US 2004/0111221 A1 · Oligonucleotide probes for genosensor chips

Abstract

Software for designing optimized sets of oligonucleotide probes for use in genosensors (oligonucleotide microarrays) is disclosed. The selection of probe sequences is based on multiple criteria including thermal stability of the probe-target pairs, similarity degree of the probes with respect to other DNA sequences, and evaluation of the secondary structure of target molecules. The programs were written in the programming language Borland Delphi by means of Object-Oriented Programming (OOP) techniques. The Genosensor Probe Design computer program disclosed herein facilitates the design of optimized arrays of probes which accurately represents the characteristics of the nucleic acid molecule under study, such as its identity or its differences in sequence or abundance with respect to other molecules.

Claims13

Dependent claims

A software system for designing and selecting oligonucleotide probes for use in DNA microarray, said software system comprising program instructions for:

(a) inputing target DNA sequences;
(b) creating an internal DNA database table that includes the entire target DNA sequences from which oligonucleotide probes are selected;
(c) generating a primary table of oligonucleotides that contains all possible probes of a defined length that can be derived from said DNA target sequences;
(d) creating a secondary table of probes that only contains probes with appropriate composition and thermodynamic properties according to user-defined selection criteria;
(e) selecting from said secondary table specific probes based on methods that evaluate similarity between the probes in said secondary table and selected targeted DNA molecules;
and
(f) performing virtual hybridization to analyze possible hybridization of said oligonucleotide probes against the DNA sequences in said internal DNA database, wherein said analysis shows target sites for perfect hybridization as well as sites that could be potential sites for ambiguous hybridization.

4 more elements

A method for designing and selecting oligonucleotide probes for use in DNA microarray, comprising the steps of:

(a) inputing target DNA sequences;
(b) creating an internal DNA database table that includes the entire target DNA sequences from which oligonucleotide probes are selected;
(c) generating a primary table of oligonucleotides that contains all possible probes of a defined length that can be derived from said DNA target sequences;
(d) creating a secondary table of probes that only contains probes with appropriate composition and thermodynamic properties according to user-defined selection criteria;
and
(e) selecting from said secondary table specific probes based on methods that evaluate similarity between the probes in said secondary table and selected targeted DNA molecules;
and
(f) performing virtual hybridization to analyze possible hybridization of said oligonucleotide probes against the DNA sequences in said internal DNA database, wherein said analysis shows target sites for perfect hybridization as well as sites that could be potential sites for ambiguous hybridization.

5 more elements

Dependencies are inferred from the claim text.

Oligonucleotide probes for genosensor chips

Life of this patent

Oligonucleotide probes for genosensor chips

Life of this patent

Abstract

Claims13