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Fractals for Multicyclic Synthesis Conditions of Biopolymers: Examples of Oligonucleotide Synthesis Measured by High-Performance Capillary Electrophoresis and Ion-Exchange High-Performance Liquid Chromatography

Z. Földes-Papp
E. Birch-Hirschfeld
H. Eickhoff
Gerd Baumann
Organization: Visual Analysis
W.-G. Peng
T. Biber
R. Seydel
A. Kleinschmidt
H. Seliger
Journal / Anthology

Journal of Chromatography A
Year: 1996
Volume: 739
Page range: 431-447

We have developed models of patterns for nucleotide chain growth. These patterns are measurable by high-performance capillary electrophoresis and ion-exchange high-performance liquid chromatography in crude products of solid-phase synthesized 30mer and 65mer oligodeoxyribonucleotide target sequences N. We introduce mathematical methods for finding characteristic values d0 and p0 for constant chemical modes of growth as well as d and p for non-constant chemical modes of growth (d = probability of propagation, p = probability of termination). These methods are employed by presenting the accompanying computer software developed by us in C code, MathematicaR languages, and Fortran.

Characteristic values of the parameters d, p, and the target nucleotide length N describe the complete composition of the crude product. From this we have developed the relation 2 - [N/(N - 1)]/Da, measurable(N,d) as a universal quantitative measure for multicyclic synthesis conditions (D, fractal dimension and similarity exponent, respectively). We use this mathematical treatment to compare the efficiency of oligodeoxyribonucleotide syntheses of different target length N on polymer support materials. Further, we analyze selected syntheses of short and long oligodeoxyribonucleotides as well as single-stranded DNA sequences by well-known empirical autocorrelation, fast Fourier transformation, and embedding-dimension techniques.

*Science > Biology
*Science > Chemistry

Oligonucleotide synthesis, chemical, Nucleotide sequence variability, Gene assembly, Fractal dimension, Data analysis, Polymerization processes, Enzymatic nucleotide growth, Oligodeoxyribonucleotides, Oligonucleotides, Oligoribonucleotides, DNA