Patent Description:
Biopolymers, such as proteins, DNA, or RNA, are often in the form of semi-flexible entwined polymeric chains. These macromolecules are normally assumed to have a random coil configuration in free solution. For double stranded DNA (dsDNA) in biological solution, the persistence length (a parameter defining its rigidity) is typically about <NUM>. In order to achieve consistent and accurate characterization of DNA and other biopolymers, it is often desirable that the biopolymer be moved through a fluidic channel to facilitate analysis or use of the biopolymer. In some instances, the biopolymer is linearized in a channel; in others, the biopolymer is directed through a fluidic flow path for other purposes. Further, to facilitate characterization of macromolecules and biopolymers, such as DNA, sequences or features of the macromolecule may be marked, for example, with fluorescent labeling techniques. Linearized, labeled biopolymers can then be optically imaged to provide certain information. However, optical mapping techniques for biopolymers have been hindered by low information density for optical maps, and conventional techniques provide only low-throughput capabilities. Although systems and methods for linearization and optical mapping providing an accurate, high-throughput characterization of biopolymer molecules are becoming more common, these systems are often hindered by the reduced throughput over time due to clogging of fluidic passageways, for example entrances into nanochannel or microchannel regions of nanofluidic and/or microfluidic linearizing systems including microfabricated structures such as pillar arrays. This clogging may occur regardless of whether the system is heavily loaded with DNA chains or lightly loaded, though in lightly loaded systems, the clogging may occur at a slower rate. Thus, systems and methods for cleaning and unclogging fluidic systems that handle biopolymers are needed.

Documents <CIT> and <CIT>disclose known systems and methods for enhancing fluid flow within devices.

The systems, methods, and devices of the invention each have several aspects, no single one of which is solely responsible for its desirable attributes. Without limiting the scope of this invention as expressed by the claims which follow, some features will now be discussed briefly. After considering this discussion, and particularly after reading the section entitled "Detailed Description," one will understand how the features of the various embodiments of this invention provide advantages that include improved cleaning and increased throughput.

One aspect of this disclosure provides a method for enhancing fluid flow. In one aspect, the method includes moving biopolymer molecules into contact with at least one fluidic channel in or on a device, whereby clogging occurs in the device due to coiling or aggregation of the biopolymer molecules or adsorption to or tangling around the channels or any other nano- or micro-patterned features inside the channel or fluidic device, and directing a light source at a region of the device in which said clogging has occurred in a manner effective to photocleave biopolymers that contribute to said clogging, thereby facilitating removal or reduction of said clogging. In some aspects, the method further includes applying a motive force to fluid in the region of the device in a manner effective to flush the photocleaved biopolymer molecules from the region of the device comprising said clogging. In some aspects, the motive force may comprise an electrostatic force, a pneumatic force, a capillary force, or any combination thereof. In some aspects, the directing a light source comprises directing a light source having a wavelength of one of about <NUM> or about <NUM> to excite YOYO-<NUM> bound to DNA. In some aspects, the biopolymer molecules being moved and photocleaved may comprise DNA or RNA.

In some aspects, the method also includes labeling the biopolymer molecules with an indicator or photon absorber to facilitate photocleavage of the biopolymer molecules when exposed to the light source. In some aspects, the light source may be configured to generate light matched to the indicator or photon absorber used to label the biopolymer molecules so as to maximize photocleavage of the biopolymer molecules when exposed to the light. In some aspects, the indicator used to label the biopolymer molecules may comprise one of YO, YOYO-<NUM>, YOYO-<NUM>, TOTO, methylene blue, Cu or Rh, compounds useful for photodynamic therapy, or any other photon absorber capable of facilitating photocleavage of the biopolymer. Each indicator can be excited with a specific wavelength or a range of wavelengths to induce photocleavage in an efficient manner. In some aspects, the method may further comprise detecting a clogged or reduced flow condition. In some aspects, the detecting comprises identifying that a transport of the biopolymer molecules through the device falls below a threshold transport value. In some aspect, the detecting comprises direct imaging of at least one fluidic channel in or on the device to indicate clogging. In some aspects, the cleaning of the region of the device in which the clogging has occurred is implemented in an automatic fashion at one of a predetermined time or a predetermined transport threshold. In some aspects, the method may further include positioning the light source in a manner effective to minimize exposure of the device to the light source.

