Quantitative <scp>SNP</scp> genotyping by affinity capillary electrophoresis using <scp>PEG</scp>‐oligodeoxyribonucleotide block copolymers with electroosmotic flow

Tsukada, Harumi; Watanabe, Takashi; Kanayama, Naoki; Takarada, Tohru; Maeda, Mizuo

doi:10.1002/elps.201200073

Cited by 9 publications

(27 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In fact, the values of i c (3) for different N remain nearly the same all the way to the highest values of p at which fitting with eq 35 can still be considered meaningful (Figure 6b). Another advantage of i c (3) is that, while for large values of p there is no solution of eq 38, the solution of eq 39 exists whenever the solution of eq 37 does. In some cases, i c (3) may exceed N/2, which is "unphysical," but is a useful estimate of the crossover point position in the N → ∞ limit.…”

Section: Macromoleculesmentioning

confidence: 81%

“…Another advantage of i c (3) is that, while for large values of p there is no solution of eq 38, the solution of eq 39 exists whenever the solution of eq 37 does. In some cases, i c (3) may exceed N/2, which is "unphysical," but is a useful estimate of the crossover point position in the N → ∞ limit. Of course, for i c ≪ N both calculations give the same result (i c (2) ≈ i c (3) ) and eventually, for even smaller i c /N, all three estimates approximately coincide: i c (1) ≈ i c (2) ≈ i c (3) .…”

Section: Macromoleculesmentioning

confidence: 99%

“…In some cases, i c (3) may exceed N/2, which is "unphysical," but is a useful estimate of the crossover point position in the N → ∞ limit. Of course, for i c ≪ N both calculations give the same result (i c (2) ≈ i c (3) ) and eventually, for even smaller i c /N, all three estimates approximately coincide: i c (1) ≈ i c (2) ≈ i c (3) . The data in Figure 6 give a more reliable confirmation of the fact we first noticed in Figure 2 that the distance of the crossover points from the ends (i c − 1 ≈ i c ) exceeds the persistence length p significantly already for quite small p and grows with p superlinearly.…”

Section: Macromoleculesmentioning

confidence: 99%

“…In Figure 7 we compare a 2 /N + 1 / 2 to i c (3) . We see, first of all, that the results for different N coincide.…”

Section: Macromoleculesmentioning

confidence: 99%

See 3 more Smart Citations

Electrophoresis of Heteropolymers. Effect of Stiffness

Chubynsky

Slater

2015

Macromolecules

View full text Add to dashboard Cite

In the limit of a small Debye length, the electrophoretic mobility of a charged heteropolymer is a weighted average of the mobilities of its parts. The weights are a function of the position along the chain that depends on the properties of the polymer, such as its stiffness. It is known that for a flexible polymer the weights diverge as a power law at the ends, while for a rodlike polymer the divergence is only logarithmic. Using the Kirkwood− Riseman approximation, we study in detail the intermediate case of a semiflexible polymer. We find that for sufficiently small persistence lengths, the position dependence of the weights matches that for flexible polymers away from the ends, but crosses over to the logarithmic dependence characteristic of rods near the ends. While this crossover is broad and the exact points at which it occurs can be defined in different ways, we give an operational definition of the distance of the crossover points from the respective end that turns out to be nearly independent of the polymer length even when it is comparable to that length. This crossover distance is proportional to the "hydrodynamic Kuhn length" defined as the polymer length at which the crossover between the "rod-like" and the "coil-like" dependences of the friction coefficient occurs. Both the crossover distance for the weights and the hydrodynamic Kuhn length scale superlinearly with the persistence length of the polymer; as a result, geometrically "coil-like" semiflexible polymers can be quite "rod-like" hydrodynamically and electrophoretically. Our results are applied to the case of a diblock copolymer with one charged and one neutral part.

show abstract

Section: Macromoleculesmentioning

confidence: 81%

Section: Macromoleculesmentioning

confidence: 99%

Section: Macromoleculesmentioning

confidence: 99%

“…In Figure 7 we compare a 2 /N + 1 / 2 to i c (3) . We see, first of all, that the results for different N coincide.…”

Section: Macromoleculesmentioning

confidence: 99%

See 2 more Smart Citations

Electrophoresis of Heteropolymers. Effect of Stiffness

Chubynsky

Slater

2015

Macromolecules

View full text Add to dashboard Cite

show abstract

“…Similar allele-specific PNA probes modified by PEG were used to estimate allele frequency of single-nucleotide polymorphisms in DNAs obtained after the pooling procedure. [19][20][21] Aptamers that bind small molecules can serve as universal biosensing tools. Measuring the values of K d and k on for interaction between an aptamer and a small molecule helps to determine the effectiveness of the aptamer-based sensors.…”

mentioning

confidence: 99%

Capillary Electrophoresis for Quantitative Studies of Biomolecular Interactions

2014

View full text Add to dashboard Cite

T he development of highly selective and sensitive analytical techniques has been a driving force for unprecedented advances in biotechnology, gene engineering, and drug discovery. Capillary electrophoresis (CE) is becoming a wider accepted analytical method in biology and medicine. CE offers short analysis time, high resolution, and minute consumption of samples and reagents, making it an attractive technique for mass bioassays and drug screening. Since the last Analytical Chemistry review in this field, 1 there have been published over 10 000 articles with CE as a topic. Within a variety of studies concerning CE, we have identified the intensively developing area of reversible biomolecular interactions which are defined as highly selective noncovalent binding of ligands with biomolecules. These affinity interactions control cell recognition, signal transduction, immune response, DNA replication, gene expression, and other cellular processes. The knowledge of quantitative parameters of binding reactions (equilibrium and/ or rate constants) is essential for understanding the mechanisms of biological processes, which these reactions regulate. The present review covers a 3-year period between January 2012 and November 2014. We have attempted to select studies that demonstrate the newest and most impactive developments in the field of biomolecular affinity interactions.

show abstract

Theory of end‐labeled free‐solution electrophoresis: Is the end effect important?

Chubynsky

Slater

2014

Electrophoresis

View full text Add to dashboard Cite

In the theory of free-solution electrophoresis of a polyelectrolyte (such as the DNA) conjugated with a "drag-tag," the conjugate is divided into segments of equal hydrodynamic friction and its electrophoretic mobility is calculated as a weighted average of the mobilities of individual segments. If all the weights are assumed equal, then for an electrically neutral drag-tag, the elution time t is predicted to depend linearly on the inverse DNA length 1/M. While it is well-known that the equal-weights assumption is approximate and in reality the weights increase toward the ends, this "end effect" has been assumed to be small, since in experiments the t(1/M) dependence seems to be nearly perfectly linear. We challenge this assumption pointing out that some experimental linear fits do not extrapolate to the free (i.e. untagged) DNA elution time in the limit 1/M→0, indicating nonlinearity outside the fitting range. We show that a theory for a flexible polymer taking the end effect into account produces a nonlinear curve that, however, can be fitted with a straight line over a limited range of 1/M typical of experiments, but with a "wrong" intercept, which explains the experimental results without additional assumptions. We also study the influence of the flexibilities of the charged and neutral parts.

show abstract

Quantitative SNP genotyping by affinity capillary electrophoresis using PEG‐oligodeoxyribonucleotide block copolymers with electroosmotic flow

Cited by 9 publications

References 60 publications

Electrophoresis of Heteropolymers. Effect of Stiffness

Electrophoresis of Heteropolymers. Effect of Stiffness

Capillary Electrophoresis for Quantitative Studies of Biomolecular Interactions

Theory of end‐labeled free‐solution electrophoresis: Is the end effect important?

Contact Info

Product

Resources

About