Detection oligomer and method for controlling quality of biochip using detection oligomer
First Claim
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1. A method of assessing biochip quality, the method comprising:
- providing a biochip comprising at least first full length polynucleotide probes and second truncated polynucleotide probes, each having first ends that are coupled to an immobilization layer, the first full length polynucleotide probes having a different number of nucleotide monomers than the second truncated polynucleotide probes;
hybridizing Quality Control (QC) probes to the first full length polynucleotide probes and second truncated polynucleotide probes, each QC probe comprising;
a template portion having a nucleotide sequence complementary to a nucleotide sequence of the first full length polynucleotide probes and second truncated polynucleotide probes; and
a hairpin connected to a first end of the template portion;
exposing the biochip to conditions suitable for ligation of polynucleotides;
washing the biochip to de-hybridize the QC probes from the first full length polynucleotide probes and second truncated polynucleotide probes, thereby removing un-ligated QC probes;
detecting a ratio of the amount of the first full length polynucleotide probes that are ligated to the QC probes to the amount of the second truncated polynucleotide probes that are ligated to the QC probes to assess biochip quality, wherein the quality of the biochip is a measure of the relative amounts of first full length polynucleotide probes and second truncated polynucleotide probes.
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Abstract
A detection oligomer and method for controlling the quality of a biochip using the detection oligomer are provided. The detection oligomer includes a template having a first and second end and having a sequence that is complementary to a specific sequence of an oligomer, and a hairpin connected to the first end of the template.
10 Citations
11 Claims
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1. A method of assessing biochip quality, the method comprising:
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providing a biochip comprising at least first full length polynucleotide probes and second truncated polynucleotide probes, each having first ends that are coupled to an immobilization layer, the first full length polynucleotide probes having a different number of nucleotide monomers than the second truncated polynucleotide probes; hybridizing Quality Control (QC) probes to the first full length polynucleotide probes and second truncated polynucleotide probes, each QC probe comprising; a template portion having a nucleotide sequence complementary to a nucleotide sequence of the first full length polynucleotide probes and second truncated polynucleotide probes; and a hairpin connected to a first end of the template portion; exposing the biochip to conditions suitable for ligation of polynucleotides; washing the biochip to de-hybridize the QC probes from the first full length polynucleotide probes and second truncated polynucleotide probes, thereby removing un-ligated QC probes; detecting a ratio of the amount of the first full length polynucleotide probes that are ligated to the QC probes to the amount of the second truncated polynucleotide probes that are ligated to the QC probes to assess biochip quality, wherein the quality of the biochip is a measure of the relative amounts of first full length polynucleotide probes and second truncated polynucleotide probes. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8)
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9. A method of assessing biochip quality, the method comprising:
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providing a biochip comprising; an immobilization layer; and at least first full length polynucleotide probes and second truncated polynucleotide probes, each having 3′
ends that are coupled to the immobilization layer, the first full length polynucleotide probes having a different number of nucleotide monomers than the second truncated polynucleotide probes;hybridizing Quality Control (QC) probes to the first full length polynucleotide probe and second truncated polynucleotide probe, each QC probe comprising a template portion having a nucleotide sequence complementary to the entire first full length polynucleotide probe; and exposing the biochip to conditions suitable for ligation of 3′
ends of the QC probes to 5′
ends of the first full length polynucleotide probe and second truncated polynucleotide probe;washing the biochip to de-hybridize the QC probes from the first full length polynucleotide probes and second truncated polynucleotide probes, thereby removing un-ligated QC probes; detecting a ratio of the first amount of the first full length polynucleotide probes that are ligated with the QC probes to the amount of the second truncated polynucleotide probes that are ligated to the QC probes to assess the quality of the biochip, wherein the quality of the biochip is a measure of the relative amounts of the first full length and second truncated polynucleotide probes. - View Dependent Claims (10, 11)
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Specification