Another aspect disclosed is an apparatus for enhancing fluid flow. In some aspects, the apparatus may include a light source configured to generate light configured to photocleave biopolymer molecules and a controller configured to control a movement of the biopolymer molecules into contact with at least one fluidic channel in or on a device, whereby clogging occurs in the device due to coiling or aggregation of the biopolymer molecules or adsorption to or tangling around the channels or other nano- or micro-patterned features inside the channel or fluidic device, direct the light source at a region of a device in which a clog of biopolymer molecules has formed, and activate the light source to generate the light beam for an amount of time to facilitate a photocleaving of the biopolymer molecules forming said clog.

In some other aspects, the apparatus further comprises a motive force generator configured to generate a motive force, wherein the controller is configured to control a movement of the biopolymer molecules via the generated motive force and wherein the controller is further configured to apply the motive force to fluid in the region of the device in which said clog occurred in a manner effective to flush the photocleaved biopolymer molecules from the region. In some other aspects, the motive force of the apparatus comprises at least one of an electrostatic force, a pneumatic force, a capillary force, or any combination thereof. In some aspects, the motive force generator is configured to generate one of an electrostatic force, a pneumatic force, a capillary force, or any combination thereof. In some aspects, the light beam generated by the light source may have a wavelength of one of about <NUM> or <NUM>. In some other aspects, wherein the biopolymer molecules or the apparatus may comprise DNA or RNA.

In some other aspects, the apparatus may further comprise a biopolymer molecule labeling device configured to label the biopolymer molecules with an indicator or photon absorber to facilitate photocleavage of the biopolymer molecules when exposed to the light beam generated by the light source. In some aspects, the indicator used to label the biopolymer molecules comprises at least one of YO, TOTO, methylene blue, Cu or RH, compounds useful for photodynamic therapy, or any other suitable photon absorber. In some aspects, the apparatus may further comprise a detector configured to detect a clog or reduced flow condition through the at least one fluidic channel in or on the device. In some aspects, the detector may be further configured to identify that a transport of biopolymer molecules through the at least one fluidic channel in or on the device falls below a threshold transport value. In some aspects, the detector may be further configured to directly image the at least one fluidic channel in or on the device to indicate the clog.

In some other aspects, the controller is further configured to operate the light source and enhance fluid flow in at automatic fashion at one of a predetermined time or a predetermined transport threshold. In some other aspects, the apparatus further comprises an x, x-y, or x-y-z translation motor configured to position the light source in a manner effective to minimize exposure of the device to the light source and further configured to allow positioning of the light source at any location in relation to the device.

In another implementation, light is directed to the region of the fluidic structure for the purposes of photocleavage by bringing a light-source such as an LED into close proximity to the fluidic structure without use of lenses or other optical systems. Either the LED or the fluidic structure could be translated into position to accomplish this. The controller would coordinate movements, light intensity and duration of exposure. A mask in between the light and the fluidic structure can be used to minimize exposure to regions that should not be subject to photocleavage or degradation, such as the sample well containing molecules that have yet to be loaded into the interrogation region of the chip.

Another implementation is to include light emitting regions into the fluidic device to apply local excitation and photocleavage to a particular region of the fluidic device that is subject to blockage or clogging.

Another aspect includes an apparatus for characterizing a biopolymer molecule. The apparatus comprises a fluidic device comprising a detection region comprising at least one channel and the biopolymer molecule. The apparatus further comprises a motive force generator that moves biopolymer molecules into the detection region, where a clog of biopolymer molecules may occur in the fluidic device and hamper further flow of new biopolymer molecules to the detection region. The apparatus further comprises a detection system for determining a characteristic of the biopolymer molecules in the detection region and a light source set to deliver a light comprising a configuration for photocleaving the biopolymer molecules forming the clog. The apparatus further comprises a light delivery system to deliver the light to any region of the fluidic device and a positioning system to target the detection system to the detection region for characterization of the biopolymer molecules, and to target the light comprising the photocleaving configuration to a region of the device where the clog has formed. The apparatus also comprises a controller configured to activate the motive force generator to move the biopolymer molecules into the detection region, direct the detection system to the detection region, activate the detection system to determine the characteristics of the biopolymer molecules, direct the light source configured for photocleaving biopolymer molecules to the region where the clog has formed, activate the light source to generate a light for photocleaving biopolymer molecules forming the clog, and activate the motive force generator to flush out the photocleaved biopolymer molecules; wherein additional new biopolymer molecules flow into the detection region for characterization.

