in π_i accompanied by anomalous effects on segment elongation and shrinkage leading to a lower value for Ψ_o which establishes a growth rate of zero and to an apparent recovery from osmotic shrinkage after 2 hours of incubation. These effects can be quantitatively attributed to uptake of MAN into the tissue. MAN is taken up into the apoplastic space and the symplast as revealed by a large temperature-dependent component of MAN uptake. It is concluded that MAN, in contrast to PEG, is unsuitable as an extemal osmoticum for the quantitative determination of water relations of growing maize coleoptiles.     

Poly(ethylene glycol)-induced and temperature-dependent phase separation in fluid binary phospholipid membranes.

Exclusion of the strongly hygroscopic polymer, poly(ethylene glycol) (PEG), from the surface of phosphatidylcholine liposomes results in an osmotic imbalance between the hydration layer of the liposome surface and the bulk polymer solution, thus causing a partial dehydration of the phospholipid polar headgroups. PEG (average molecular weight of 6000 and in concentrations ranging from 5 to 20%, w/w) was added to the outside of large unilamellar liposomes (LUVs). This leads to, in addition to the dehydration of the outer monolayer, an osmotically driven water outflow and shrinkage of liposomes. Under these conditions phase separation of the fluorescent lipid 1-palmitoyl-2[6-(pyren-1-yl)]decanoyl-sn-glycero-3-phosphocholine (PPDPC) embedded in various phosphatidylcholine matrices was observed, evident as an increase in the excimer-to-monomer fluorescence intensity ratio (IE/IM). Enhanced segregation of the fluorescent lipid was seen upon increasing and equal concentrations of PEG both inside and outside of the LUVs, revealing that osmotic gradient across the membrane is not required, and phase separation results from the dehydration of the lipid. Importantly, phase separation of PPDPC could be induced by PEG also in binary mixtures with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), for which temperature-induced phase segregation of the fluorescent lipid below Tm was otherwise not achieved. In the different lipid matrices the segregation of PPDPC caused by PEG was abolished above characteristic temperatures T0 well above their respective main phase transition temperatures Tm. For 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), DMPC, SOPC, and POPC, T0 was observed at approximately 50, 32, 24, and 20 degrees C, respectively. Notably, the observed phase separation of PPDPC cannot be accounted for the 1 degree C increase in Tm for DMPC or for the increase by 0.5 degrees C for DPPC observed in the presence of 20% (w/w) PEG. At a given PEG concentration maximal increase in IE/IM (correlating to the extent of segregation of PPDPC in the different lipid matrices) decreased in the sequence 1,2-dihexadecyl-sn-glycero-3-phosphocholine (DHPC) > DPPC > DMPC > SOPC > POPC, whereas no evidence for phase separation in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) LUV was observed (Lehtonen and Kinnunen, 1994, Biophys. J. 66: 1981-1990). Our results indicate that PEG-induced dehydration of liposomal membranes provides the driving force for the segregation of the pyrene lipid.(ABSTRACT TRUNCATED AT 400 WORDS)     

Inhibition of Gibberellic Acid-induced alpha-Amylase Formation by Polyethylene Glycol and Mannitol

Both polyethylene glycol (PEG) and mannitol inhibit gibberellic acid-induced α-amylase production in barley aleurone layers. The effect of the osmotic solution is on enzyme synthesis rather than α-amylase secretion. The inhibition of α-amylase synthesis does not appear to be mediated via an indirect effect on respiration or protein synthesis. Rather it seems that the osmotic solutions reduce the extent of proteolysis of the stored aleurone grain protein thus making available less substrate for new protein synthesis.     

