Nano-PCR: methods and devices for nucleic acid amplification and detection

A method for amplifying a nucleic acid, comprising:

• (a) contacting one or more template strands of single-stranded nucleic acid with one or more oligonucleotide primers complementary to a portion of the one or more template strands, wherein at least one primer of the one or more primers comprises one or more complexing groups capable of binding one or more molecules bound to a substrate;
• (b) annealing the at least one primer with the one or more complexing groups to the portion of the one or more template strands to which the primer is complementary, thereby binding the one or more template strands to the substrate;
• (c) contacting the one or more template strands with a nucleic acid polymerase and at least four different nucleoside triphosphates;
• (d) extending the one or more primers by the nucleic acid polymerase thereby forming one or more extension products bound to the one or more template strands;
• (e) separating the one or more extension products from the one or more template strands;
• and
• (f) repeating steps (a), (b), (c), (d) and (e) to amplify the nucleic acid, wherein, in the last cycle, step (e) is optional,
• wherein at least one of the one or more extension products in step (e) is used as template strands in a subsequent cycle of steps (a)-(e), and
• wherein at least one of steps (b), (d), and (e) comprises applying tension that tends to stretch the nucleic acid to the one or more template strands.

A method for amplifying a nucleic acid, comprising:

• (a) denaturing a double-stranded nucleic acid molecule by applying tension that tends to stretch the nucleic acid to one or both strands of the double-stranded nucleic acid molecule sufficient to cause separation of the double-stranded nucleic acid molecule into two single-stranded nucleic acid molecules, wherein the one or both single-stranded nucleic acid molecules to which the tension is applied becomes a template strand;
• (b) contacting the one or both template strands with one or more oligonucleotide primers complementary to a portion of the template strands, a nucleic acid polymerase and at least four different nucleoside triphosphates;
• (c) reducing the tension applied to the one or both template strands in step a) to permit the one or more primers to anneal to the corresponding portions of the template strands to which the one or more primers are complementary;
• (d) controlling the tension applied to the one or both template strands so as to permit extension of the one or more primers by the nucleic acid polymerase, thereby forming one or more double-stranded nucleic acid molecules in which one or more extension products are bound to the one or more template strands;
• and
• (e) repeating steps (a), (b), (c), and (d) to amplify the nucleic acid,
• wherein at least one of the one or more double-stranded nucleic acid molecules formed in step (d) in a cycle of steps (a)-(d) is used as the double-stranded nucleic acid molecule in step (a) in a subsequent cycle of steps (a)-(d), so that at least one extension product formed in step (d) is used as a template strand in a subsequent cycle of steps (a)-(d).

A method comprising:

• (a) providing a sample of double-stranded DNA (dsDNA) containing a target sequence, oligonucleotide primers complimentary to the 3′ ends of the target sequence and its complement;
• at least four different nucleoside triphosphates and a DNA polymerase;
• (b) denaturing the dsDNA into single-stranded DNA (ssDNA) molecules by applying tension that tends to stretch the nucleic acid to one or both strands of the dsDNA sufficient to cause the dsDNA to melt, wherein the one or both resulting ssDNA molecules becomes a template strand;
• (c) reducing the tension applied to the one or both template strands sufficient to permit hybridization of at least one of the primers to its complementary sequence in the template strands;
• (d) modulating the tension applied to the one or both template strands to a level allowing the DNA polymerase to extend the at least one primer to form an extension product, thereby forming one or more molecules of dsDNA;
• and
• (e) repeating steps (b) through (d) to amplify the dsDNA provided in step (a), wherein at least one of the one or more molecules of dsDNA formed in step (d) in a cycle of steps (b) through (d) is denatured in step (b) in a subsequent cycle of steps (b) through (d), so that at least one extension product formed in step (d) is used as a template strand in a subsequent cycle of steps (a)-(d).