Another aspect may include a method for characterizing a biopolymer. The method may comprise moving biopolymer molecules into a detection region of a fluidic device, whereby clogging may occur in the device, hampering further flow of biopolymers to the detection region. The method may further comprise detecting a characteristic of the biopolymer molecules in the detection region. The method may further comprise directing a light source at a region of the device where the clog has formed and photocleaving the biopolymer molecules causing the clogging. Then, the method may comprise applying a motive force to flush the photocleaved biopolymer molecules and applying a motive force to flow additional biopolymer molecules for characterization.

Another aspect may include another method for characterizing a biopolymer. The method may comprise moving biopolymer molecules into a detection region of a fluidic device and detecting a characteristic of the biopolymer molecules in the detection region. The method may further comprise directing a light source at the detection region wherein the light source comprises a configuration for photocleaving biopolymer molecules. The method further comprises photocleaving biopolymer molecules which have been characterized and flushing photocleaved molecules, allowing entry of new molecules for characterization.

Another aspect may include a system for characterizing a biopolymer. The system may comprise a fluidic device comprising a detection region comprising at least one channel, and further comprising the biopolymer and a detection system for determining a characteristic of the biopolymer molecule in the detection region. The system may further comprise a photo cleaving system comprising a light source set to deliver a light comprising a configuration for photocleaving biopolymer molecules that have already been interrogated or were not interrogated and do not need to be, for loading new molecules for characterization.

In the description provided herein, reference is made to the accompanying drawings, which form a part hereof. The illustrative embodiments described in the detailed description, and drawings are not meant to be limiting. It will be readily understood that the aspects of the present disclosure, as generally described herein, and illustrated in the Figures, can be arranged, substituted, combined, and designed in a wide variety of different configurations, all of which are explicitly contemplated and made part of this disclosure.

Reference to values in ranges includes each and every value within that range.

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

As used herein, the term "channel" means a region defined by borders. Such borders may be physical, electrical, chemical, magnetic, and the like. The term "nanochannel" is used to clarify that certain channels are considered nanoscale in certain dimensions; similarly, the term "microchannel" is used to clarify that certain channels are considered microscale in certain dimensions. Also as used herein, nanofluidic may mean a fluid system having components whose dimensions are on the nanoscale, while microfluidic may mean a fluid system having components whose dimensions are on the microscale. As used herein, biopolymer analysis may refer to analysis of a macromolecule or biopolymer, such as DNA or RNA, using a nanoscale structure, such as a nanochannel, e.g., a nanofluidic system, and microanalysis may refer to analysis of a macromolecule or biopolymer, such as DNA or RNA, using a microscale structure, such a microchannel, e.g., a microfluidic system. In some embodiments, biopolymer analysis may comprise biopolymer characterization, wherein a characteristic of the biopolymer molecule may include a physical dimension (i.e. length, width, etc.), a landmark periodicity, shape, enumerating molecules, size, density, electrical property, light scattering/refraction, etc..

As used herein, the term "nanochannel" may also refer to "microchannel. " Thus, a device, system, or method that utilizes a nanochannel may be inferred to also apply to or be capable of utilizing a microchannel. Furthermore, any term utilizing the prefix "nano" may be replaced with the prefix "micro. " For example, discussions of "nanochannels" or "nanofluidic" include "microchannels" and "microfluidic.

As used herein, the term "DNA" refers to DNA of any length (e.g., <NUM>. 1Kb to <NUM> megabase). The DNA can be a highly pure preparation, crude, or semi crude material. The DNA can come from any biological source or can be synthetic.

