Fractal dimension of error sequence dynamics in quantitative modeling of syntheses of short oligonucleotide and single-stranded DNA sequences
Identifieur interne : 001873 ( Istex/Checkpoint ); précédent : 001872; suivant : 001874Fractal dimension of error sequence dynamics in quantitative modeling of syntheses of short oligonucleotide and single-stranded DNA sequences
Auteurs : Zeno Földes-Papp [Allemagne] ; Wei-Guo Peng [Allemagne] ; Hartmut Seliger [Allemagne] ; Albrecht K. Kleinschmidt [Allemagne]Source :
- Journal of Theoretical Biology [ 0022-5193 ] ; 1995.
English descriptors
- Teeft :
- Academic press, Agarose, Aqueous ammonium hydroxide, Average values, Biomedical application, Biosystems, Capillary electrophoresis, Cassette, Chain length, Chaotic dynamics, Chemical oligonucleotide synthesis, Chemical synthesis, Cluster analysis, Computer program, Crude product, Crude products, Data points, Data sets, Dynamical, Dynamical system, Dynamical system complexity, Dynamics, Electrophoresis, Error accumulation, Error propagation, Error sequence, Error sequence dynamics, Error sequences, Error sequences dynamics, Ethidium agarose, Ethidium bromide, Experimental curve, Experimental frequency distribution, External synthesis conditions, Fmc8 biozym diagnostik, Fractal, Fractal dimension, Fractal dimensions, Fractal geometry, Frequency distribution, Frequency distributions, Fusion protein cleavage, Genetics computer group, Growth dependence, Growth phenomena, Growth term, Hplc, Initial conditions, Inset, Internal conditions, Internal standards, Inverse power, Johnson faunt, Last reaction cycle, Long oligonucleotides, Lower limit, Main text, Mathematical model, Methods enzymol, Microconcentrator columns, Mmol scale, Molecular biology, Molecular growth process, Nonlinear equations, Nucleic acids, Nucleotide, Nucleotide length, Nucleotide length scale, Nucleotide length standards, Nucleotide lengths, Nucleotide sequence, Oligonucleotide, Oligonucleotide growth, Oligonucleotide syntheses, Oligonucleotide synthesis, Oligonucleotides, Overall pattern, Phosphoramidite chemistry, Polymer, Polymer support, Polymer support synthesis, Polymerase chain reaction, Primer, Probability function, Probability functions, Quantitative electrophoresis, Quantitative measure, Reaction conditions, Reaction cycle, Reaction cycles, Reaction step, Recursive relations, Relation limd, Relative yields, Room temperature, Routine syntheses, Sequence, Sequence analysis, Sequence analysis software package, Short oligonucleotides, Short target oligonucleotides, Sodium acetate, Software, Software package, Solid phase, Splint ligation, Synthesis, Synthesis conditions, Synthetic dynamics, Synthetic genes, System complexity, Target nucleotide length, Target nucleotides, Target sequence, Target sequences, Tetrahedron lett, Theoretical curve, Theoretical curves, Total amount, Unambiguous peaks, Variation generator, Visual inspection, Warren vella.
Abstract
Oligonucleotides are becoming more and more important in molecular biomedicine; for example, they are used as defined primers in polymerase chain reaction and as antisense oligonucleotides in gene therapy. In this paper, we model the dynamics of polymer-supported oligonucleotide synthesis to an inverse power law of driven multi-cycle synthesis on fixed starting sites. The mathematical model is employed by presenting the accompanying view of error sequences dynamics. This model is a practical one, and is applicable beyond oligonucleotide synthesis to dynamics of biological diversity.Computer simulations show that the polymer support synthesis of oligonucleotides and single-stranded DNA sequences in iterated cyclic format can be assumed as scale-invariant. This synthesis is quantitatively described by nonlinear equations. From these the fractal dimension Da(N, d) is derived as the growth term (N = number of target nucleotides, d = coupling probability function). Da(N, d) is directly measurable from oligonucleotide yields via high-performance liquid chromatography or capillary electrophoresis, and quantitative gel electrophoresis. Different oligonucleotide syntheses, including those with large-scale products can be directly compared with regard to error sequences dynamics. In addition, for short sequences the fractal dimension Da(N, d) is characteristic for the efficiency with which a polymer support of a given load allows oligonucleotide chain growth.We analyze the results of separations of crude oligonucleotide product from the synthesis of a 30 mer. Preliminary analysis of a 238 mer single-stranded DNA sequence is consistent with a simulated estimate of crude synthesis product, although the target sequence itself is not detectable. We characterize the oligonucleotide support syntheses by simulated and experimentally determined values of the fractal dimension Da(N, d0) within limitations (d0 = constant (average) coupling probability).