Size‐selective DNA separation: Recovery spectra help determine the sodium chloride (NaCl) and polyethylene glycol (PEG) concentrations required

In the presence of sodium chloride (NaCl), DNA fragments can be size‐selectively separated by varying the final concentration of polyethylene glycol (PEG). This separation strategy in combination with the use of paramagnetic particles provides a valuable platform for achieving the desired DNA size interval, which is important in automated library preparation for high‐throughput DNA sequencing. Here, we report the establishment of recovery spectra of DNA fragments that enable the determination of suitable NaCl and PEG concentrations for size‐selective separation. Firstly, at a given NaCl concentration, the recovery equation was obtained by fitting the DNA recovery ratios versus the PEG concentrations using the logistic function to determine the required parameters. Secondly, the slope function of the recovery equation was achieved by deducing its first derivative. Therefore, the recovery spectrum can be generated using the slope function based on those parameters. According to the recovery spectra of different length DNA fragments, suitable NaCl and PEG concentrations can be determined, respectively, by calculating their resolution values and recovery ratios. The strategy was effectively applied to the size‐selective separation of 532‐, 400‐, and 307‐bp fragments at the selected reagent concentrations with recoveries of 96.9, 64.7, and 85.9%, respectively. Our method enables good predictions of NaCl and PEG concentrations for size‐selective DNA separation.     

Nonosmotic Effects of Polyethylene Glycols upon Sodium Transport and Sodium-Potassium Selectivity by Rice Roots

Addition of polyethylene glycol (PEG) as an osmotic agent (at −230 kilopascals) dramatically lessened the toxicity of NaCl (at 50 moles per cubic meter) to rice (Oryza sativa L.) seedlings. This was explained by a reduction in the uptake of NaCl. This reduction was much greater than could be accounted for by the lowered transpiration rate resulting from the solute potential changes due to the PEG.

Low concentrations of PEG (−33 kilopascals and less) had no effect upon transpiration rate but reduced sodium uptake (from 10-50 moles per cubic meter NaCl) by up to 80%. PEG (at −33 kilopascals) also reduced chloride uptake but had no effect upon the uptake of potassium from low (0.5-2.0 moles per cubic meter) external concentrations. However, the increased uptake of potassium occurring between 2 and 10 moles per cubic meter external concentration was abolished by PEG. Similar concentrations of mannitol had no effect upon sodium uptake in rice. PEG, in similar conditions, had much less effect upon sodium uptake by the more salt-resistant species, barley.

²²Na studies showed that PEG reduced the transport of sodium from root to shoot, but had a long half time for maximal effect (several days).

¹⁴C-labeled PEG was shown to bind to microsomal membranes isolated from rice roots; it is suggested that this is due to multipoint attachment of the complex ions of PEG which exist in aqueous solutions. It is argued that this reduces passive membrane permeability, which accounts for the large effect of PEG on sodium influx in rice and the different effects on sodium influx and (carrier-dependent) potassium influx.

     

Root Growth and Oxygen Relations at Low Water Potentials. Impact of Oxygen Availability in Polyethylene Glycol Solutions

Polyethylene glycol (PEG), which is often used to impose low water potentials (ψ_w) in solution culture, decreases O₂ movement by increasing solution viscosity. We investigated whether this property causes O₂ deficiency that affects the elongation or metabolism of maize (Zea mays L.) primary roots. Seedlings grown in vigorously aerated PEG solutions at ambient solution O₂ partial pressure (pO₂) had decreased steady-state root elongation rates, increased root-tip alanine concentrations, and decreased root-tip proline concentrations relative to seedlings grown in PEG solutions of above-ambient pO₂ (alanine and proline accumulation are responses to hypoxia and low ψ_w, respectively). Measurements of root pO₂ were made using an O₂ microsensor to ensure that increased solution pO₂ did not increase root pO₂ above physiological levels. In oxygenated PEG solutions that gave maximal root elongation rates, root pO₂ was similar to or less than (depending on depth in the tissue) pO₂ of roots growing in vermiculite at the same ψ_w. Even without PEG, high solution pO₂ was necessary to raise root pO₂ to the levels found in vermiculite-grown roots. Vermiculite was used for comparison because it has large air spaces that allow free movement of O₂ to the root surface. The results show that supplemental oxygenation is required to avoid hypoxia in PEG solutions. Also, the data suggest that the O₂ demand of the root elongation zone may be greater at low relative to high ψ_w, compounding the effect of PEG on O₂ supply. Under O₂-sufficient conditions root elongation was substantially less sensitive to the low ψ_w imposed by PEG than that imposed by dry vermiculite.     