As used herein, a "sample" may include any fluid containing a biopolymer that can be introduced into a microfluidic or nanofluidic device. The sample may include any fluid that contains a biopolymer of interest, for example purified and labeled DNA to be analyzed for optical genome mapping or sequencing. In some embodiments, the sample may be highly processed fluid that is applied to the nano- or microfluidic chip for analysis (i.e., an analyte). The sample can contain buffers and additives to modify the surface of the fluidic device to facilitate electrophoresis or prevent adsorption. In some embodiments, the sample can, for example, include one or more components of blood, serum, plasma, sputum, lavage fluid, cerebrospinal fluid, tissue, microorganisms, urine, semen, sweat, tears, saliva, and the like, including any fractions or processed portions thereof. Similarly, where a sample is taken from a biopsy, swab, smear, etc., the "sample" expressly encompasses a processed fraction or portion derived from the biopsy, swab, smear, etc. Linearizing biopolymers may be beneficial in various biopolymer analysis systems. For example, linearization may be used in systems that image biopolymers, biopolymer optical mapping systems, sequencing systems, or in biopolymer transfection systems. Such linearization may be critical for studying, using, and/or analyzing the physical and biological properties of the biopolymer molecules. Some biopolymer analysis systems may use various methods or structures to linearize the biopolymers. In some embodiments, the biopolymer analysis system may include a fluidic device having a detection region, while in some embodiments, the biopolymer analysis system may include an apparatus having the fluidic device. The detection region may comprise at least one channel (e.g., a nanofluidic or microfluidic channel) through which the biopolymer flow. In some embodiments, the fluidic device may be a disposable, detachable unit (i.e., a chip as described below), a detachable, reusable unit, or a permanent or detachable part of the biopolymer analysis system or apparatus. For example, the fluidic device may be a Mapcard or similar unit. The detection region may comprise one or more fluidic channels (e.g., nano- or microfluidic channels). For example, some systems may utilize a tapered region to facilitate linearization and to introduce biopolymers into fluidic channels. Others may use a variety of obstacles or pillar regions or arrays through which the biopolymer molecules are fed via a motive force, the pillar regions or arrays causing the biopolymer molecules to straighten as they move through and around the pillars. Other systems may use confinement in nano- or microchannels, may feed the biopolymer molecules through nanoslits, nanopores, microslits, or micropores, or may insert the biopolymer molecules within reconfigurable tunable/elastomeric channels to linearize the biopolymers. Some may use open-topped channels on a surface of a substrate. Some systems may utilize other linearization methods or combinations of linearization methods and structures to linearize biopolymers. In the discussion below, various embodiments may be described. One of ordinary skill in the art would understand that these embodiments are a subset of the examples of fluidic systems in which biopolymers are directed and are not intended to be limiting except as specifically called out in claims.

For example, in a system for linearizing biopolymer molecules, nanochannels (or microchannels) can be used to straighten or transport the biopolymer molecules (e.g., DNA molecules) or maintain them in a linearized form to allow for imaging, mapping and/or sequencing of the biopolymer molecule. Such channels may be formed on or in nanofluidic (or microfluidic) chips or similar structures that may be easily replaceable or removable from a biopolymer analysis system or may be permanent fixtures of a biopolymer analysis system. In some embodiments, the nanofluidic or microfluidic structures may comprise one or more of the linearizing systems or methods discussed above. In other embodiments, the nanofluidic or microfluidic structures may comprise the linearizing systems or methods above and additional structures used by the biopolymer analysis system, e.g., a sample well or reservoir. The nanofluidic or microfluidic structures may comprise a plurality or an array of the nanochannels (or microchannels) therein that are used to translocate or straighten the biopolymers. High efficiency and high throughput imaging devices may have a large number of parallel arrays of nanochannels used for the linearization process, e.g., <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM> or more nanochannels in an array. In operation, the biopolymer analysis system may be repeatedly loaded with biopolymer molecules, and the biopolymer molecules may be directed to flow through the biopolymer analysis system (e.g., the fluidic device) under a motive force, e.g., an electrokinetic force, pneumatic force, a capillary force, or any combination thereof, to move the biopolymer molecules into the detection region. For example, flow of biopolymer molecules, through a biopolymer analysis imaging system may comprise flow through one or more linearization regions and the plurality of nanochannels may comprise an imaging region, where the biopolymer molecules, now having been linearized, may be effectively and efficiently imaged using imaging devices. In the biopolymer analysis system, a motive force, e.g., fluid pressure or an electric field, may be used to drive the biopolymer molecules through the system.

Further, the biopolymer analysis system or apparatus therein may comprise a detection system configured to determine a characteristic of the biopolymer molecules in the detection region of the fluidic device. In some embodiments, the detection system may comprise an optically-based device configured to use fluorescence to interrogate the biopolymer molecules. In some embodiments, the detection system may be an electrochemical detection system configured to operate independently of or in conjunction with the optically-based detection system (for example, for defining stretched biopolymer molecules). In some embodiments, the optically-based device configured to use fluorescence to interrogate the biopolymer molecules may use a same light source used for interrogation for photocleaving purposes. For example, when being used for photocleaving as opposed to interrogation, the light source may be tuned up (as is the case with the blue laser, <NUM> or <NUM>, used for backbone DNA detection and photocleaving. In some embodiments, the amount of energy required for photocleaving may be <NUM> to <NUM> times greater than the energy required for imaging. However, one or more optical detection components used for biopolymer molecule imaging (e.g., the CCD or CMOS camera) may not be used for biopolymer photocleavage.

