Multiplex Capture of Nucleic Acids

A method of capturing ten or more different target nucleic acids, the method comprising:

• providing a sample comprising or suspected of comprising the ten or more different target nucleic acids;
• providing a solid support having associated therewith a support capture probe;
• providing ten or more subsets of n different target capture probes, wherein n is at least two, wherein a different subset of target capture probes is provided for each different target nucleic acid, wherein the target capture probes in each subset are capable of hybridizing to nonoverlapping polynucleotide sequences in the corresponding target nucleic acid, and wherein the target capture probes in each subset are capable of hybridizing to the support capture probe;
• hybridizing any target nucleic acid present in the sample to its corresponding subset of n target capture probes and hybridizing the subset of n target capture probes to the support capture probe, thereby capturing the target nucleic acid on the solid support,
• wherein the hybridizing the subset of n target capture probes to the support capture probe is performed at a hybridization temperature which is greater than a melting temperature Tm of a complex between each individual target capture probe and the support capture probe;
• after hybridizing any target nucleic acid present in the sample to its corresponding subset of n target capture probes and hybridizing the subset of n target capture probes to the support capture probe, removing the captured target nucleic acids from the solid support;
• and
• after removing the captured target nucleic acids from the solid support, manipulating the captured target nucleic acids.

A method of capturing and sequencing nucleic acids, the method comprising:

• providing a sample comprising or suspected of comprising ten or more different target nucleic acids;
• providing a solid support having associated therewith a support capture probe;
• providing ten or more subsets of n different target capture probes, wherein n is at least two, wherein a different subset of target capture probes is provided for each different target nucleic acid, wherein the target capture probes in each subset are capable of hybridizing to nonoverlapping polynucleotide sequences in the corresponding target nucleic acid, and wherein the target capture probes in each subset are capable of hybridizing to the support capture probe;
• hybridizing any target nucleic acid present in the sample to its corresponding subset of n target capture probes and hybridizing the subset of n target capture probes to the support capture probe, thereby capturing the target nucleic acid on the solid support,
• wherein the hybridizing the subset of n target capture probes to the support capture probe is performed at a hybridization temperature which is greater than a melting temperature Tm of a complex between each individual target capture probe and the support capture probe;
• and
• after capturing the target nucleic acids on the solid support, determining a polynucleotide sequence of one or more of the captured target nucleic acids or a portion thereof.

A method of identifying the presence of target nucleic acids in a sample, the method comprising:

• providing a sample comprising or suspected of comprising ten or more different target nucleic acids;
• providing a solid support having associated therewith a support capture probe;
• providing ten or more subsets of n different target capture probes, wherein n is at least two, wherein a different subset of target capture probes is provided for each different target nucleic acid, wherein the target capture probes in each subset are capable of hybridizing to nonoverlapping polynucleotide sequences in the corresponding target nucleic acid, and wherein the target capture probes in each subset are capable of hybridizing to the support capture probe;
• hybridizing any target nucleic acid present in the sample to its corresponding subset of n target capture probes and hybridizing the subset of n target capture probes to the support capture probe, thereby capturing the target nucleic acid on the solid support,
• wherein the hybridizing the subset of n target capture probes to the support capture probe is performed at a hybridization temperature which is greater than a melting temperature Tm of a complex between each individual target capture probe and the support capture probe;
• and
• after hybridizing any target nucleic acid present in the sample to its corresponding subset of n target capture probes and hybridizing the subset of n target capture probes to the support capture probe, identifying the captured target nucleic acids, thereby determining which of the ten or more different target nucleic acids were present in the sample.