Method and compositions for efficient and specific rolling circle amplification

A method of amplifying nucleic acid sequences, the method comprising

• a DNA ligation operation and an amplification operation,
• wherein the DNA ligation operation comprises circularization of one or more open circle probes,
• wherein the ligation operation is carried out in the presence of a set of open circle probes, wherein the set of open circle probes comprises a plurality of different open circle probes,
• wherein the amplification operation comprises rolling circle replication of the circularized open circle probes,
• wherein the amplification operation is carried out in the presence of a plurality of detection rolling circle replication primers, a secondary DNA strand displacement primer, and a common rolling circle replication primer,
• wherein each detection rolling circle replication primer corresponds to a different open circle probe in the set of open circle probes, wherein the secondary DNA strand displacement primer corresponds to all of the open circle probes in the set of open circle probes, wherein the common rolling circle replication primer corresponds to all of the open circle probes in the set of open circle probes.

A method of amplifying nucleic acid sequences, the method comprising

• an amplification operation,
• wherein the amplification operation is carried out in the presence of a set of amplification target circles, wherein the set of amplification target circles comprises a plurality of different amplification target circles,
• wherein the amplification operation comprises rolling circle replication of the amplification target circles,
• wherein the amplification operation is carried out in the presence of a plurality of detection rolling circle replication primers, a secondary DNA strand displacement primer, and a common rolling circle replication primer,
• wherein each detection rolling circle replication primer corresponds to a different amplification target circle in the set of amplification target circles, wherein the secondary DNA strand displacement primer corresponds to all of the amplification target circles in the set of amplification target circles, wherein the common rolling circle replication primer corresponds to all of the amplification target circles in the set of amplification target circles.

A method of amplifying nucleic acid sequences, the method comprising

• a DNA ligation operation and an amplification operation,
• wherein the DNA ligation operation comprises circularization of one or more open circle probes,
• wherein the ligation operation is carried out in the presence of a set of open circle probes, wherein the set of open circle probes comprises a plurality of different open circle probes,
• wherein the amplification operation comprises rolling circle replication of the circularized open circle probes, wherein two or more of the open circle probes in the set of open circle probes constitute a matched open circle probe set.

A method of amplifying nucleic acid sequences, the method comprising

• a DNA ligation operation and an amplification operation,
• wherein the DNA ligation operation comprises circularization of one or more open circle probes,
• wherein the amplification operation comprises rolling circle replication of the circularized open circle probes,
• wherein the amplification operation is carried out in the presence of one or more rolling circle replication primers,
• wherein at least one of the rolling circle replication primers is associated with a peptide nucleic acid quencher or a peptide nucleic acid fluor.

A method of amplifying nucleic acid sequences, the method comprising

• an amplification operation,
• wherein the amplification operation comprises rolling circle replication of the amplification target circles,
• wherein the amplification operation is carried out in the presence of one or more rolling circle replication primers,
• wherein at least one of the rolling circle replication primers is associated with a peptide nucleic acid quencher or a peptide nucleic acid fluor.

A method of selectively amplifying nucleic acid sequences related to one or more target sequences, the method comprising,

• (a) mixing a set of open circle probes with a target sample, to produce an OCP-target sample mixture, and incubating the OCP-target sample mixture under conditions that promote hybridization between the open circle probes and the target sequences in the OCP-target sample mixture, wherein the set of open circle probes comprises a plurality of different open circle probes,
• wherein each open circle probe comprises two ends, wherein at least one of the ends of at least one of the open circle probes can form an intramolecular stem structure, wherein circularization of the open circle probes that can form an intramolecular stem structure is dependent on hybridization of the open circle probe to a target sequence, wherein two or more of the open circle probes in the set of open circle probes constitute a matched open circle probe set,
• (b) mixing ligase with the OCP-target sample mixture, to produce a ligation mixture, and incubating the ligation mixture under conditions that promote ligation of the open circle probes to form amplification target circles, wherein the amplification target circles formed from the open circle probes in the set of open circle probes comprise a set of amplification target circles,
• (c) mixing a plurality of detection rolling circle replication primers, a secondary DNA strand displacement primer, and a common rolling circle replication primer with the ligation mixture, to produce a primer-ATC mixture, and incubating the primer-ATC mixture under conditions that promote hybridization between the amplification target circles and the rolling circle replication primers in the primer-ATC mixture, wherein each detection rolling circle replication primer is associated with a peptide nucleic acid quencher, wherein each detection rolling circle replication primer corresponds to a different open circle probe in the set of open circle probes, wherein the secondary DNA strand displacement primer corresponds to all of the open circle probes in the set of open circle probes, wherein the common rolling circle replication primer corresponds to all of the open circle probes in the set of open circle probes, and
• (d) mixing DNA polymerase with the primer-ATC mixture, to produce a polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote replication of the amplification target circles,
• wherein replication of the amplification target circles results in the formation of tandem sequence DNA.

A kit for selectively detecting one or more target sequences or selectively amplifying nucleic acid sequences related to one or more target sequences, the kit comprising,

• a set of open circle probes each comprising two ends, wherein at least one of the ends of one of the open circle probe can form an intramolecular stem structure, wherein portions of each open circle probe are complementary to the one or more target sequences,
• a plurality of detection rolling circle replication primers, wherein all or a portion of each detection rolling circle replication primer is complementary to a portion of one or more of the open circle probes,
• one or more secondary DNA strand displacement primers, wherein all or a portion of each secondary DNA strand displacement primer matches a portion of one or more of the open circle probes, and
• one or more common rolling circle replication primers, wherein all or a portion of each common rolling circle replication primer is complementary to a portion of one or more of the open circle probes.