The biopolymer analysis system may further comprise a motive force generator and a detection system, the detection system configured to determine a characteristic of the biopolymer molecules in the detection region. The light source described above may be configured to deliver a light comprising a configuration for interrogating biopolymer molecules or photocleaving biopolymer molecules forming a clog in the fluidic device. In some embodiments, the light source may comprise one or more lasers with a specific or adjustable wavelength, an LED/OLED, an incandescent lamp, a mercury lamp, a UV lamp, an arc lamp, an argon lamp, or any other gas lamp (e.g., neon and krypton). The light source can be pulsating (i.e., turned on for a finite amount of time in bursts) or continuous, gated by physical shutters, filtered, amplified, dampened, polarized, or otherwise manipulated to generate a light used to interrogate biopolymer molecules at a variety of different wavelengths and intensities.

In some embodiments, the energy used for photocleavage may be destructive to multiple species of label. For example, labels that are red-shifted in emission, such as Cy3 or Atto <NUM>, may be destroyed or damaged by a <NUM> light source used to photocleave biopolymer molecules labeled with YOYO-<NUM>. Thus, the use of photocleavage processes and energies may inhibit subsequent attempts to image such biopolymer molecules that have been photocleaved, and care must be used to ensure the photocleavage has minimal effects on non-targeted biopolymer molecules and labels. In some embodiments, matching of the light generated by the light source to the label to be photocleaved may reduce the destructive effects of the light on non-targeted species of label. Additionally, in an optical detection system using fluorescence, additional wavelengths may be used for target multiplexing (targets being landmarks within a molecule, i.e. a defined sequence in a DNA), or sample multiplexing (different samples labeled with different colors or color combinations).

In some embodiments, the optically-based detection system may further comprise mirrors, objectives, lenses, filters, shutters, fiber optic cable, or any combination thereof. The optically-based detection system may further comprise a focusing mechanism to ensure maximum photon delivery for photocleaving (where the light source of the detection system is used for photocleaving and interrogating) and to provide tight focus for maximum clarity when interrogating biopolymers.

In some embodiments, a light delivery system may be configured to deliver the light generated by the light source to any region of the fluidic device. The light delivery system may comprise an optical system, or close proximity based delivery system bypassing the optical system, or a combination of the two, wherein DNA detection and interrogation of biopolymer molecules may occur via the optical system and photocleaving may occur by direct irradiation while protecting biopolymer molecules outside the interrogation zone.

The biopolymer analysis system may further include a positioning system and a controller, wherein the positioning system may be configured to target the detection system to the detection region for characterization of biopolymer molecules and to target a photocleaving light to a region of the fluidic device where the clog has formed. In some embodiments, the positioning system may be capable of movement in one or more of the x-, y-, and z-directions. In some embodiments, the positioning system may include a lag-screw based motion system or a piezo or stick-slip motion system. In some embodiments, the positioning system may include an internal or external encoder or another feedback mechanism to achieve accurate positioning.

In some embodiments, a controller may be configured to activate the motive force generator to move biopolymer molecules into the detection region and to direct the detection system to the detection region. The controller may be further configured to activate the detection system to determine characteristics of the biopolymer molecules. When a clog has formed in the fluidic device, the controller may direct the light source configured for photocleaving biopolymer molecules to the region where the clog has formed and activate the light source to generate a light for photocleaving biopolymer molecules forming the clog. Thereafter, the controller may activate the motive force generator to flush out the photocleaved biopolymer molecules so that additional new molecules can flow into the detection region for characterization.