Url:
DOI: 10.1006/jtbi.1995.0107
Affiliations:
- Allemagne
- Bade-Wurtemberg, Bavière, District de Haute-Bavière, District de Tübingen
- Munich, Ulm
- Université d'Ulm
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Kleinschmidt</name><affiliation wicri:level="1"><country xml:lang="fr">Allemagne</country><wicri:regionArea>Abteilung für Experimentelle Physik</wicri:regionArea></affiliation></author></analytic><monogr></monogr><series><title level="j">Journal of Theoretical Biology</title><title level="j" type="abbrev">YJTBI</title><idno type="ISSN">0022-5193</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1995">1995</date><biblScope unit="volume">174</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="391">391</biblScope><biblScope unit="page" to="408">408</biblScope></imprint><idno type="ISSN">0022-5193</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0022-5193</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Academic press</term><term>Agarose</term><term>Aqueous ammonium hydroxide</term><term>Average values</term><term>Biomedical application</term><term>Biosystems</term><term>Capillary electrophoresis</term><term>Cassette</term><term>Chain length</term><term>Chaotic dynamics</term><term>Chemical oligonucleotide synthesis</term><term>Chemical synthesis</term><term>Cluster analysis</term><term>Computer program</term><term>Crude product</term><term>Crude products</term><term>Data points</term><term>Data sets</term><term>Dynamical</term><term>Dynamical system</term><term>Dynamical system complexity</term><term>Dynamics</term><term>Electrophoresis</term><term>Error accumulation</term><term>Error propagation</term><term>Error sequence</term><term>Error sequence dynamics</term><term>Error sequences</term><term>Error sequences dynamics</term><term>Ethidium agarose</term><term>Ethidium bromide</term><term>Experimental curve</term><term>Experimental frequency distribution</term><term>External synthesis conditions</term><term>Fmc8 biozym diagnostik</term><term>Fractal</term><term>Fractal dimension</term><term>Fractal dimensions</term><term>Fractal geometry</term><term>Frequency distribution</term><term>Frequency distributions</term><term>Fusion protein cleavage</term><term>Genetics computer group</term><term>Growth dependence</term><term>Growth phenomena</term><term>Growth term</term><term>Hplc</term><term>Initial conditions</term><term>Inset</term><term>Internal conditions</term><term>Internal standards</term><term>Inverse power</term><term>Johnson faunt</term><term>Last reaction cycle</term><term>Long oligonucleotides</term><term>Lower limit</term><term>Main text</term><term>Mathematical model</term><term>Methods enzymol</term><term>Microconcentrator columns</term><term>Mmol scale</term><term>Molecular biology</term><term>Molecular growth process</term><term>Nonlinear equations</term><term>Nucleic acids</term><term>Nucleotide</term><term>Nucleotide length</term><term>Nucleotide length scale</term><term>Nucleotide length standards</term><term>Nucleotide lengths</term><term>Nucleotide sequence</term><term>Oligonucleotide</term><term>Oligonucleotide growth</term><term>Oligonucleotide syntheses</term><term>Oligonucleotide synthesis</term><term>Oligonucleotides</term><term>Overall pattern</term><term>Phosphoramidite chemistry</term><term>Polymer</term><term>Polymer support</term><term>Polymer support synthesis</term><term>Polymerase chain reaction</term><term>Primer</term><term>Probability function</term><term>Probability functions</term><term>Quantitative electrophoresis</term><term>Quantitative measure</term><term>Reaction conditions</term><term>Reaction cycle</term><term>Reaction cycles</term><term>Reaction step</term><term>Recursive relations</term><term>Relation limd</term><term>Relative yields</term><term>Room temperature</term><term>Routine syntheses</term><term>Sequence</term><term>Sequence analysis</term><term>Sequence