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Maeda M. Sequence-Specific Aggregation Behavior of DNA-Carrying Colloidal Nanoparticles Prepared from Poly(N-isopropylacrylamide)-graft-Oligodeoxyribonucleotide. Polym J 2006. [DOI: 10.1295/polymj.pj2006107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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2
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Oba S, Hatakeyama M, Handa H, Kawaguchi H. Development of Polymer Latex Particles for Selective Cleavage of Mismatched DNA and Their Application for DNA Diagnosis. Bioconjug Chem 2005; 16:551-8. [PMID: 15898721 DOI: 10.1021/bc049728l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed functional polymer latex particles that can catch and cleave mismatched DNA selectively and propose a new mismatch detection system using the functional particles. The aimed particles possess two functional units composed of mismatch binding protein (MutS) and an anthraquinone derivative (AQ), a light-activated agent that photocleaves dsDNA. Use of the functional particles made it possible to discriminate complementary and mismatched DNAs and photocleave mismatched DNA selectively. The efficiency of photocleavage of mismatched DNA by the functional particles increased with UV irradiation time. It was also found that the functional particles were reusable and had dissociation constants (K(d)) of 1000 and 68.5 nM for G/C homoduplex and G/T heteroduplex, respectively. Using the functional particles and a dsDNA-binding fluorescent dye, SYBR-Gold, we could construct the system for detection of mismatched DNA that was 40 base pairs. The functional particles prepared in this study will be an absolutely new tool for mismatch detection in DNA diagnosis.
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Affiliation(s)
- Shinsuke Oba
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Kouhoku-ku, Yokohama 223-8522, Japan
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3
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Extended Langmuir approach to analyze the telomeric sequence using a biochromatographic concept. Anal Chim Acta 2004. [DOI: 10.1016/j.aca.2004.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Elaissari A, Ganachaud F, Pichot C. Biorelevant Latexes and Microgels for the Interaction with Nucleic Acids. Top Curr Chem (Cham) 2003. [DOI: 10.1007/3-540-36412-9_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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5
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Lee GY, Chen CH, Wang TH, Lee WC. Affinity chromatography of DNA on nonporous copolymerized particles of styrene and glycidyl methacrylate with immobilized polynucleotide. Anal Biochem 2003; 312:235-41. [PMID: 12531211 DOI: 10.1016/s0003-2697(02)00507-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Nonporous particles of microsize were prepared by the dispersion polymerization of styrene and glycidyl methacrylate and chemically modified to introduce amino groups on the surface by grafting with either hexamethylenediamine or N-methyl-1,3-propanediamine. Aminated particles were then coupled with phosphorylated single-stranded polynucleotides at the 5'-end through covalent linkages. The affinity columns packed with these prepared polynucleotide-immobilized particles effectively retained single-stranded DNA, which could base-pair with the immobilized sequence. Bound DNAs could be eluted to yield a sharp peak by using an aqueous solution of 0.4M NaOH. The nonspecific adsorption due to the electrostatic interaction between the polynucleotide and the residual amino groups on the particle surface via the amination with hexamethylenediamine was significant and could only be reduced by using a high salt (NaCl) concentration. A higher salt concentration in the elution solution could result in a portion of complementary polynucleotide eluted in the nonretained fraction. However, the nonspecific adsorption of polynucleotides was insignificant in the column packed with DNA-immobilized particles prepared via amination using N-methyl-1,3-propanediamine. The column was effective for microanalysis of sequence-specific DNA.
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Affiliation(s)
- Gow-Yuan Lee
- Department of Chemical Engineering, National Chung Cheng University, Chiayi 621, Taiwan
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Ganachaud F, Laayoun A, Chaix C, Delair T, Pichot C, Elaïssari A. Oligodeoxyribonucleotide Activation with 2,4-Phenylenediisothiocyanate and Their Covalent Grafting onto Amine-Functionalized Latex Microspheres. J DISPER SCI TECHNOL 2001. [DOI: 10.1081/dis-100107856] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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Ganachaud F, Elaissari A, Pichot C. Covalent grafting of polythymidylic acid onto amine-containing polystyrene latex particles. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2001; 11:931-45. [PMID: 11211087 DOI: 10.1163/156856200744110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The covalent grafting of a 35-base poly(thymidylic) acid (dT35) onto aminated polystyrene latex has been studied. The oligonucleotide was activated by 1,4-phenylene diisothiocyanate (PDC) prior to grafting reaction. The influence of various experimental conditions related either to the medium (pH, ionic strength) or to the latex (nature and surface charge density, presence of adsorbed nonionic surfactant) was studied. Discrimination between covalent grafting and adsorption was achieved by desorbing the non-covalently grafted dT35 induced by consecutive washings with a suitable buffer solution. The amount of covalently grafted oligonucleotide directly correlated to the concentration and accessible functional groups at the particle surface.
