Oligonucleotide probes for genosensor chips

• US 20040111221A1
• Filed: 04/09/2003
• Published: 06/10/2004
• Est. Priority Date: 04/09/2002
• Status: Active Grant

• Current Assignee: UT-Battelle LLC
• Original Assignee: UT-Battelle LLC
• Inventors: Guerra-Trejo, Armando, Mendez-Tenorio, Alfonso, Doktycz, Mitchel J., Beattie, Kenneth L., Maldonado-Rodriguez, Rogelio
• Granted Patent: US 7,539,579 B2
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search

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.

Claims

1. 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.

2. The software system of claim 1, wherein said target DNA sequences are selected from the group consisting of single DNA sequence, multiple DNA sequences, DNA sequence database, oligonucleotide sequences and oligonucleotide database.

3. The software system of claim 1, wherein said user-defined selection criteria comprise criteria for rejecting or accepting oligonucleotide probes based upon user-specified criteria selected from the group consisting of [A+T] composition, [G+C] composition, melting temperature (Tm) range, enthalpy, entropy, free energy, internal repeated sequences, sequence symmetry of probes, and frequency of occurrence.

4. The software system of claim 1, wherein said software system comprises program instructions for selecting oligonucleotide probes according to a program application selected from the group consisting of simple selection application, mapping application, non-aligned sequences application, aligned sequences application and tandem hybridization application.

5. The software system of claim 1, wherein said virtual hybridization is performed according the algorithm comprising the steps of:

(a) selecting a minimal value (minbasescom) for the number of complementary bases between probes and potential hybridization sites, wherein said minbasescom is defined as 2≦

minbasescom≦

L (a given probe length);

(b) selecting a minimal value (minblocksize) for the length of contiguously paired bases within potential hybridization sites, wherein said minblocksize is specified as 2≦

minblocksize≦

L (a given probe length);

(c) selecting potential hybridization sites by evaluating the complementarity degree between said oligonucleotide probes and potential hybridization sites along the target sequences, wherein said potential hybridization sites are defined as sites where the number of complementary bases between the probe and the evaluated sites is equal to or greater than minbasescom or sites where a block of contiguously paired bases is equal to or greater than minblocksize;

(d) calculating the free energy value (Δ

G°

) for the thermal stability of probes paired with their respective potential hybridization sites using the nearest-neighbor model; and

(e) selecting sites of high hybridization probability, wherein said sites of high hybridization probability are potential hybridization sites with Δ

G°

values equal to or greater than pre-determined Δ

G°

cutoff values.

6. The software system of claim 1, wherein said selection of oligonucleotide probes from said specific probes comprises adding or deleting nucleotides from one or both ends of said specific probes.

7. 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.

8. The method of claim 7, wherein said target DNA sequences are selected from the group consisting of single DNA sequence, multiple DNA sequences, DNA sequence database, oligonucleotide sequences and oligonucleotide database.

9. The method of claim 7, wherein said user-defined selection criteria comprise criteria for rejecting or accepting oligonucleotide probes based upon user-specified criteria selected from the group consisting of [A+T] composition, [G+C] composition, melting temperature (Tm) range, enthalpy, entropy, free energy, internal repeated sequences, sequence symmetry of probes, and frequency of occurrence.

10. The method of claim 7, wherein said software system comprises program instructions for selecting oligonucleotide probes according to a program application selected from the group consisting of simple selection application, mapping application, non-aligned sequences application, aligned sequences application and tandem hybridization application.

11. The method of claim 7, wherein said virtual hybridization is performed according the algorithm comprising the steps of:

(a) selecting a minimal value (minbasescom) for the number of complementary bases between probes and potential hybridization sites, wherein said minbasescom is defined as 2≦

minbasescom≦

L (a given probe length);

(b) selecting a minimal value (minblocksize) for the length of contiguously paired bases within potential hybridization sites, wherein said minblocksize is specified as 2≦

minblocksize≦

L (a given probe length);

(c) selecting potential hybridization sites by evaluating the complementarity degree between probes and potential hybridization sites along the target sequences, wherein said potential hybridization sites are defined as sites where the number of complementary bases between the probe and the evaluated sites is equal to or greater than minbasescom or sites where a block of contiguously paired bases is equal to or greater than minblocksize;

(d) calculating the free energy value (Δ

G°

) for the thermal stability of probes paired with their respective potential hybridization sites using the nearest-neighbor model; and

(e) selecting sites of high hybridization probability, wherein said sites of high hybridization probability are potential hybridization sites with Δ

G°

values equal to or greater than pre-determined Δ

G°

cutoff values.

12. The software system of claim 7, wherein said selection of oligonucleotide probes from said specific probes comprises adding or deleting nucleotides from one or both ends of said specific probes.

13. A method for designing and selecting optimized sets of 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;

(e) performing virtual hybridization to predict the hybridization pattern of probes contained in said secondary table; and

(f) eliminating probes which have the potential for ambiguous hybridization, thereby yielding an optimized set of specific probes for use in DNA microarray.