PubMed Health⌕ Search

Biomedical subjects

Earle Stellwagen

Publications and source records attributed to Earle Stellwagen.

12 recordsLinked to original sources
PubMed2006

Effect of organic cosolvents on the free solution mobility of curved and normal DNA molecules.

The free solution mobilities of curved and normal 199-bp DNA fragments have been measured in buffer solutions containing various quantities of the organic cosolvents methanol, ethanol, 2-propanol, 2-methyl-2,4-pentanediol (MPD), ethylene glycol, and ACN, using CE. The curved fragment, taken from the VP1 gene of SV40, contains five unevenly spaced A- and T-tracts in a centrally located "curvature module"; the A- and T-tracts have been mutated to other sequences in the normal 199-bp fragment. The free solution mobility of the curved 199-bp fragment is significantly lower than that of its normal counterpart in aqueous solutions [Stellwagen, E., Lu, Y. J., Stellwagen, N. C., Nucleic Acids Res. 2005, 33, 4425-4432]. The mobilities of both the curved and normal fragments decrease with increasing cosolvent concentration, due to the effect of the cosolvent on the viscosity and dielectric constant of the solution. The mobility differences between the curved and normal 199-bp fragments and the mobility ratios decrease approximately linearly with the increasing mole fraction of cosolvent in the solution. Hence, MPD and other organic cosolvents affect DNA electrophoretic mobility by a common mechanism, most likely the preferential hydration of the DNA surface that occurs in aqueous cosolvents. The gradual loss of the anomalously slow mobility of the curved 199-bp fragment with increasing cosolvent concentration, combined with other data in the literature, suggests that preferential hydration gradually widens the narrow A-tract minor groove, releasing site-bound counterions in the minor groove and shifting the conformation toward that of normal DNA.

Alcohols↗
PubMed2005

Curved DNA molecules migrate anomalously slowly in free solution.

The electrophoretic mobility of a curved DNA restriction fragment taken from the VP1 gene in the SV40 minichromosome has been measured in polyacrylamide gels and free solution, using capillary electrophoresis. The 199 bp restriction fragment has an apparent bend angle of 46 +/- 2 degrees located at SV40 sequence position 1922 +/- 2 bp [Lu Y.J., Weers B.D. and Stellwagen N. C. (2005) Biophys. J., 88, 1191-1206]. The 'curvature module' surrounding the apparent bend center contains five unevenly spaced A- and T-tracts, which are responsible for the observed curvature. The parent 199 bp fragment and sequence mutants containing at least one A-tract in the curvature module migrate anomalously slowly in free solution, as well as in polyacrylamide gels. Hence, the anomalously slow mobilities observed for curved DNA molecules in polyacrylamide gels are due in part to their anomalously slow mobilities in free solution. Analysis of the gel and free solution mobility decrements indicates that each A- or T-tract contributes independently, but not equally, to the curvature of the 199 bp fragment and its A-tract mutants. The relative contribution of each A- or T-tract to the observed curvature depends on its spacing with respect to the first A-tract in the curvature module.

AT Rich Sequence↗
PubMed2005

Monovalent cations affect the free solution mobility of DNA by perturbing the hydrogen-bonded structure of water.

The free solution mobilities of single- and double-stranded DNA molecules of various molecular weights have been measured by capillary electrophoresis in solutions of constant ionic strength containing a common anion and fifteen different monovalent cations. In solutions with the same ionic composition, the mobilities of different DNA molecules can vary by up to 20%, depending on molecular weight, the number of strands, and the presence or absence of A-tracts, runs of four or more contiguous adenine residues. Importantly, the mobilities observed for the same DNA sample can vary by up to 40% in solutions containing different cations. The mobility differences observed for the same DNA in solutions containing different cations cannot be rationalized by differences in the anhydrous radii or intrinsic conductivities of the various cations, or by the sequence-dependent binding of certain cations to A-tracts. Instead, the observed mobilities are linearly correlated with the average number of water-water hydrogen bonds that are present in solutions containing different cations. The mobilities are also correlated with the viscosity B coefficients of the various cations and with the rotational correlation times frictional coefficients observed for water molecules in solutions containing different cations. Hence, monovalent cations modify the free solution mobility of DNA primarily by perturbing the hydrogen-bonded structure of water, affecting the friction experienced by the migrating DNA molecules during electrophoresis.