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Affiliation(s)
- F Ganachaud
- Unité Mixte CNRS-bioMérieux ENS, Lyon, France
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Mori T, Umeno D, Maeda M. Sequence-specific affinity precipitation of oligonucleotide using poly(N-isopropylacrylamide)-oligonucleotide conjugate. Biotechnol Bioeng 2001; 72:261-8. [PMID: 11135195 DOI: 10.1002/1097-0290(20010205)72:3<261::aid-bit2>3.0.co;2-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this study we develop a sequence-specific precipitation separation system of oligonucleotide (ODN) using a conjugate between poly(N-isopropylacrylamide) (PNIPAM) and ODN. PNIPAM is known as a thermoresponsive polymer and dehydrates to precipitate above its phase transition temperature in an aqueous milieu. The principal advantage of this separation system using the conjugate is that the hybridization reaction between the conjugate and oligonucleotide is conducted in homogeneous solution. The conjugate was prepared by copolymerization between N-isopropylacrylamide and a vinyl-derivatized (dT)(8). The obtained conjugate efficiently precipitated (dA)(8) from solution when the solution contained more than 1.5 M NaCl. The conjugate containing 3 nmol of (dT)(8) residue was able to precipitate 1.4 nmol of (dA)(8), suggesting that the (dT)(8) residue of the conjugate formed a triple helix with (dA)(8). From an equimolar mixture of (dA)(8) and its one point mutant, the conjugate selectively precipitated (dA)(8): the highest selectivity was obtained for the isolation of (dA)(8) from the mixture consisting of (dA)(4)dT(dA)(3) and (dA)(8). When the conjugate was applied for the precipitation of five oligo(dA)s having different chain lengths, the longer oligo(dA)s tended to be precipitated by the conjugate more efficiently than the shorter ones. The conjugate could be used repeatedly for precipitation of (dA)(8) without showing any loss in precipitation efficiency.
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Affiliation(s)
- T Mori
- Department of Materials Physics and Chemistry, Graduate School of Engineering, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Mori T, Maeda M. Formation of DNA-Carrying Colloidal Particle from Poly(N-isopropylacrylamide)-graft-DNA Copolymer and Its Assembly through Hybridization. Polym J 2001. [DOI: 10.1295/polymj.33.830] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Ma GH, Nagai M, Omi S. Study on preparation of monodispersed poly(styrene-co-N-dimethylaminoethyl methacrylate) composite microspheres by SPG (Shirasu Porous Glass) emulsification technique. J Appl Polym Sci 2001. [DOI: 10.1002/1097-4628(20010328)79:13<2408::aid-app1048>3.0.co;2-q] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Spiro A, Lowe M, Brown D. A bead-based method for multiplexed identification and quantitation of DNA sequences using flow cytometry. Appl Environ Microbiol 2000; 66:4258-65. [PMID: 11010868 PMCID: PMC92294 DOI: 10.1128/aem.66.10.4258-4265.2000] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new multiplexed, bead-based method which utilizes nucleic acid hybridizations on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences is described. The method consists of three elements: beads (5.6-microm diameter) with oligomer capture probes attached to the surface, three fluorophores for multiplexed detection, and flow cytometry instrumentation. Two fluorophores are impregnated within each bead in varying amounts to create different bead types, each associated with a unique probe. The third fluorophore is a reporter. Following capture of fluorescent cDNA sequences from environmental samples, the beads are analyzed by flow cytometric techniques which yield a signal intensity for each capture probe proportional to the amount of target sequences in the analyte. In this study, a direct hybrid capture assay was developed and evaluated with regard to sequence discrimination and quantitation of abundances. The target sequences (628 to 728 bp in length) were obtained from the 16S/23S intergenic spacer region of microorganisms collected from polluted groundwater at the nuclear waste site in Hanford, Wash. A fluorescence standard consisting of beads with a known number of fluorescent DNA molecules on the surface was developed, and the resolution, sensitivity, and lower detection limit for measuring abundances were determined. The results were compared with those of a DNA microarray using the same sequences. The bead method exhibited far superior sequence discrimination and possesses features which facilitate accurate quantitation.
