Deterministic stepping of polymers through a nanopore

A method for characterizing a target polymer molecule, the target polymer molecule selected from nucleic acid polymer molecules and protein polymer molecules and having polymer subunits along a target polymer molecule length, comprising:

• reversibly binding an enzyme clamp to a plurality of sequential polymer subunits along the target polymer molecule length;
• disposing the target polymer molecule and reversibly bound clamp in an ionic solution that is in fluidic communication with the nanopore, the nanopore having an aperture diameter less than an outer diameter of the clamp;
• applying a constant translocation force across the nanopore to induce travel of the target polymer molecule in the ionic solution into the nanopore until the clamp on the target polymer molecule abuts the nanopore aperture and stops further travel of the target polymer molecule into the nanopore;
• applying a control pulse comprising at least one of a voltage control pulse across the nanopore and a thermal control pulse at the nanopore, the control pulse having a control pulse duration that steps the clamp along the target polymer molecule by no more than one polymer subunit in a direction opposite that of travel into the nanopore, with no fuel provided to the clamp, to step the target polymer molecule further into the nanopore by no more than one polymer subunit;
• acquiring a characteristic indication of a polymer subunit when the polymer subunit is in the nanopore;
• and
• repeatedly applying the control pulse to cause a sequential plurality of polymer subunits of the target polymer molecule to translocate through the nanopore into an ionic solution while acquiring a characteristic indication of each polymer subunit that translocates through the nanopore.

A nanopore system for characterizing a target polymer molecule selected from nucleic acid polymer molecules and protein polymer molecules and including a sequential plurality of polymer subunits along a target polymer molecule length, comprising:

• a first fluidic reservoir and a second fluidic reservoir, the first and second fluidic reservoirs in fluidic communication with a nanopore that forms a sole fluidic path between the first fluidic reservoir and the second fluidic reservoir;
• an enzyme clamp provided in the first fluidic reservoir, the clamp abutting the nanopore and reversibly bound to a sequential plurality of polymer subunits of the target polymer molecule in ionic solution in the first fluidic reservoir;
• a circuit comprising an electrode in the first reservoir, an electrode in the second reservoir, and a current amplifier for applying a constant voltage bias across the nanopore, between the first reservoir and the second reservoir to induce travel of the target polymer molecule into the nanopore;
• a voltage pulse generator connected to the circuit to apply voltage control pulses across the nanopore, between the first reservoir and the second reservoir, to step the clamp along sequential polymer subunits of the target polymer molecule, polymer subunit by polymer subunit, in a direction away from the nanopore, and step the polymer molecule further into the nanopore, the system including no fuel for the clamp and no source of fuel for the clamp;
• and
• a computer controller connected to the circuit to collect an electrical indication of ionic current through nanopore while a sequential plurality of polymer subunits of the target polymer molecule steps through the nanopore.

A nanopore system for characterizing a target polymer molecule selected from nucleic acid polymer molecules and protein polymer molecules and including a sequential plurality of polymer subunits along a target polymer molecule length, comprising:

• a first fluidic reservoir and a second fluidic reservoir, the first and second fluidic reservoirs in fluidic communication with a nanopore that forms a sole fluidic path between the first fluidic reservoir and the second fluidic reservoir;
• an enzyme clamp provided in the first fluidic reservoir abutting the nanopore and being reversibly bound to a sequential plurality of polymer subunits of the target polymer molecule;
• a circuit comprising an electrode in the first reservoir, an electrode in the second reservoir, and a current amplifier for applying a constant voltage bias across the nanopore, between the first reservoir and the second reservoir to induce travel of the target polymer molecule into the nanopore;
• a laser connected to the computer controller to produce laser pulses;
• optics disposed adjacent to the laser and oriented to direct the laser pulses to the nanopore;
• a material element, disposed at the nanopore, that is absorptive of energy from the laser pulses to heat the ionic solution during each laser pulse and in turn to step the clamp along sequential polymer subunits of the target polymer molecule, polymer subunit by polymer subunit, in a direction away from the nanopore, and to step the target polymer molecule further into the nanopore, the system including no fuel for the clamp and no source of fuel;
• and
• a computer controller connected to the circuit to collect electrical indications of ionic current through nanopore while the sequential plurality of polymer subunits of the target polymer molecule steps through the nanopore.