Base Sequence↗
PubMed2005

The sensitivity of the cis/trans-isomerization of enalapril and enalaprilat to solvent conditions.

The cis- and trans-isomers of enalapril and enalaprilat can be resolved by HPLC and by capillary electrophoresis. The isomeric content of enalapril is perturbed by the ionization of both its carboxyl and amine groups, while the isomeric content of enalaprilat is only perturbed by the ionization of its amine group. Increasing the hydrophobicity of the analyte solvent, as reflected in its molar polarization, increases the Z (cis) content of enalapril and markedly decreases the kinetics for isomerization. Far UV circular dichroic measurements suggest that the increase in Z (cis) content of enalapril is due to protonation of its carboxylate group. Taken together, the in-vitro properties of enalapril and enalaprilat suggest that the in-vivo transformation of the prodrug enalapril to the inhibitor enalaprilat and its delivery to angiotensin-converting enzyme should not be significantly limited by cis/trans-isomerization.

Antihypertensive Agents↗
PubMed2003

Analysis of the isomeric composition of the proline peptide bond in an angiotensin-converting enzyme inhibitor using capillary electrophoresis.

The cis and trans isomeric composition of a proline peptide bond can be determined by routine free-solution capillary electrophoresis measurements provided that one isomeric form is preferentially stabilized by a dissociable ionic group. This capability is illustrated using the angiotensin converting enzyme (ACE) inhibitor (S)-1-N-[1-(ethoxycarbonyl)-3-phenylpropyl]-L-ala-L-pro, which has the trade name enalapril. Electropherograms indicate that the two isomeric forms of enalapril can be separated with baseline resolution at 15 degrees C using capillary buffers having pH values in the dissociation ranges of the enalapril carboxyl group, pK(cis) and pK(trans) of 2.6 and 3.1, and of the enalapril amine group, pK(cis) and pK(trans) of 5.9 and 5.6. Such baseline resolution indicates that the isomeric composition does not change during analysis, facilitating measurement of the isomer composition of a sample prior to its injection into the capillary. Thus the effect of pH, ionic strength, or an aprotic solvent on the isomeric composition of enalapril can be measured under uniform analytical conditions. The trans isomer composition changes from 68% in the cationic form, pH <2, to 50% in the isoelectric form, pH approximately 4.5, to 60% in the anionic form, pH >7. Addition of salt to the isoelectric form or addition of an aprotic solvent to any form prior to analysis increases the trans isomer composition. Similar analyses can be made using the alternative ACE inhibitors captopril and enalaprilat.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2003

Unified description of electrophoresis and diffusion for DNA and other polyions.

The electrophoretic mobilities and diffusion coefficients of single- and double-stranded DNA molecules up to 50,000 bases or base pairs in size have been analyzed, using mobilities and diffusion coefficients either measured by capillary electrophoresis or taken from the literature. The Einstein equation suggests that the electrophoretic mobilities (mu) and diffusion coefficients (D) should be related by the expression mu/D = Q/k(B)T, where Q is the charge of the polyion (Q = ze(o), where z is the number of charged residues and e(o) is the fundamental electronic charge), k(B) is Boltzmann's constant, and T is the absolute temperature. If this equation were true, the ratio mu/zD should be a constant equal to e(o)/k(B)T (39.6 V(-1)) at 20 degrees C. However, the ratio mu/zD decreases with an increase in molecular weight for both single- and double-stranded DNAs. The mobilities and diffusion coefficients are better described by the modified Einstein equation mu/N(m)D = e(o)/k(B)T, where N is the number of repeat units (bases or base pairs) in the DNA and m is a constant equal to the power law dependence of the diffusion coefficients on molecular weight. The average value of the ratio mu/N(m)D is 40 +/- 4 V(-1) for 36 single- and double-stranded DNA molecules of different sizes, close to the theoretically expected value. The generality of the modified Einstein equation is demonstrated by analyzing literature values for sodium polystyrenesulfonate (PSS). The average value of the ratio mu/N(m)D is 35 +/- 6 V(-1) for 14 PSS samples containing up to 855 monomers.

