Poly(ethylene glycol)-oligodeoxyribonucleotide block copolymers for affinity capillary electrophoretic separation of single-stranded DNAs with a single-base difference

Kanayama, Naoki; Takarada, Tohru; Kimura, Akihiko; Shibata, Hirobumi; Maeda, Mizuo

doi:10.1016/j.reactfunctpolym.2007.07.036

Cited by 13 publications

(30 citation statements)

References 29 publications

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“…These results support the working principle that the electrophoretic separation is based on the reversible hybridization between sample ssDNA and PEG-b-ODN. The similar dependences were observed when using PEG-b-ODN(7)-or PEG-b-ODN(8)-introduced capillary tube [23].…”

Section: Determination Of Thermodynamic Parameterssupporting

confidence: 78%

“…A mixture of equal amounts of chemically synthesized 59-6-carboxyfluorescein-labeled 20 mer ssDNA (normal ssDNA) and its single-base-substituted 20 mer ssDNA (mutant ssDNA) was used as sample ssDNA. PEG-b-ODN was synthesized by the method reported previously [23]. Briefly, 59-thiol-terminated ODN was coupled with maleimide-terminated PEG (M n = 5500, M w /M n = 1.03), and the product was purified by gel filtration chromatography and anion exchange chromatography.…”

Section: Methodsmentioning

confidence: 99%

“…The PEG segment is water soluble, electrically neutral, and free from nonspecific interaction with biomolecules including DNA [24]. Block type conjugation of end-functionalized PEG with ODN gave a size-and composition-controlled affinity ligand; the reproducibility of migration time in the PEG-b-ODNbased system was higher than that in the previous PAAmg-ODN system [23]. Although it was clearly shown that PEG-b-ODN was a promising separation medium for a single-base mutation assay, the separation principle has still not been addressed.…”

Section: Introductionmentioning

confidence: 94%

“…Size-and composition-controlled PEG-b-ODN copolymers were synthesized by the method previously reported [23].…”

Section: Determination Of Thermodynamic Parametersmentioning

confidence: 99%

“…Quite recently, we reported that a size-and composition-defined PEG-ODN block copolymer (PEG-b-ODN) also served as an affinity ligand for the discrimination of single-base difference [23]. The PEG segment is water soluble, electrically neutral, and free from nonspecific interaction with biomolecules including DNA [24].…”

Section: Introductionmentioning

confidence: 99%

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Affinity capillary electrophoretic DNA separation using PEG‐oligodeoxyribonucleotide block copolymers: Relationship between peak resolution and affinity strength

Kanayama

Takarada²,

Kimura

et al. 2008

J of Separation Science

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Capillary electrophoretic separation of chemically synthesized ssDNA and a single-base-substituted one (normal and mutant ssDNA, respectively) was demonstrated using a PEG-oligodeoxyribonucleotide block copolymer (PEG-b-ODN) as an affinity ligand. When the base sequence of PEG-b-ODN was designed to be complementary to part of normal ssDNA including the base-substituted site, the electrophoretic mobility of normal ssDNA significantly decreased whereas that of mutant ssDNA slightly changed. Resolution of the separation strongly depended on the ODN length of the copolymer, the capillary temperature, and the Mg2+ concentration in the running buffer, indicating that the retardation of migration of normal ssDNA was induced by the reversible hybridization with PEG-b-ODN. It was found that the dissociation constant (K(d)) of the duplex between normal ssDNA and the affinity probe ODN should be smaller than 10(-6) M to achieve the good peak separation. In addition, we calculated the mobility of the complex (mu(C)) between normal ssDNA and PEG-b-ODN using a two-state model. The base sequence of affinity probe ODN appropriate to achieve the sufficient resolution will be predicted on the basis of the mu(C) and K(d )values.