<FIG> depicts an embodiment of a nanofluidic or microfluidic structure <NUM> that may be used in a biopolymer fluidic system. The components of an embodiment of the nanofluidic or microfluidic structure <NUM> are depicted. The nanofluidic or microfluidic structure <NUM> is adjacent to a sample well <NUM> or other sample source, such as a larger fluidic channel. The sample well <NUM> may be filled with a liquid sample containing a biopolymer or macromolecule, for example DNA molecules <NUM>. The fluid sample can also contain buffer for purposes of electrophoresis and surfactants and other additives for surface modification. The movement of DNA molecules <NUM> through the nanofluidic or microfluidic structure <NUM> is described herein as an example, and embodiments of the present disclosure are not limited thereto. While the biopolymers or macromolecules described herein are exemplified by DNA molecules <NUM>, one of skill in the art will understand this is merely an example of a biopolymer and not limiting.

The nanofluidic or microfluidic structure <NUM> may be divided into various zones, such as a transition zone 150a and a nanochannel zone 150b. The transition zone 150a can include a lip region <NUM>, one or more feeder channels <NUM>, a pillar or deconvolution or linearizing region <NUM>, and one or more relaxation channels <NUM>. The lip region <NUM> is advantageously adjacent to a sample well <NUM> and may comprise a raised portion with respect to the sample well <NUM>. The lip region <NUM> can be the first part of the nanofluidic or microfluidic structure <NUM> that the DNA molecule <NUM> encounters when being moved, translocated, or otherwise driven from the sample well <NUM> using, for example, electrophoresis. The lip region <NUM> provides a transition area for DNA molecules <NUM> leaving the sample well <NUM> and entering the subsequent regions of the nanofluidic or microfluidic structure <NUM>. A coiled or entangled DNA molecule <NUM> is depicted in the lip region <NUM>, having been driven from the sample well <NUM>. The lip region <NUM> may have a depth of from about <NUM> microns to about <NUM> microns, as measured from a top surface of the well structure <NUM>. The lip region may be from about <NUM> micron to about <NUM> microns in length, wherein length is defined as being in the direction transversing the nanofluidic or microfluidic structure <NUM> from one sample well <NUM> to another. In some embodiments, the lip region is about <NUM> microns deep and about <NUM> microns in length. The dimensions provided herein are exemplary only, and the dimension may be construed to be any value within the listed ranges.

Adjacent to the lip region <NUM> are the one or more feeder channels <NUM>. The feeder channels <NUM> funnel or direct the coiled or entangled DNA molecules <NUM> into a pillar region <NUM>. The one or more feeder channels <NUM> run parallel to each other, and are wide channels, relative to the nanochannels <NUM>. The feeder channels <NUM> may have a width of about <NUM> microns to about <NUM> microns, or any value therebetween, wherein width is understood to be in a direction perpendicular to length as described above. The feeder channels <NUM> may have a depth of from about <NUM> to about <NUM>, or any value therebetween. In some embodiments, the feeder channel is about <NUM> in depth and about <NUM> microns wide.

In one embodiment, the feeder channels <NUM> may lead to the pillar region <NUM>. The pillar region <NUM> includes a floor <NUM> which, in some embodiments, is contiguous with the bottom surface of the feeder channels <NUM>. The pillar region <NUM> also includes one or more pillars <NUM>. The pillars <NUM> may be silicon formations which are interspersed throughout the pillar region, with the pillars <NUM> extending from the floor <NUM> of the pillar region to a top portion which is raised above the floor <NUM>. In some embodiments, the top portion of the pillar region is in the same plane as the top surface of the well structure <NUM>, and may be in contact with the substrate (not shown). The pillars <NUM> may be of any shape, that is, the pillars may have a cross-sectional shape which is round, square, diamond, ovoid, rectangular, or any other desired shape. The pillars <NUM> may vary from one to another in size, shape, height, and distance from other pillars <NUM>. The pillars <NUM> may be evenly spaced or unevenly spaced throughout the pillar region <NUM>. In some embodiments, the pillar region <NUM> may include multiple zones (e.g., two or more zones) of pillars <NUM>, wherein a first zone comprises pillars of one a first dimension, shape, and/or height, and a second zone of pillars comprises pillars <NUM> of a second dimension, shape, and/or height, different from the first dimension. In one embodiment, the pillars <NUM> vary from larger to smaller dimension as they are further removed from the feeder channels <NUM> and closer to the nanochannels <NUM>.

