Diffusion coefficients of oligonucleotides in capillary gel electrophoresis

Yin, Hongfeng; Kleemiss, Maria Helen.; Lux, Jürgen A.; Schomburg, G.

doi:10.1002/mcs.1220030407

Cited by 21 publications

(5 citation statements)

References 12 publications

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“…For our ssDNA (which similarly to polyethylene glycol behaves as a random coil), this would reduce the diffusion coefficient to 23 μm 2 /s. A similar value of approximately 30 μm 2 /s was reported for ssDNA of corresponding molecular weight in polyacrylamide hydrogels (of somewhat different composition than ours, 6%T, 5%C, compared with our approximately 10%T, 2%C, where %T is the total concentration of monomers and %C is the weight percentage of cross-linker).…”

Section: Results and Discussionsupporting

confidence: 88%

Toehold Length of Target ssDNA Affects Its Reaction-Diffusion Behavior in DNA-Responsive DNA-co-Acrylamide Hydrogels

2019

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In the present study, we expand on the understanding of hydrogels with embedded deoxyribonucleic acid (DNA) cross-links, from the overall swelling to characterization of processes that precede the swelling. The hydrogels respond to target DNA strands because of a toehold-mediated strand displacement reaction in which the target strand binds to and opens the dsDNA cross-link. The spatiotemporal evolution of the diffusing target ssDNA was determined using confocal laser scanning microscopy (CLSM). The concentration profiles revealed diverse partitioning of the target DNA inside the hydrogel as compared with the immersing solution: excluding a nonbinding DNA, while accumulating a binding target. The data show that a longer toehold results in faster cross-link opening but reduced diffusion of the target, thus resulting in only a moderate increase in the overall swelling rate. The parameters obtained by fitting the data using a reaction-diffusion model were discussed in view of the molecular parameters of the target ssDNA and hydrogels.

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Section: Results and Discussionsupporting

confidence: 88%

Toehold Length of Target ssDNA Affects Its Reaction-Diffusion Behavior in DNA-Responsive DNA-co-Acrylamide Hydrogels

2019

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“…The diffusion coefficient of DNA fragments was measured at different pHs using a “stop migration technique” to investigate the effect of pH on DNA during these separations. , In this technique, two runs were employed to measure the variance contributed by molecular diffusion. The first run was uninterrupted and completed by applying a voltage of 6 kV.…”

Section: Resultsmentioning

confidence: 99%

Separation of Double- and Single-Stranded DNA Restriction Fragments: Capillary Electrophoresis with Polymer Solutions under Alkaline Conditions

Liu

Kuhr

1999

Anal. Chem.

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Capillary electrophoresis in buffers containing hydroxyethyl cellulose (HEC) was used to separate double- and single-stranded DNA restriction fragments under neutral and alkaline conditions in epoxy-coated capillaries. It was found that better resolution was achieved using highly entangled HEC solutions for a narrow range of DNA fragment sizes, while lower resolution was obtained over a wide separation range using diluted HEC solutions. Optimal resolution of these DNA fragments was obtained using buffers containing 0.5% HEC at pH 11 with plate numbers exceeding 3 x 10(6) plates/m. It was also found that the diffusion coefficients and electrophoretic mobilities of DNA fragments decreased with increasing pH. This may indicate a more extended DNA conformation and, therefore, enhancement of transient entanglement coupling between DNA and HEC polymers under alkaline condition. At pH 12, ss-DNA were well separated in entangled HEC solutions; however, the resolution of ss-DNA was significantly decreased in diluted polymer solution.

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“…In cases where the two latter broadenings are negligible, the diffusion constant can be estimated. However, it might be more appropriate to let the solute zone migrate 1-3 cm inside the column, then switch off the voltage to determine the diffusion constant of the solute from the peak broadening [16]. An experiment similar to that in Fig.…”

Section: Methodsmentioning

confidence: 99%

Capillary zone electrophoresis in agarose gels using absorption imaging detection

Palm¹,

Lindh²,

Pawliszyn³

1996

Electrophoresis

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A simple home-built electrophoretic unit and a commercially available charge-coupled device (CCD) camera with image acquisition and analysis software were used to study the separation process in zone electrophoresis experiments in 4 cm long, round capillaries (inside diameter 0.2 mm). Several capillaries could be investigated simultaneously. The absorption imaging system was used not only to follow the course of the separation but also to study the interaction between biologically active substances (proteins, detergents, enzymes and-substrate). Since the system allows visual on-line observation of the separation one can rapidly decide when the analysis is finished, which often shortens the analysis time. The electrophoresis method presented is suitable also for preparative runs, since direct visualizations of a solute zone allows it to be excised and then used for further studies.

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Diffusion coefficients of oligonucleotides in capillary gel electrophoresis

Cited by 21 publications

References 12 publications

Toehold Length of Target ssDNA Affects Its Reaction-Diffusion Behavior in DNA-Responsive DNA-co-Acrylamide Hydrogels

Toehold Length of Target ssDNA Affects Its Reaction-Diffusion Behavior in DNA-Responsive DNA-co-Acrylamide Hydrogels

Separation of Double- and Single-Stranded DNA Restriction Fragments: Capillary Electrophoresis with Polymer Solutions under Alkaline Conditions

Capillary zone electrophoresis in agarose gels using absorption imaging detection

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