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Section: Determination Of Thermodynamic Parameterssupporting

confidence: 78%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 94%

“…Size-and composition-controlled PEG-b-ODN copolymers were synthesized by the method previously reported [23].…”

Section: Determination Of Thermodynamic Parametersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Affinity capillary electrophoretic DNA separation using PEG‐oligodeoxyribonucleotide block copolymers: Relationship between peak resolution and affinity strength

Kanayama

Takarada²,

Kimura

et al. 2008

J of Separation Science

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

et al. 2012

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Quantitative SNP detection was demonstrated with an ACE using a PEG-oligodeoxyribonucleotide block copolymer (PEG-b-ODN) as a probe in the presence of an EOF. The probe's PEG segment with large molecular weight and small polydispersity yielded a high resolution in the separation of a chemically synthesized 60-base ssDNA (WT) and its single-base-substituted mutant (MT). A mixture of WT and MT was clearly separated within 10 min by simultaneously using two types of PEG-b-ODN probes whose ODN segments were complementary to WT and MT and whose PEG segments were of different lengths. The peak area ratio between WT and MT was in good agreement with the feed ratio. The averaged difference between the feed and observed ratio of MT was determined to be 0.23%, which is lower than that of any other methods. The ACE using the PEG-b-ODN probes in the presence of EOF could be utilized as a facile method for estimating SNP allele frequency in various research fields.

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Capillary electrophoresis–based immunoassay and aptamer assay: A review

2020

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Capillary electrophoresis-based immunoassay and aptamer assay: A reviewOver the last two decades, the group of techniques called affinity probe CE has been widely used for the detection and the determination of several types of biomolecules with high sensitivity. These techniques combine the low sample consumption and high separation power of CE with the selectivity of the probe to the target molecule. The assays can be defined according to the type of probe used: CE immunoassays, with an antibody as the probe, or aptamer-based CE, with an aptamer as the probe. Immunoassays are generally divided into homogeneous and heterogeneous groups, and homogeneous variant can be further performed in competitive or noncompetitive formats. Interacting partners are free in solution at homogeneous assay, as opposed to heterogeneous analyses, where one of them is immobilized onto a solid support. Highly sensitive fluorescence, chemiluminescence or electrochemical detections were typically used in this type of study. The use of the aptamers as probes has several advantages over antibodies such as shorter generation time, higher thermal stability, lower price, and lower variability. The aptamer-based CE technique was in practice utilized for the determination of proteins in biological fluids and environmentally or clinically important small molecules. Both techniques were also transferred to microchip. This review is focused on theoretical principles of these techniques and a summary of their applications in research.Abbreviations: Ag, antigen; CEIA, CE immunoassay; MCE, microchip CE; SELEX, systematic evolution of ligands by exponential enrichment and they are produced by the immune system of living organisms. Ag that start the immunological response are also called immunogens. These Ab-Ag complexes are stabilized by dipole-dipole, van der Waals or hydrophobic interactions and hydrogen bonds [5,6].The most often used immunoassays are ELISA with Ab or Ag immobilized onto solid support (plates, glass fibers, or plastic tubes), immunofluorescence assay, fluorescence polarization immunoassay, luminescence immunoassay, microparticle enzyme immunoassay, and biosensors. The major disadvantages of immunoassays are the tedious process, time-consuming reactions, and problems with reproducibility and nonspecific interactions [6].CE is a powerful analytical method for the separation of a wide range of molecules. The coupling of CE and immunoassay in the new CE immunoassay (CEIA) technique provided both separation power and specificity of interactions. Other advantages are the possibility of multianalyte analyses, automation, low sample consumption, high speed, flexibility, a lower amount of false-positive results, and also the possibility of connection with highly sensitive detectors [5].In CEIA, the Fab fragments of Ab containing Ag-specific regions are more often used than the whole monoclonal and Color online: See article online to view Figs. 4 and 7 in color.

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Poly(ethylene glycol)-oligodeoxyribonucleotide block copolymers for affinity capillary electrophoretic separation of single-stranded DNAs with a single-base difference

Cited by 13 publications

References 29 publications

Affinity capillary electrophoretic DNA separation using PEG‐oligodeoxyribonucleotide block copolymers: Relationship between peak resolution and affinity strength

Affinity capillary electrophoretic DNA separation using PEG‐oligodeoxyribonucleotide block copolymers: Relationship between peak resolution and affinity strength

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

Capillary electrophoresis–based immunoassay and aptamer assay: A review

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