A method of performing nucleic acid amplification by a polymerase chain reaction, comprising:

• (a) denaturing a double-stranded nucleic acid to produce single-stranded template strands;
• (b) annealing primers to the template strands;
• and
• (c) extending the primers by a template-strand-driven polymerase to produce extension products, thereby forming double-stranded nucleic acid molecules;
• and
• (d) repeating steps (a)-(c) to amplify the double-stranded nucleic acid,
• wherein at least one of the double-stranded nucleic acid molecules produced in step (c) in a cycle of steps (a)-(c) is denatured in step (a) in a subsequent cycle of steps (a)-(c), so that at least one extension product formed in step (c) is used as a template strand in a subsequent cycle of steps (a)-(d), and
• wherein at least one of steps (b) and (c) comprises applying tension that tends to stretch the nucleic acid to the nucleic acid.

A method of performing nucleic acid amplification, comprising:

• (a) denaturing a double-stranded nucleic acid to produce single-stranded template strands;
• (b) annealing primers to the template strands;
• (c) extending the primers by a template-strand-driven polymerase to produce extension products while applying mechanical tension to the primer or the template strands, thereby forming double-stranded nucleic acid molecules;
• and
• (d) repeating steps (a)-(c) to amplify the double-stranded nucleic acid,
• wherein at least one of the double-stranded nucleic acid molecules produced in step (c) in a cycle, of steps (a)-(c) is denatured in step (a) in a subsequent cycle of steps (a)-(c), so that at least one extension product formed in step (c) is used as a template strand in a subsequent cycle of steps (a)-(d).

A method of performing nucleic acid amplification, comprising:

• (a) denaturing a double-stranded nucleic acid to produce single-stranded template strands;
• (b) annealing primers to the template strands;
• (c) extending the primers by a template-strand-driven polymerase to produce extension products, thereby forming double- stranded nucleic acid molecules;
• and
• (d) repeating steps (a)-(c) to amplify the double-stranded nucleic acid,
• wherein at least one of the double-stranded nucleic acid molecules produced in step (c) in a cycle of steps (a)-(c) is denatured in step (a) in a subsequent cycle of steps (a)-(c), so that at least one extension product formed in step (c) is used as a template strand in a subsequent cycle of steps (a)-(d), and
• wherein at least one of steps (a)-(c) comprises applying hydrodynamic tension to the nucleic acid.

A method of performing nucleic acid amplification, comprising:

• (a) denaturing a double-stranded nucleic acid to produce single-stranded template strands;
• (b) annealing primers to the template strands;
• (c) extending the primers by a template-strand-driven polymerase to produce extension products while applying electromagnetic tension to the primer or the template strands, thereby forming double-stranded nucleic acid molecules;
• and
• (d) repeating steps (a)-(c) to amplify the double-stranded nucleic acid,
• wherein at least one of the double-stranded nucleic acid molecules produced in step (c) in a cycle of steps (a)-(c) is denatured in step (a) in a subsequent cycle of steps (a)-(c), so that at least one extension product formed in step (c) is used as a template strand in a subsequent cycle of steps (a)-(d).

A method of performing nucleic acid amplification, comprising:

• (a) denaturing a double-stranded nucleic acid to produce single-stranded template strands;
• (b) annealing primers to the template strands;
• (c) extending the primers by a template-strand-driven polymerase to. produce extension products, thereby forming double-stranded nucleic acid molecules;
• and
• (d) repeating steps (a)-(c) to amplify the double-stranded nucleic acid,
• wherein step (a) is isothermal and comprises applying mechanical or hydrodynamic tension to the nucleic acid;
• and wherein at least one of the double-stranded nucleic acid molecules produced in step (c) in a cycle of steps (a)-(c) is denatured in step (a) in a subsequent cycle of steps (a)-(c), so that at least one extension product formed in step (c) is used as a template strand in a subsequent cycle of steps (a)-(d).

A method of performing nucleic acid amplification, comprising:

• (a) denaturing a double-stranded nucleic acid to produce single-stranded template strands;
• (b) annealing primers to the template strands;
• (c) extending the primers by a template-strand-driven polymerase to produce extension products, thereby forming double- stranded nucleic acid molecules;
• and
• (d) repeating steps (a)-(c) to amplify the double-stranded nucleic acid,
• wherein at least one of the extension products in step (c) is used as a template strand in a subsequent cycle of steps (a)-(d), and
• wherein step (c) comprises applying adjustable tension that tends to stretch the nucleic acid to the nucleic acid, said adjustable tension modulating proofreading exonuclease activity of the nucleic acid polymerase.

