FRACTAL DIMENSION OF ERROR SEQUENCE DYNAMICS IN QUANTITATIVE MODELING OF SYNTHESES OF SHORT OLIGONUCLEOTIDE AND SINGLE-STRANDED-DNA SEQUENCES

被引：7

作者：

FOLDESPAPP, Z ^{[1
]}

PENG, WG ^{[1
]}

SELIGER, H ^{[1
]}

KLEINSCHMIDT, AK ^{[1
]}

机构：

[1] UNIV ULM, EXPTL PHYS ABT, ULM, GERMANY

来源：

JOURNAL OF THEORETICAL BIOLOGY | 1995年 / 174卷 / 04期

关键词：

D O I：

10.1006/jtbi.1995.0107

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 D-u (N, d) is derived as the growth term (N = number of target nucleotides, d = coupling probability function). D-u (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 D-u (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 D-u (N, d(o)) within imitations (d(o) = constant (average) coupling probability).

引用

页码：391 / 408

页数：18

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