Oligonucleotide retention time prediction method

An oligonucleotide and retention time technology, which can be used in biochemical equipment and methods, measuring devices, and microbial determination/inspection. big effect

Inactive Publication Date: 2010-09-29
CHONGQING UNIV
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Problems solved by technology

Large-scale purification using liquid chromatography requires the selection of suitable experimental conditions and parameters. Optimizing through experiments is theoretically feasible, but practically difficult (Gilar et al., J Chromatogr A, 2002, 958: 167)

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  • Oligonucleotide retention time prediction method
  • Oligonucleotide retention time prediction method
  • Oligonucleotide retention time prediction method

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Embodiment Construction

[0013] The following is a detailed description of the use of the method of the present invention for oligonucleotide chromatographic retention time prediction as an example, including the following steps:

[0014] a) Select 585 three-dimensional property parameters of 5 kinds of bases (A, C, G, T and U), including: Randic molecular profile parameters, geometric feature parameters, radial basis function descriptors (RDF) based on different atomic distances ), the descriptor obtained by the molecular structure characterization (MoRSE) based on the electric diffraction method, the descriptor of the weighted whole invariant molecule (WHIM) and the set of geometry, topology and atomic weight (GETAWAY) parameters;

[0015] Principal component analysis is used to process 585 kinds of property parameters, and 4 principal components are obtained, which accumulatively explain 99.68% of the variance of the original data matrix (5×585). The scores of the principal components are shown in T...

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Abstract

The invention discloses an oligonucleotide retention time prediction method which comprises the following steps that: (a) based on a main component analysis method, a DNA sequence structure characterization method i.e. the score of alkali-based three-dimensional nature is established; (b) the score of the alkali-based three-dimensional nature characterizes the structures of oligonucleotides; (c) the characterization variables of each oligonucleotide are normalized through a self-crossing covariance method; (d) nature parameters which are closely related to the chromatogram retention index of the oligonucleotide are picked through genetic algorithm; and (e) RBF-SVR is applied to build an oligonucleotide retention time prediction model so as to validate the prediction capability of the model respectively through self-replacement test, LOO interactive test and external test. The method can be used for predicting the oligonucleotide retention time and oligonucleotide quantitative structure retention relationship analysis, and optimize and select appropriate chromatographic conditions and parameters.

Description

technical field [0001] The invention relates to a method for predicting DNA quantitative chromatographic retention, in particular to a method for predicting oligonucleotide chromatographic retention time. Background technique [0002] Oligonucleotides are often used as probes to determine the structure of DNA or RNA, and are widely used in processes such as gene chips, electrophoresis, and fluorescence in situ hybridization. Among its many separation and analysis methods, reversed-phase high-pressure liquid chromatography has the advantages of quickness, high efficiency and high selectivity (Huber, et al., J Chromatogr A, 1998, 806: 1). Large-scale purification using liquid chromatography requires the selection of suitable experimental conditions and parameters. It is theoretically feasible to optimize through experiments, but it is difficult in practice (Gilar et al., J Chromatogr A, 2002, 958: 167). Quantitative structure-retention relationship models provide an important...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G01N30/02C12Q1/68
Inventor 梁桂兆赵巍马秀岩杨力
Owner CHONGQING UNIV
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