Optical detection of position of oligonucleotides on large DNA molecules
First Claim
1. A method for analyzing a sample oligonucleotide sequence comprising:
- (a) contacting a said sample oligonucleotide sequence with an anchor sequence comprising an oligonucleotide sequence which is immobilized to a support and which hybridizes with said sample oligonucleotide sequence and with a probe comprising an oligonucleotide sequence which hybridizes to a target oligonucleotide sequence to be detected in a suitable buffer to form a complex;
(b) subjecting said complex to a field which moves unbound oligonucleotide sequences away from said anchor sequence in the direction of said field, wherein said field is a magnetic field and a magnetic particle is attached to said sample oligonucleotide sequence or said probe or said field is an electric field; and
(c) determining whether said probe is bound to said sample oligonucleotide sequence.
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Abstract
A method for analyzing a sample oligonucleotide sequence is described. The method comprises contacting the sample oligonucleotide sequence with an anchor sequence which comprises an immobilized oligonucleotide sequence which hybridizes with the sample. The sample is also contacted with a probe comprising an oligonucleotide sequence which hybridizes to a target oligonucleotide sequence to be detected in a suitable buffer to form a complex. The complex is subjected to a field which moves unbound oligonucleotide sequences away from the anchor sequence in the direction of the field, and preferably, extends the sample sequence. Whether the probe is bound to the sample oligonucleotide sequence, and preferably, the position of the probe, is determined to determine whether the target oligonucleotide sequence is present in the sample. The method can be used for mapping, for identity typing, and to determine whether a test oligonucleotide sequence is present in the sample. A device for performing the method and reagents are also described.
154 Citations
30 Claims
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1. A method for analyzing a sample oligonucleotide sequence comprising:
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(a) contacting a said sample oligonucleotide sequence with an anchor sequence comprising an oligonucleotide sequence which is immobilized to a support and which hybridizes with said sample oligonucleotide sequence and with a probe comprising an oligonucleotide sequence which hybridizes to a target oligonucleotide sequence to be detected in a suitable buffer to form a complex; (b) subjecting said complex to a field which moves unbound oligonucleotide sequences away from said anchor sequence in the direction of said field, wherein said field is a magnetic field and a magnetic particle is attached to said sample oligonucleotide sequence or said probe or said field is an electric field; and (c) determining whether said probe is bound to said sample oligonucleotide sequence. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10)
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11. A method for determining whether a first and a second target oligonucleotide sequence are on a molecule of sample DNA comprising:
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(a) contacting said sample DNA with an anchor sequence comprising an oligonucleotide sequence which is immobilized to a support and which hybridizes with said first target oligonucleotide sequence and with a probe which hybridizes with said second target oligonucleotide sequence in a suitable buffer to form a complex; (b) subjecting said complex to an electric field which moves unbound oligonucleotide sequences away from said anchor sequence in the direction of said field; and (c) determining whether said probe is bound to said sample DNA. - View Dependent Claims (12, 13, 14, 15, 16)
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17. A method for obtaining a pattern characteristic of sample DNA comprising:
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(a) contacting said sample DNA with an anchor sequence comprising an immobilized, conserved oligonucleotide sequence which hybridizes with said sample DNA and with a plurality of probes, each of said probes comprising an oligonucleotide sequence of from about 5 to about 15 bases in a suitable buffer to form a complex; (b) subjecting said complex to an electric field which moves unbound oligonucleotide sequences away from said anchor sequence and extends said sample DNA in the direction of said field; and (c) determining the positions of said probes from said anchor sequence. - View Dependent Claims (18, 19, 20, 21)
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22. A method for determining whether sample DNA and test DNA are from the same individual comprising:
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(a) contacting said sample DNA and said test DNA with an anchor sequence comprising an immobilized, conserved oligonucleotide sequence which hybridizes with said test DNA and with a plurality of probes, each of said probes comprising an oligonucleotide sequence of from about 5 to about 15 bases in a suitable buffer to form a complex; (b) subjecting said complex to an electric field which moves unbound oligonucleotide sequences away from said anchor sequence and extends said sample DNA in the direction of said field; (c) determining the positions of said probes from said anchor sequence for said sample DNA and said test DNA; and (d) comparing the positions of said probes for said test DNA to said probes for said sample DNA.
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23. A method for determining whether a putative father is the father of a child comprising:
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(a) contacting said sample DNA from said putative father, said child and the mother of said child with an anchor sequence comprising an immobilized, conserved oligonucleotide sequence which hybridizes with said putative father'"'"'s DNA and with a plurality of probes, each of said probes comprising an oligonucleotide sequence of from about 5 to about 15 bases in a suitable buffer to form a complex; (b) subjecting said complex to an electric field which moves unbound oligonucleotide sequences away from said anchor sequence and extends said sample DNA in the direction of said field; (c) determining the positions of said probes from said anchor sequence for said DNA from said putative father, said child, and said mother; (d) comparing the positions of said probes for said child'"'"'s DNA to those of said mother; and (e) comparing any positions of the probes of said child which do not match with the probes of said mother to said probes of said putative father.
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24. A method for determining whether a test oligonucleotide sequence is present in sample oligonucleotide sequence comprising:
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(a) contacting said sample oligonucleotide sequence with an anchor sequence comprising an immobilized, conserved oligonucleotide sequence known to hybridize with an oligonucleotide sequence present in said sample oligonucleotide sequence and with a probe comprising an oligonucleotide sequence which binds to said test oligonucleotide sequence in a suitable buffer to form a complex; (b) subjecting said complex to an electric field which moves unbound oligonucleotide sequences away from said anchor sequence and extends said sample DNA in the direction of said field; and (c) determining whether said probe is bound to said sample oligonucleotide sequence. - View Dependent Claims (25, 26, 27, 28, 29, 30)
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Specification