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Affiliation(s)
- A Spiro
- Physics Department, Loyola College in Maryland, Baltimore, Maryland 21210, USA
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Hatakeyama M, Iwato S, Hanashita H, Nakamura K, Fujimoto K, Kawaguchi H. DNA-carrying latex particles for DNA diagnosis 3. Detection of point mutant DNA using an indirect labeled probe. Colloids Surf A Physicochem Eng Asp 1999. [DOI: 10.1016/s0927-7757(98)00466-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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13
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Elaissari A, Holt L, Meunier F, Voisset C, Pichot C, Mandrand B, Mabilat C. Hydrophilic and cationic latex particles for the specific extraction of nucleic acids. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 1999; 10:403-20. [PMID: 10227464 DOI: 10.1163/156856299x00171] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The adsorption of BSA and RNA onto hydrophilic and thermosensitive poly(N-isopropyl-acrylamide) (NIPAM) latex particles was described as a function of pH, ionic strength and temperature. The hydrogel poly(NIPAM) latex was synthesized by precipitation polymerization in the presence of a cationic amino-containing monomer. The latex obtained was characterized in terms of particle size, and electrophoretic mobility as a function of pertinent variables: pH, temperature and ionic strength. The adsorption of BSA onto the latex was investigated to identify the conditions at which the adsorbed amount of BSA was negligible. The adsorption of RNA was studied to establish the conditions which give rise to maximal adsorption of RNA. In order to favor the desorption of RNA, desorption was investigated by changing the pH, ionic strength, and temperature. The adsorption of BSA was found to be lower at 20 than at 40 degrees C. However, the adsorption of RNA is drastically affected by the pH and the ionic strength of the medium. Maximal adsorbed amounts were obtained at acidic pH, 20 degrees C, and low ionic strength. The adsorption is shown to decrease when the pH, temperature and ionic strength increase, implying that the adsorption was mainly governed by electrostatic interactions. Maximal release of RNA molecules was obtained at high ionic strength and basic pH.
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Umeno D, Maeda M. Temperature-Induced Precipitation of Specific DNA Fragments Using DNA-Poly(N-isopropylacrylamide) Conjugate. CHEM LETT 1999. [DOI: 10.1246/cl.1999.381] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Dorsey JG, Cooper WT, Siles BA, Foley JP, Barth HG. Liquid Chromatography: Theory and Methodology. Anal Chem 1998. [DOI: 10.1021/a1980022h] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- John G. Dorsey
- Department of Chemistry, Florida State University, Tallahassee, Florida 32306-4390
| | - William T. Cooper
- Department of Chemistry, Florida State University, Tallahassee, Florida 32306-4390
| | - Barbara A. Siles
- Department of Chemistry, College of William and Mary, Williamsburg, Virginia 23187-8795
| | - Joe P. Foley
- Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085-1699
| | - Howard G. Barth
- Central Research and Development Department, E. I. du Pont de Nemours & Company, P.O. Box 80228, Experimental Station, Wilmington, Delaware 19880
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DNA-carrying latex particles for DNA diagnosis. 1. Separation of normal and point mutant DNAs according to the difference in hybridization efficiency. Colloids Surf B Biointerfaces 1998. [DOI: 10.1016/s0927-7765(97)00059-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Hatakeyama M, Nakamura K, Iwato S, Handa H, Fujimoto K, Kawaguchi H. DNA-carrying latex particles for DNA diagnosis 2. Distinction of normal and point mutant DNA using S1 nuclease. Colloids Surf B Biointerfaces 1998. [DOI: 10.1016/s0927-7765(97)00058-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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18
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Preparation of dimerized polypeptide-carrying microspheres and purification of specific proteins bound to these microspheres. Colloids Surf B Biointerfaces 1997. [DOI: 10.1016/s0927-7765(97)00042-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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