Provided is a method capable of simply and exponentially amplifying circular DNA, and particularly, long-chain circular DNA, in a cell-free system. Specifically, provided herein is a method for amplifying circular DNA which comprises mixing circular DNA having a replication origin sequence (origin of chromosome (oriC)) with a reaction solution comprising: a first enzyme group that catalyzes replication of circular DNA; a second enzyme group that catalyzes an Okazaki fragment maturation and synthesizes two sister circular DNAs constituting a catenane; a third enzyme group that catalyzes a separation of two sister circular DNAs; and also, a buffer, NTP, dNTP, a magnesium ion source, and an alkali metal ion source, to form a reaction mixture, which is then reacted.

Provided is a method capable of replicating or amplifying circular DNA, and particularly, long-chain circular DNA, in a cell-free system. Specifically, provided is a method for suppressing generation of a DNA multimer as a by-product, when circular DNA having a replication origin sequence (origin of chromosome (oriC)) is replicated or amplified by using the following enzyme groups: (1) a first enzyme group that catalyzes replication of circular DNA; (2) a second enzyme group that catalyzes an Okazaki fragment maturation and synthesizes two sister circular DNAs constituting a catenane; and (3) a third enzyme group that catalyzes a separation of two sister circular DNAs. Moreover, also provided is a method comprising introducing oriC into circular DNA by using a transposon.

Provided is a method capable of replicating or amplifying circular DNA, and particularly, long-chain circular DNA, in a cell-free system. Specifically, provided is a method for suppressing generation of a DNA multimer as a by-product, when circular DNA having a replication origin sequence (origin of chromosome (oriC)) is replicated or amplified by using the following enzyme groups: (1) a first enzyme group that catalyzes replication of circular DNA; (2) a second enzyme group that catalyzes an Okazaki fragment maturation and synthesizes two sister circular DNAs constituting a catenane; and (3) a third enzyme group that catalyzes a separation of two sister circular DNAs. Moreover, also provided is a method comprising introducing oriC into circular DNA by using a transposon.

The invention provides a method of identifying a microorganism that expresses a nucleic acid-modifying enzyme, in sample, the method comprising: (a) contacting a nucleic acid substrate targeted by the nucleic acid-modifying enzyme with the sample; (b) adding a further nucleic acid molecule to the sample which nucleic acid molecule is ligated to the nucleic acid substrate in the presence of the nucleic acid-modifying enzyme to form a ligation product which comprises a linear single strand of nucleic acid that is capable of being detected; and (c) detecting the presence of the ligation product.

The invention provides a method of identifying a microorganism that expresses a nucleic acid-modifying enzyme, in sample, the method comprising: (a) contacting a nucleic acid substrate targeted by the nucleic acid-modifying enzyme with the sample; (b) adding a further nucleic acid molecule to the sample which nucleic acid molecule is ligated to the nucleic acid substrate in the presence of the nucleic acid-modifying enzyme to form a ligation product which comprises a linear single strand of nucleic acid that is capable of being detected; and (c) detecting the presence of the ligation product.

The present invention provides labeled circular plasmid DNA molecules for studying DNA topology and topoisomerases. The molecules of the present invention also provide tools for high throughput drug screening for inhibitors of DNA gyrases and DNA topoisomerases for anticancer drug discovery and antibiotics discovery.

The present invention provides labeled circular plasmid DNA molecules for studying DNA topology and topoisomerases. The molecules of the present invention also provide tools for high throughput drug screening for inhibitors of DNA gyrases and DNA topoisomerases for anticancer drug discovery and antibiotics discovery.

The present invention provides for methods, reagents, apparatuses, and systems for the replication or amplification of nucleic acid molecules from biological samples. In one embodiment of the invention, the nucleic molecules are isolated from the sample, and subjected to fragmenting and joining using ligating agents of one or more hairpin structures to each end of the fragmented nucleic molecules to form one or more dumbbell templates. The one or more dumbbell templates are contacted with at least one substantially complementary primer attached to a substrate, and subjected to rolling circle replication or rolling circle amplification. The resulting replicated dumbbell templates or amplified dumbbell templates are used in numerous genomic applications, including whole genome de novo sequencing; sequence variant detection, structural variant detection, determining the phase of molecular haplotypes, molecular counting for aneuploidy detection; targeted sequencing of gene panels, whole exome, or chromosomal regions for sequence variant detection, structural variant detection, determining the phase of molecular haplotypes and/or molecular counting for aneuploidy detection; study of nucleic acid-nucleic acid binding interactions, nucleic acid-protein binding interactions, and nucleic acid molecule expression arrays; and testing of the effects of small molecule inhibitors or activators or nucleic acid therapeutics.

Live cells of a microorganism in a test sample are detected by the following steps: a) the step of treating the test sample with a topoisomerase poison and/or a DNA gyrase poison, b) the step of extracting DNA from the test sample, and amplifying a target region of the extracted DNA by PCR, and c) the step of analyzing an amplification product.

Live cells of a microorganism in a test sample are detected by the following steps: a) the step of treating the test sample with a topoisomerase poison and/or a DNA gyrase poison, b) the step of extracting DNA from the test sample, and amplifying a target region of the extracted DNA by PCR, and c) the step of analyzing an amplification product.