Method and system for imaging a molecular strand

1. Method for imaging a molecular strand, the method comprising

providing a sample volume comprising the strand with trapping beads attached on opposite ends of the strand;

providing an excitation beam having an excitation focus in the sample volume wherein an excitation of a fluorophore on the strand by the excitation focus results in a fluorescence response when the excitation focus coincides with the fluorophore;

scanning the excitation focus in the sample volume along a one dimensional scanning line;

providing optical traps, trapping the trapping beads at the ends of the strand in the sample volume and extending the strand between the optical traps to form a one-dimensional trapping line parallel to the scanning line;

aligning the trapping line to coincide with the scanning line to have the scanning excitation focus coincide with the strand; and

recording the fluorescence response as a function of a plurality of distinct scanning positions of the excitation focus along the scanning line.

2. Method according to claim 1 , comprising providing a depletion beam having a depletion focus with a depletion profile coinciding with an excitation profile of the excitation focus and causing stimulated emission depletion of the excitation of the fluorophore according to the depletion profile, wherein the depletion profile has a minimum intensity at a centre of the excitation focus for reducing the area where spontaneous fluorescent emission occurs wherein the depletion profile comprises a region of minimum intensity coinciding with the trapping line.

3. Method according to claim 1 , comprising providing a depletion beam having a depletion focus with a depletion profile coinciding with an excitation profile of the excitation focus and causing stimulated emission depletion of the excitation of the fluorophore according to the depletion profile, wherein the depletion profile has a minimum intensity at a centre of the excitation focus for reducing a profile size of excited fluorophores by the stimulated emission depletion wherein the depletion profile comprises a plane of minimum intensity extending perpendicular to the trapping line.

4. Method according to claim 1 , wherein one or more optically trapped beads are attached to the strand for trapping the strand, wherein the beads exert a tensile force on the strand to suppress thermal fluctuations of the strand to a value below the diffraction limit.

5. Method according to claim 1 , wherein optically trapped beads are attached to the strand, wherein the beads have a diameter larger than a waist of a trapping beam trapping the beads.

6. Method according to claim 1 , wherein the fluorescence response is recorded at an image plane which image plane is a conjugate focal plane of an object plane in the sample volume, wherein the object plane extends in the first direction and wherein the excitation focus and trapping line are aligned to coincide with the object plane wherein a spatial pinhole is provided in the image plane, wherein the spatial pinhole is aligned to coincide with a conjugate focal point of the excitation focus for passing the fluorescence response through the spatial pinhole to a fluorescence detector.

7. Method according to claim 1 , wherein the excitation focus is repeatedly scanned back and forth along the scanning line wherein the fluorescence response is distinguished between the plurality of distinct scanning positions along the scanning line and/or integrated over multiple scans and/or recorded as a function of time.

8. Method according to claim 1 , wherein the sample volume is comprised in a sample cell comprising a sample window transparent to incoming excitation and/or depletion beams, wherein the sample cell comprises rotational actuators for tilting and/or rotating the sample cell, wherein the method further comprises aligning the sample window to be perpendicular to the incoming beams for optimizing a profile of the excitation focus and/or depletion focus.

9. Method according to claim 1 , further comprising measuring interaction of a fluorescent reagent with a molecular strand by;

providing a microfluidic flow cell FC wherein separate input channels of the flow cell provide a plurality of separate laminar flows in a sample volume of the flow cell, wherein

a first laminar flow comprises a plurality of beads arranged for attaching to opposite ends of the molecular strand;

a second laminar flow comprises a plurality of the molecular strands; and

a third laminar flow comprises the reagent;

providing an optical trap in the first laminar flow and trapping a bead with the optical trap;

positioning the optical trap to the second laminar flow and attaching the bead to a strand;

positioning the optical trap to the third laminar flow; and

using a method according to any of the previous claims for recording the fluorescence response of the reagent.

10. Method according to claim 9 , wherein the molecular strand is a DNA or RNA strand and the fluorescent reagent comprises a reagent that associates with the molecular strand such as protein molecules.

11. System for imaging a molecular strand, the system comprising

a sample cell arranged for providing a sample volume comprising the strand;

an excitation light source arranged for providing an excitation beam having an excitation focus in the sample volume wherein an excitation of a fluorophore on the strand by the excitation focus results in a fluorescence response when the excitation focus coincides with the fluorophore;

a beam scanner arranged for scanning the excitation focus in the sample volume along a one dimensional scanning line;

a trap arranged for trapping an end of the strand in the sample volume and extending the strand along a one-dimensional trapping line parallel to the scanning line, wherein the trap comprises a trapping light source and trapping beam optics arranged for providing optical traps trapping beads attached on opposite ends of the strand, wherein the optical traps are arrange to form the trapping line between the beads;

a beam aligner arranged for aligning the trapping line to coincide with the scanning line to have the scanning excitation focus coincide with the strand; and

a fluorescence detector arranged for recording the fluorescence response as a function of a plurality of distinct scanning positions of the excitation focus along the scanning line; and

a processor programmed to provide a scanning mode wherein

the processor controls the trap to extend the strand along a one-dimensional trapping line in the first direction;

the processor controls the beam aligner to have the trapping line coincide with the scanning line;

the processor controls the beam scanner to scan the excitation focus along the scanning line;

the processor receives the recorded fluorescence response from the fluorescence detector; and

the processor stores the fluorescence response at one or more positions of the excitation focus along the scanning line.

12. System according to claim 11 , further comprising

a depletion light source and depletion beam optics arranged for providing a depletion beam having a depletion focus with a depletion profile coinciding with an excitation profile of the excitation focus and causing stimulated emission depletion of the excitation of the fluorophore according to the depletion profile, wherein the depletion profile has a minimum intensity at a centre of the excitation focus for reducing a profile size of excited fluorophores by the stimulated emission depletion;

a depletion focus shaper arranged for shaping the depletion profile wherein the depletion profile comprises a plane of minimum intensity extending perpendicular to the trapping line.

13. System according to claim 11 , wherein

the sample cell comprises a microfluidic flow cell FC wherein separate input channels of the flow cell provide a plurality of separate laminar flows in a sample volume of the flow cell;

the trap comprises optical traps trapping beads attached on opposite ends of the strand, wherein the optical traps are arranged to form the trapping line between the beads;

wherein the optical traps are moveable between the laminar flows.