analysis software package</term><term>Short oligonucleotides</term><term>Short target oligonucleotides</term><term>Sodium acetate</term><term>Software</term><term>Software package</term><term>Solid phase</term><term>Splint ligation</term><term>Synthesis</term><term>Synthesis conditions</term><term>Synthetic dynamics</term><term>Synthetic genes</term><term>System complexity</term><term>Target nucleotide length</term><term>Target nucleotides</term><term>Target sequence</term><term>Target sequences</term><term>Tetrahedron lett</term><term>Theoretical curve</term><term>Theoretical curves</term><term>Total amount</term><term>Unambiguous peaks</term><term>Variation generator</term><term>Visual inspection</term><term>Warren vella</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Oligonucleotides are becoming more and more important in molecular biomedicine; for example, they are used as defined primers in polymerase chain reaction and as antisense oligonucleotides in gene therapy. In this paper, we model the dynamics of polymer-supported oligonucleotide synthesis to an inverse power law of driven multi-cycle synthesis on fixed starting sites. The mathematical model is employed by presenting the accompanying view of error sequences dynamics. This model is a practical one, and is applicable beyond oligonucleotide synthesis to dynamics of biological diversity.Computer simulations show that the polymer support synthesis of oligonucleotides and single-stranded DNA sequences in iterated cyclic format can be assumed as scale-invariant. This synthesis is quantitatively described by nonlinear equations. From these the fractal dimension Da(N, d) is derived as the growth term (N = number of target nucleotides, d = coupling probability function). Da(N, d) is directly measurable from oligonucleotide yields via high-performance liquid chromatography or capillary electrophoresis, and quantitative gel electrophoresis. Different oligonucleotide syntheses, including those with large-scale products can be directly compared with regard to error sequences dynamics. In addition, for short sequences the fractal dimension Da(N, d) is characteristic for the efficiency with which a polymer support of a given load allows oligonucleotide chain growth.We analyze the results of separations of crude oligonucleotide product from the synthesis of a 30 mer. Preliminary analysis of a 238 mer single-stranded DNA sequence is consistent with a simulated estimate of crude synthesis product, although the target sequence itself is not detectable. We characterize the oligonucleotide support syntheses by simulated and experimentally determined values of the fractal dimension Da(N, d0) within limitations (d0 = constant (average) coupling probability).</div></front></TEI><affiliations><list><country><li>Allemagne</li></country><region><li>Bade-Wurtemberg</li><li>Bavière</li><li>District de Haute-Bavière</li><li>District de Tübingen</li></region><settlement><li>Munich</li><li>Ulm</li></settlement><orgName><li>Université d'Ulm</li></orgName></list><tree><country name="Allemagne"><region name="Bade-Wurtemberg"><name sortKey="Foldes Papp, Zeno" sort="Foldes Papp, Zeno" uniqKey="Foldes Papp Z" first="Zeno" last="Földes-Papp">Zeno Földes-Papp</name></region><name sortKey="Kleinschmidt, Albrecht K" sort="Kleinschmidt, Albrecht K" uniqKey="Kleinschmidt A" first="Albrecht K." last="Kleinschmidt">Albrecht K. Kleinschmidt</name><name sortKey="Peng, Wei Guo" sort="Peng, Wei Guo" uniqKey="Peng W" first="Wei-Guo" last="Peng">Wei-Guo Peng</name><name sortKey="Peng, Wei Guo" sort="Peng, Wei Guo" uniqKey="Peng W" first="Wei-Guo" last="Peng">Wei-Guo Peng</name><name sortKey="Seliger, Hartmut" sort="Seliger, Hartmut" uniqKey="Seliger H" first="Hartmut" last="Seliger">Hartmut Seliger</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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