A method of performing nucleic acid amplification, comprising:

• (a) denaturing a double-stranded nucleic acid to produce single-stranded template strands;
• (b) annealing primers to the template strands;
• (c) extending the primers by a template-strand-driven polymerase to produce extension products, thereby forming double-stranded nucleic acid molecules;
• and
• (d) repeating steps (a)-(c) to amplify the double-stranded nucleic acid,
• wherein at least one extension product in step (c) is used as a template strand in a subsequent cycle of steps (a)-(c), and
• wherein primers used in step (b) are activatable primers comprising complexing groups for immobilizing extension products obtained in step (c) wherein tension that tends to stretch the nucleic acid is applied in at least one cycle.

A method of performing nucleic acid amplification, comprising:

• (a) denaturing a double-stranded nucleic acid to produce single-stranded template strands;
• (b) annealing primers to the template strands;
• (c) extending the primers by a template-strand-driven polymerase to produce extension products, thereby forming double-stranded nucleic acid molecules;
• and
• (d) repeating steps (a)-(c) to amplify the double-stranded nucleic acid,
• wherein at least one extension product in step (c) is used as a template strand in a subsequent cycle of steps (a)-(c), and
• wherein at least one of steps (a)-(c) comprises applying tension that tends to stretch the nucleic acid to the nucleic acid;
• and
• wherein primers used in step (b) are activatable primers comprising complexing groups for immobilizing extension products obtained in step (c).

A method of performing nucleic acid amplification, comprising:

• (a) denaturing a double-stranded nucleic acid to produce single-stranded template strands;
• (b) annealing primers to the template strands;
• and
• (c) extending the primers by a template-strand-driven polymerase to produce extension products, thereby forming double-stranded nucleic acid molecules;
• and
• (d) repeating steps (a)-(c) to amplify the double-stranded nucleic acid,
• wherein at least one of the double-stranded nucleic acid molecules produced in step (c) in a cycle of steps (a)-(c) is denatured in step (a) in a subsequent cycle of steps (a)-(c), so that at least one extension product formed in step (c) is used as a template strand in a subsequent cycle of steps (a)-(d),
• wherein at least one of steps (b) and (c) comprises applying tension that tends to stretch the nucleic acid to the nucleic acid, and
• wherein the number of copies of the template strand increases exponentially, as a power of n, after steps (a) through (c) are repeated n times, wherein n is an integer greater than 1.

A method for controlling the stringency of annealing of a primer to a nucleic acid template strand, comprising:

• in a plurality of cycles of nucleic acid amplification,
• annealing a primer to a nucleic acid template strand, wherein tension that tends to stretch the nucleic acid is adjustably applied to said nucleic acid template strand or to said primer to control the stringency of annealing of said primer to said nucleic acid template strand;
• and
• wherein an extension product formed by extending the primer by a nucleic acid polymerase is used as a nucleic acid template strand in a subsequent cycle of nucleic acid amplification.

A method for controlling the stringency of annealing of a primer to a GC-rich nucleic acid template strand, comprising:

• in a plurality of cycles of nucleic acid amplification,
• annealing a primer to a GC-rich nucleic acid template strand, wherein tension that tends to stretch the nucleic acid is adjustably applied to said GC-rich nucleic acid template strand or to said primer to control the stringency of annealing of said primer to said GC-rich nucleic acid template strand;
• and
• wherein an extension product formed by a nucleic acid polymerase is used as a nucleic acid template strand in a subsequent cycle of nucleic acid amplification.

A method of improving fidelity of nucleic acid amplification, comprising:

• (a) denaturing a double-stranded nucleic acid to produce single-stranded template strands;
• (b) annealing primers to the template strands;
• and
• (c) extending the primers by a template-strand-driven polymerase to produce extension products, thereby forming double-stranded nucleic acid molecules;
• and
• (d) repeating steps (a)-(c) to amplify the double-stranded nucleic acid,
• wherein at least one of the double-stranded nucleic acid molecules produced in step (c) in a cycle of steps (a)-(c) is denatured in step (a) in a subsequent cycle of steps (a)-(c), so that at least one extension product formed in step (c) is used as a template strand in a subsequent cycle of steps (a)-(d), and
• wherein at least one of steps (a) through (c) comprises adjustably applying tension that tends to stretch the nucleic acid to the nucleic acid to improve fidelity of nucleic acid amplification.