Base Composition↗
PubMed2003

Free solution mobility of small single-stranded oligonucleotides with variable charge densities.

The free solution mobilities of six single-stranded 16-nucleotide DNA oligomers with the same sequence, containing up to 11 neutral phosphoramidate internucleoside linkages, have been measured by capillary electrophoresis. The mobilities of the partially charged oligomers increase linearly with the logarithm of increasing charge density, as predicted by the Manning theory of electrophoresis (G. S. Manning, J. Phys. Chem. 1981, 85, 1506-1515). For comparison, the mobilities of eight fully charged single-stranded oligomers containing similar numbers of charged phosphate residues have also been measured. The mobilities of the variable length, fully charged oligomers increase more rapidly with the increasing number of charged phosphate residues than the mobilities of the constant size, partially charged phosphoramidate derivatives, because of the larger diffusion coefficients of the modified oligomers.

Amides↗
PubMed2003

Probing the electrostatic shielding of DNA with capillary electrophoresis.

The free solution mobility of a 20-bp double-stranded DNA oligomer has been measured in diethylmalonate (DM) and Tris-acetate buffers, with and without added NaCl or TrisCl. DM buffers have the advantage that the buffering ion is anionic, so the cation composition in the solution can be varied at will. The results indicate that the free solution mobility of DNA decreases linearly with the logarithm of ionic strength when the ionic strength is increased by increasing the buffer concentration. The mobility also decreases linearly with the logarithm of ionic strength when NaCl is added to NaDM buffer or TrisCl is added to TrisDM buffer. Nonlinear effects are observed if the counterion in the added salt differs from the counterion in the buffer. The dependence of the mobility on ionic strength cannot be predicted using the Henry, Debye-Hückel-Onsager, or Pitts equations for electrophoresis. However, the mobilities observed in all buffer and buffer/salt solutions can be predicted within approximately 20% by the Manning equation for electrophoresis, using no adjustable parameters. The results suggest that the electrostatic shielding of DNA is determined not only by the relative concentrations of the various ions in the solution, but also by their equivalent conductivities.

Computer Simulation↗
PubMed2002

Salt-promoted protein folding, preferential binding, or electrostatic screening?

The extended coil/molten globule conformational equilibrium exhibited by ferricytochrome c in 10 to 20 mM HCl was examined using free boundary capillary electrophoresis. Addition of the osmolyte glucitol, also called sorbitol, to shift the conformational equilibrium toward the molten globule markedly diminished the mobility of the protein. This diminution can be entirely assigned to the relative viscosity of the added glucitol. The insensitivity of the viscosity corrected protein mobility to added glucitol suggests that both the extended coil and molten globule conformations of cytochrome c are free draining in an electrophoresis measurement. Addition of a neutral salt to shift the conformational equilibrium toward the molten globule conformation also markedly diminished the mobility of the protein. This diminution can be entirely assigned to the electrostatic screening afforded by the added salt. The onset of the conformational transition observed by optical measurements and the onset of electrostatic screening observed by mobility measurements appear to be in common for some but not all neutral salts. The exception suggests that preferential binding of the anion of a neutral salt to the molten globule conformation and not electrostatic screening is principally responsible for the shift in the conformational equilibrium of cytochrome c in acidic solutions.

