Nucleic acid amplification

A method of amplifying a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence, wherein nucleic acids in the target sample are not separated from other material in the target sample,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

A method of amplifying a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence, wherein the target sample is a crude cell lysate,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

A method of amplifying a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence, wherein the primers are 5, 6, 7, 8, 9, or 10 nucleotides long,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

A method of amplifying a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence, wherein the primers each contain at least one modified nucleotide such that the primers are nuclease resistant,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

A method of amplifying a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence, wherein the primer-target sample is not subjected to denaturing conditions, wherein the primers are 6 nucleotides long, wherein the primers each contain at least one modified nucleotides such that the primers are nuclease resistant, and wherein DNA polymerase is φ29 DNA polymerase,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

A method of amplifying a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence, wherein the target sample is not subjected to denaturing conditions,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

A method of amplifying a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence, wherein the target sample is not subjected to denaturing conditions,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand, wherein the target sequence is a nucleic acid sample of substantial complexity, and wherein the set of primers comprises primers having random nucleotide sequences.

A method of amplifying a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence, wherein the target sample is not subjected to denaturing conditions,
• wherein all of the primers in the set of primers are complementary to the same strand in the target sequence,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

A method of amplifying a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence, wherein the target sample is not subjected to heat denaturing conditions,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

A method of labeling nucleic acids produced by strand displacement replication, the method comprising

• labeling nucleic acids produced by strand displacement replication using terminal deoxynucleotidyl transferase.

A method of labeling nucleic acids produced by strand displacement replication, the method comprising

• incorporating modified nucleotides into nucleic acids produced by strand displacement replication during replication.

A method of attaching nucleic acids produced by strand displacement replication, the method comprising

• adding modified nucleotides to the 3′ ends of nucleic acids produced by strand displacement replication using terminal deoxynucleotidyl transferase, and
• reacting the modified nucleotides with a solid-state support thereby attaching the nucleic acids to the solid-state support.

A microarray comprising nucleic acids produced by strand displacement replication coupled or adhered to a solid-state substrate.

A method of generating probes based on a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand,
• wherein the replicated strands are used as hybridization probes.

A method of amplifying messenger RNA, the method comprising,

• reverse transcribing messenger RNA to produce a first strand cDNA,
• bringing into contact a set of primers, DNA polymerase, and the first strand cDNA, and incubating under conditions that promote replication of the first strand cDNA,
• wherein replication of the first strand cDNA results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the first strand cDNA by strand displacement replication of another replicated strand.

A method of amplifying a target nucleic acid sequence, the method comprising,

• partially degrading RNA in a target sample,
• bringing into contact DNA polymerase, and the target sample, and incubating the target sample under conditions that promote replication of the target sequence,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

A method of comparative genome hybridization, the method comprising,

• hybridizing nucleic acids produced by strand displacement replication of a first sample with nucleic acids produced by strand displacement replication of a second sample.

A method of amplifying a target nucleic acid sequence, the method comprising,

• bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence, wherein a circular nucleic acid molecule comprises the target sequence,
• wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.