Evaluation of the water potentials of solutions of polyethylene glycol 8000 both in the absence and presence of other solutes

Published and additional data for polyethylene glycol 8000 (PEG), formerly PEG 6000, solution water potentials (Ψ) are compared. Actual bars Ψ over the concentration range of 0 to 0.8 gram PEG per gram H₂O and temperature (T) range of 5 to 40°C are best predicted (probably within ± 5%) by this equation: Ψ = 1.29[PEG]²T − 140[PEG]² − 4.0[PEG]. Although transformable through division by [PEG] to virial equation form, results indicate that the coefficients are not virial. Mannitol (MAN) interacts with PEG to produce Ψ significantly lower than additive. Vapor pressure osmometer (VPO) data for MAN-PEG synergism compared favorably with those from thermocouple hygrometry; and VPO data showing the interactions between PEG and four salts are presented. The synergism of MAN-PEG and of NaCl-PEG are related linearly to the concentration of solute added with PEG.     

Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli

Evidence is accumulating that small, noncoding RNAs are important regulatory molecules. Computational and experimental searches have led to the identification of ~60 small RNA genes in Escherichia coli. However, most of these studies focused on the intergenic regions and assumed that small RNAs were >50 nt. Thus, the previous screens missed small RNAs encoded on the antisense strand of protein-coding genes and small RNAs of <50 nt. To identify additional small RNAs, we carried out a cloning-based screen focused on RNAs of 30–65 nt. In this screen, we identified RNA species corresponding to fragments of rRNAs, tRNAs and known small RNAs. Several of the small RNAs also corresponded to 5′- and 3′-untranslated regions (UTRs) and internal fragments of mRNAs. Four of the 3′-UTR-derived RNAs were highly abundant and two showed expression patterns that differed from the corresponding mRNAs, suggesting independent functions for the 3′-UTR-derived small RNAs. We also detected three previously unidentified RNAs encoded in intergenic regions and RNAs from the long direct repeat and hok/sok elements. In addition, we identified a few small RNAs that are expressed opposite protein-coding genes and could base pair with 5′ or 3′ ends of the mRNAs with perfect complementarity.     

Primer-dependent synthesis by poliovirus RNA-dependent RNA polymerase (3Dpol)

Properties of poliovirus RNA-dependent RNA polymerase (3D^pol) including optimal conditions for primer extension, processivity and the rate of dissociation from primer-template (k_off) were examined in the presence and absence of viral protein 3AB. Primer-dependent polymerization was examined on templates of 407 or 1499 nt primed such that fully extended products would be 296 or 1388 nt, respectively. Maximal primer extension was achieved with low rNTP concentrations (50–100 µM) using pH 7 and low (<1 mM) MgCl₂ and KCl (<20 mM) concentrations. However, high activity (about half maximal) was also observed with 500 µM rNTPs providing that higher MgCl₂ levels (3–5 mM) were used. The enhancement observed with the former conditions appeared to result from a large increase in the initial level or active enzyme that associated with the primer. 3AB increased the number of extended primers at all conditions with no apparent change in processivity. The k_off values for the polymerase bound to primer-template were 0.011 ± 0.005 and 0.037 ± 0.006 min^–1 (average of four or more experiments ± SD) in the presence or absence of 3AB, respectively. The decrease in the presence of 3AB suggested an enhancement of polymerase binding or stability. However, binding was tight even without 3AB, consistent with the highly processive (at least several hundred nucleotides) nature of 3D^pol. The results support a mechanism whereby 3AB enhances the ability of 3D^pol to form a productive complex with the primer-template. Once formed, this complex is very stable resulting in highly processive synthesis.     

Downstream processing of luciferase from fireflies (Photinus pyralis) using aqueous two-phase extraction

The firefly luciferase has been extensively used for sensitive detection of bacteria, gene expression and environmental toxins (biosensors). The aim of the present study was to design a simple and more efficient method for the purification and concentration of luciferase using aqueous two-phase extraction (ATPE). Downstream processing of luciferase from North American Firefly Photinus pyralis was carried out, for the first time, using polymer/salt aqueous two phase system (ATPS) at 4 °C. The enzyme was observed to preferentially partition to the polyethylene glycol (PEG) rich top phase. The best results of purification (13.69 fold) and enzyme activity recovery (118.34%) were observed in the system containing 4.0% (w/w) PEG (1500) and 20.5% (w/w) (NH₄)₂SO₄ with a phase volume ratio of 0.21.     