Animals↗
PubMed2002

The free solution mobility of DNA in Tris-acetate-EDTA buffers of different concentrations, with and without added NaCl.

The free solution mobility of a high-molecular-weight DNA, linear pUC19, and a 20-bp oligomer called dsA5 have been studied as a function of Tris-acetate-EDTA (TAE) buffer concentration, with and without added NaCl. The two DNAs migrate as separate peaks during capillary electrophoresis, because the mobility of linear pUC19 is higher than that of the 20-bp oligomer. In TAE buffers ranging from 10-400 mM in concentration, the migration times and peak areas of the two DNAs are independent of whether they are electrophoresed separately or in mixtures, indicating that DNA-DNA and DNA-buffer interactions are absent in these solutions. The migration times of the two DNAs vary and the peak areas are not additive when the TAE buffer concentration is reduced to 5 mM or below, indicating that DNA-DNA and DNA-buffer interactions are occurring at very low TAE buffer concentrations. The mobilities of linear pUC19 and dsA5 decrease slowly with increasing conductivity or ionic strength when the conductivity is increased by increasing the TAE buffer concentration. When the Tris buffer concentration is held constant and the conductivity is increased by adding various concentrations of NaCl to the solution, the mobilities of linear pUC19 and dsA5 first increase slightly, then become independent of solution conductivity (or ionic strength), and finally decrease when the NaCl concentration is increased above approximately 50 mM. The mobility variations observed in the various TAE and TAE-NaCl solutions are described qualitatively by Manning's theory, although quantitative agreement is not achieved. The free solution mobilities of single-stranded pUC19 and two 20-base oligonucleotides have also been measured. The free solution mobility of single-stranded pUC19 is approximately 15% lower than that of native pUC19, in agreement with other results in the literature. Somewhat surprisingly, the mobilities of the single- and double-stranded 20-mers are equal to each other in TAE buffers with and without added NaCl.

Acetates↗
PubMed2002

Determining the electrophoretic mobility and translational diffusion coefficients of DNA molecules in free solution.

The free solution mobility of DNA molecules of different molecular weights, the sequence dependence of the mobility, and the diffusion coefficients of small single- and double-stranded DNA (ss- and dsDNA) molecules can be measured accurately by capillary zone electrophoresis, using coated capillaries to minimize the electroosmotic flow (EOF) of the solvent. Very small differences in mobility between various analytes can be quantified if a mobility marker is used to correct for small differences in EOF between successive experiments. Using mobility markers, the molecular weight at which the free solution mobility of dsDNA becomes independent of molecular weight is found to be approximately 170 bp in 40 mM Tris-acetate-EDTA buffer. A DNA fragment containing 170 bp has a contour length of approximately 58 nm, close to the persistence length of DNA under these buffer conditions. Hence, the approach of the free solution mobility of DNA to a plateau value may be associated with the transition from a rod-like to a coil-like conformation in solution. Markers have also been used to determine that the free solution mobilities of ss- and dsDNA oligomers are sequence-dependent. Double-stranded 20-bp oligomers containing runs of three or more adenine residues in a row (A-tracts) migrate somewhat more slowly than 20-mers without A-tracts, suggesting that somewhat larger numbers of counterions are condensed in the ion atmospheres of A-tract DNAs, decreasing their net effective charge. Single-stranded 20-mers with symmetric sequences migrate approximately 1% faster than their double-stranded counterparts, and faster than single-stranded 20-mers containing A(5)- or T(5)-tracts. Interestingly, the average mobility of two complementary single-stranded 20-mers is equal to the mobility of the double-stranded oligomer formed upon annealing. Finally, the stopped migration method has been used to measure the diffusion coefficients of single- and double-stranded oligomers. The diffusion coefficients of ssDNA oligomers containing 20 nucleotides are approximately 50% larger than those of double-stranded DNA oligomers of the same size, reflecting the greater flexibility of ssDNA molecules. The methods used to carry out these experiments are also described in detail.

Base Sequence↗