A method for amplifying a nucleic acid, comprising:

• (a) contracting one or more template strands of single-stranded nucleic acid with one or more oglinucleotide primers complementary to a portion of the one or more template strands;
• (b) annealing at least one primer of the one or more primers to the portion of the one or more template strands to which the primer is complementary;
• (c) contacting the one or more template strands with a nucleic acid polymerase and at least four different nucleoside triphosphates;
• (d) extending the at least one annealed primer by the nucleic acid polymerase while applying mechanical tension, hydrodynamic tension, or electromagnetic tension to the one or more primer or the one or more template strands, thereby forming one or more extension products bound to the one or more template strands, wherein mechanical tension, hydrodynamic tension, or electromagnetic tension tends to stretch the nucleic acid;
• (e) separating the one or more extension products from the one or more template strands;
• and
• (f) repeating steps (a)-(e) to amplify the nucleic acid,
• wherein at least one of the one or more extension products in step (e) is used as template strands in a subsequent cycle of steps (a)-(e), wherein, for the last cycle, step (e) is optional.

A method for amplifying nucleic acid, comprising:

• (a) contacting one or more template strands of single-stranded nucleic acid with one or more oligonucleotide primers complementary to a portion of the one or more template strands;
• (b) annealing at least one primer of the one or more primers to the portion of the one or more template strands to which the primer is complementary;
• (c) contacting the one or more template strands with a nucleic acid polymerase and at least four different nucleoside triphosphates;
• (d) extending the at least one annealed primer by the nucleic acid polymerase thereby forming one or more extension products bound to the one or more template strands;
• (e) separating the one or more extension products from the one or more template strands;
• and
• (f) repeating steps (a)-(e) to amplify the nucleic acid,
• wherein at least one of the one or more extension products in step (e) is used as template strands in a subsequent cycle of steps (a)-(e),
• wherein, for the last cycle, step (e) is optional, and
• wherein at least one of steps (a)-(e) comprises applying hydrodynamic tension to the one or more template strands.

A method for amplifying a nucleic acid, comprising:

• (a) contacting one or more template strands of single-stranded nucleic acid with one or more oligonucleotide primers complementary to a portion of the one or more template strands;
• (b) annealing at least one primer of the one or more primers to the portion of the one or more template strands to which the primer is complementary;
• (c) contacting the one or more template strands with a nucleic acid polymerase and at least four different nucleoside triphosphates;
• (d) extending the at least one annealed primer by the nucleic acid polymerase, thereby forming one or more extension products bound to the one or more template strands;
• (e) separating the one or more extension products from the one or more template strands;
• and
• (f) repeating steps (a)-(e) to amplify the nucleic acid,
• wherein at least one of the one or more extension products in step (e) is used as template strands in a subsequent cycle of steps (a)-(e),
• wherein, for the last cycle, step (e) is optional, and
• wherein tension that tends to stretch the nucleic acid is applied and varied during each cycle of steps (a)-(e).

A method for amplifying a nucleic acid, comprising:

• (a) contacting one or more template strands of single-stranded nucleic acid with one or more oligonucleotide primers complementary to a portion of the one or more template strands;
• (b) annealing at least one primer of the one or more primers to the portion of the one or more template strands to which the primer is complementary;
• (c) contacting the one or more template strands with a nucleic acid polymerase and at least four different nucleoside triphosphates;
• (d) extending the at least one annealed primer by the nucleic acid polymerase, thereby forming one or more extension products bound to the one or more template strands;
• (e) separating the one or more extension products from the one or more template strands;
• and
• (f) repeating steps (a)-(e) to amplify the nucleic acid,
• wherein at least one of the one or more extension products in step (e) is used as template strands in a subsequent cycle of steps (a)-(e),
• wherein, for the last cycle, step (e) is optional,
• wherein tension that tends to stretch the nucleic acid is applied and varied during each cycle of steps (a)-(e), and
• wherein each step (a) through (e) is isothermal.