From small charged molecules to oligomers: A semiempirical approach to the modeling of actual mobility in free solution

Cottet, Hervé; Gareil, Pierre

doi:10.1002/(sici)1522-2683(20000501)21:8<1493::aid-elps1493>3.0.co;2-e

Cited by 48 publications

(51 citation statements)

References 36 publications

(28 reference statements)

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“…This behavior appears to be a general polyelectrolyte effect, because it has been observed for double-stranded DNAs [1,2], poly(acrylamide/acrylic acid) copolymers [3], polyphosphates [4], poly(deoxythymidines) [5], and poly(styrenesulfonates) [5][6][7]. The mobilities of poly(deoxythymidines) and poly(styrenesulfonates) actually go through a maximum at intermediate molecular weights before leveling off at high molecular weights [5,7].…”

Section: Introductionsupporting

confidence: 59%

Do orientation effects contribute to the molecular weight dependence of the free solution mobility of DNA?

et al. 2001

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The free solution mobility of DNA increases with increasing molecular weight and then levels off and becomes constant at molecular weights above approximately 400 bp (Stellwagen, N. C., Gelfi, C., Righetti, P. G., Biopolymers 1997,42, 687-703). To investigate whether the increase in mobility could be attributed to an increased orientation of the larger DNA molecules in the electric field, the free solution mobility of DNA was measured by capillary electrophoresis as a function of electric field strength. Mixtures containing 20-, 118- and 422-bp DNA molecules, and 20-, 422- and 2116-bp DNAs, were studied. If the larger DNA molecules in each mixture were oriented by the electric field, their mobilities should increase with electric field strength faster than the mobility of the 20-bp oligomer, which is too small to be oriented by the electric fields used in this study. Instead, the ratios of the mobilities of the 118-, 422- and 2116-bp fragments to the mobility of the 20-bp oligomer were independent of electric field strength. Hence, orientation effects are not important for DNA molecules up to 2 kbp in size, in electric fields up to 500 V/cm in amplitude. An explanation is suggested.

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Section: Introductionsupporting

confidence: 59%

Do orientation effects contribute to the molecular weight dependence of the free solution mobility of DNA?

et al. 2001

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“…Previous CE measurements of the free solution mobility of DNA have shown that the mobility increases with increasing molecular weight and then levels off and becomes constant for DNA molecules larger than , 400 bp [3]. Similar increases in mobility with increasing molecular weight have been observed for small polyphosphates [6], polylysines [7], poly(styrenesulfonates) [8][9][10], poly(acrylamide/acrylic acid) copolymers [11], single-stranded DNAs [12], and poly(deoxythymidines) [8,12]. Hence, the molecular weight dependence of the mobility of small DNA molecules is a general polyelectrolyte effect, unrelated to the structure of the specific polyion.…”

Section: General Aspectsmentioning

confidence: 99%

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

2002

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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.

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“…8 In addition, a number of methods of predicting µep have been reported. [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28] The molecular weights (MW) have been reported to correspond to the µep values for amides. [9][10][11][12][13][14] In addition, for some organic and metal complex ions, the MWs correspond to the µep values.…”

mentioning

confidence: 81%

Section: Introductionmentioning

confidence: 99%

“…[24][25][26] The effects of the µep values on the friction coefficients for small charged molecules to oligomers with carboxylate and sulfonate groups have also been reported. 27 The friction coefficients of carboxylate and sulfonate groups similarly contributed to the µep values, since the electric charge was thought to more heavily influence the µep values than the The capillary electrophoretic behavior of 44 aromatic organic ions was investigated. The observed ionic radii (robs0) for the aromatic organic ions were obtained from the electrophoretic mobilities of sodium tetraborate (pH 9.2), potassium tetraborate (pH 9.2), ammonium borate (pH 9.2), and trisodium phosphate (pH 11.7) buffers with zero ionic strength.…”

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confidence: 99%

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Relation between Electrophoretic Behavior and Molecular Shapes of Aromatic Anions

et al. 2004

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Capillary electrophoresis (CE) has been applied to the separation of various analyte ions. [1][2][3][4][5][6] Theoretically, the capillary electrophoretic mobility (µep) is calculated bywhere q, η and r are the electric charge of the ionized solute, the buffer viscosity and the solute radius, respectively. 7 Therefore, the CE separation of analyte ions is primarily dependent on the ionic charge and the ionic radius, unless there are any other interactions in the analyte ions, such as those with the capillary wall or counterions. When the ionic shape is not spherical, it is difficult to predict µep from Eq. (1). In addition, the Stokes radius of the ion is necessary in order to determine the r-value. However, the observed µep values of non-spherical ions are expected to provide some information regarding the ionic shapes.Factors affecting the selectivity of inorganic anions have been reviewed. 8 In addition, a number of methods of predicting µep have been reported. [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28] The molecular weights (MW) have been reported to correspond to the µep values for amides. [9][10][11][12][13][14] In addition, for some organic and metal complex ions, the MWs correspond to the µep values. 15 The MW value is thought to depend on the molecular volume; therefore, it could be used as an index of molecular size. However, the separation of a number of aminonaphthalenesulfonate ions having the same molecular weight and electric charge at pH 9.2 has been accomplished. 16 Moreover, empirically good linear relationships between the µep values and MW -2/3 have been reported. [10][11][12][13][14] The MW 1/3 value indirectly corresponds to the third power of the molecular volume, that is, the r-value, because the MW value generally depends on the molecular volume. Therefore, the MW -2/3 value indirectly corresponds to r -2. In other words, the r -2 -values show a good linear relationship with the µep values. A correlation between the µep values for the localized electric charge of non-spherical aromatic anions with the MW -2/3 and r -2 -values has yet to be reported. Accordingly, the MW -2/3 and r -2 -values were evaluated as the indexes to determine whether or not they would be a useful means of predicting the µep values of these anions.A simulation of the µep values with the pH of the buffer has been reported for phenolic acids. 17,18 In addition, a simulation of the µep values with the pH and the 2-hydroxyisobutyric acid (HIBA) concentration of the buffer has been reported for metal HIBA complex ions. 19The effects of the µep values on a number of water-soluble organic solvents (such as methanol) for aromatic carboxylates with various functional groups (such as hydroxyl groups) have been reported. [20][21][22][23] These results showed that the differing viscosities of the buffers and the differing pKas for phenolic acids and aromatic carboxylates largely influenced the µep values. Although it has been reported that the change in the Walden product (µepη) value is de...

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From small charged molecules to oligomers: A semiempirical approach to the modeling of actual mobility in free solution

Cited by 48 publications

References 36 publications

Do orientation effects contribute to the molecular weight dependence of the free solution mobility of DNA?

Do orientation effects contribute to the molecular weight dependence of the free solution mobility of DNA?

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

Relation between Electrophoretic Behavior and Molecular Shapes of Aromatic Anions

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