Polyethylene glycol behaves like weak organic solvent

Effect of polyethylene glycol (PEG) on protein solubility has been primarily ascribed to its large hydrodynamic size and thereby molecular crowding effect. However, PEG also shows characteristics of organic solvents. Here, we have examined the solubility of glycine and aliphatic and aromatic amino acids in PEG solutions. PEG400, PEG4000, and PEG20000 decreased the solubility of glycine, though to a much smaller magnitude than the level achieved by typical organic solvents, including ethanol and dimethyl sulfoxide. PEG4000 showed varying degree of interactions with amino acid side chains. The free energy of aliphatic side chains marginally increased by the addition of PEG4000, indicating their weak unfavorable interactions. However, it significantly decreased the free energy of the aromatic side chains and hence stabilized them. Thus, it was concluded that PEG behaves like weak organic solvents; namely PEG destabilized (interacted unfavorably with) polar and charged groups and stabilized (interacted favorably with) aromatic groups. Interestingly, the interaction of PEG20000, but neither PEG400 nor PEG4000, with glycine resulted in phase separation under the saturated concentration of glycine.     

Effect of Drug Solubility on Polymer Hydration and Drug Dissolution from Polyethylene Oxide (PEO) Matrix Tablets

The purpose of the study was to investigate the effect of drug solubility on polymer hydration and drug dissolution from modified release matrix tablets of polyethylene oxide (PEO). Different PEO matrix tablets were prepared using acetaminophen (ACE) and ibuprofen (IBU) as study compounds and Polyox WSR301 (PEO) as primary hydrophilic matrix polymer. Tablet dissolution was tested using the USP Apparatus II, and the hydration of PEO polymer during dissolution was recorded using a texture analyzer. Drug dissolution from the preparations was dependent upon drug solubility, hydrogel formation and polymer proportion in the preparation. Delayed drug release was attributed to the formation of hydrogel layer on the surface of the tablet and the penetration of water into matrix core through drug dissolution and diffusion. A multiple linear regression model could be used to describe the relationship among drug dissolution, polymer ratio, hydrogel formation and drug solubility; the mathematical correlation was also proven to be valid and adaptable to a series of study compounds. The developed methodology would be beneficial to formulation scientists in dosage form design and optimization.     

Influence of the long-chain/short-chain amphiphile ratio on lateral diffusion of PEG-lipid in magnetically aligned lipid bilayers as measured via pulsed-field-gradient NMR

Lateral diffusion measurements of polyethylene glycol(PEG)-lipid incorporated into magnetically aligned lipid bilayers, composed of dimyristoyl phosphatidylcholine (DMPC) plus dihexanoyl phosphatidylcholine (DHPC) plus 1 mol % (relative to DMPC) dimyristoyl phosphatidylethanolamine-n-[methoxy(polyethylene glycol)-2000] (DMPE-PEG 2000), were performed using stimulated-echo pulsed-field-gradient proton (¹H) nuclear magnetic resonance spectroscopy. The DMPE-PEG 2000 (1 mol %, 35°C) lateral diffusion coefficient D varied directly with the mole fraction of DMPC, X_DMPC = q/(1+q) where q = DMPC/DHPC molar ratio, decreasing progressively from D = 1.65 × 10⁻¹¹ m² s⁻¹ at q ≈ 4.7 to D = 0.65 × 10⁻¹¹ m² s⁻¹ at q ≈ 2.5. Possible sources of this dependence, including orientational disorder, obstruction, and PEG-lipid sequestration, were simulated using, respectively, a diffusion-in-a-cone model, percolation theory, and a two-phase PEG distribution model. Orientational disorder alone was not capable of reproducing the observations, but in combination with either obstruction or PEG-lipid two-phase distribution models did so satisfactorily. A combination of all three models yielded the most reasonable fit to the observed dependence of lateral diffusion on q. These same effects would be expected to influence lateral diffusion of any bilayer-associating species in such systems.