The pillars <NUM> within the pillar region <NUM> are sized, shaped, and positioned to untangle, uncoil, or otherwise straighten tangled or coiled biopolymers or macromolecules. For example, the size of the pillars <NUM> and the spacing between the pillars <NUM> creates a tortuous flow path through which the coiled or tangled DNA molecule <NUM> cannot fit. Thus, as a motive force, such as an electrostatic field, is applied across the nanofluidic or microfluidic structure <NUM>, the coiled or tangled DNA molecule <NUM> is mechanically forced to uncoil as the molecule interacts with the pillars <NUM>. As shown, there may be more than one zone of pillars <NUM>, and the pillars <NUM> of the different zones may have different properties. For example, in some embodiments, the spacing between the pillars <NUM> of the first zone may be larger than the spacing of the pillars <NUM> of the second zone. In this way, the first zone causes an initial partial untangling or uncoiling, before the molecules reach the second zone. In the second zone, the molecules are forced through narrower spaces, which can cause a further untangling or uncoiling of the molecules. The distance between pillars <NUM> can vary. For example, the distance between two pillars <NUM> can be about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, about <NUM>, or a range between any two of these values. In some embodiments, the distance between pillars <NUM> is about <NUM> micron to about <NUM> microns.

The pillars <NUM> may have a height, that is, a distance from the floor <NUM> to their top surfaces of from about <NUM> to about <NUM>, or any value therebetween. In some embodiments, the pillars <NUM> may have a width, diameter, or long dimension, depending on their shape, of from about <NUM> to about <NUM>, or any value therebetween. In some embodiments, the pillars <NUM> have a height of about <NUM> and a width, diameter, or long dimension, of from about <NUM> to about <NUM>. As shown, the pillars <NUM> of the different zones may be of different diameters, where the pillars <NUM> of the first zone may have a larger diameter than the pillars <NUM> of the second zone. Additionally, the density of the pillars <NUM> in the pillar region <NUM> may increase as pillar region <NUM> nears the nanochannel wells <NUM>.

The pillar region <NUM> adjoins a plurality of relaxation channels <NUM>. The relaxation channels <NUM> are channels that act as inlets to the plurality of nanochannels <NUM>. In some embodiments, the relaxation channels <NUM> are funnel shaped channels. The relaxation channels <NUM> have a wider dimension at an end adjacent to the pillar region <NUM> and a narrower dimension at an end proximate to the nanochannels <NUM>. The relaxation channels <NUM> receive uncoiled and untangled or partially uncoiled and untangled molecules and help to further linearize the molecules as the molecules enter the plurality of nanochannels <NUM>. A linearized DNA molecule <NUM> is depicted entering one nanochannel <NUM> from the associated relaxation channel <NUM>. The relaxation channels <NUM> may be from about <NUM> to about <NUM> microns long, about <NUM> to <NUM> deep, and about <NUM>-<NUM> wide. In some embodiments, the relaxation channels <NUM> may be about <NUM> microns long, <NUM> deep, and <NUM> wide, at their widest point.

The plurality of nanochannels <NUM> receive the linearized DNA molecules, and are sized such that only linearized molecules can fit into and can be transported or moved through the nanochannels <NUM>. The nanochannels <NUM> may be from about <NUM> to about <NUM> wide, about <NUM> to about <NUM> deep, and from about <NUM> to about <NUM> microns long. In some embodiments, the nanochannels are about <NUM> wide, about <NUM> deep, and about <NUM> microns long.

During use, it is possible for the nanochannel <NUM> to become clogged with the biopolymer molecule <NUM> that is being translocated through the nanochannel <NUM> (see clog <NUM>). The clog may hamper further flow of new biopolymer molecules through the nanochannel <NUM> and/or the fluidic device. In other instances, the nanochannel <NUM> may be clogged where they meet with the relaxation channel <NUM> (see clog <NUM>) or the relaxation channels <NUM> may become clogged or blocked by DNA molecules <NUM> that do not fully uncoil through the pillar region <NUM> or that re-coil once they pass through the pillar region <NUM> (see clog <NUM>). Alternatively, the pillar region <NUM> may become clogged by DNA molecules <NUM> that do not properly uncoil or that wrap around one or more pillars <NUM> and accumulate (see clog <NUM>). Additionally, a clog <NUM> may form where the sample well <NUM> meets the feeder channels <NUM>.

In a more general sense, as applied to fluidic devices in general, DNA or other biopolymer may accumulate or clog in any region of fluid flow, but more usually in branch points, valves, transitions from larger to smaller channels, points where turbulent flow occurs, entrances to channels smaller than the dimension of coiled biopolymer, waste channels, flow passages of low velocity, regions where flow is stopped for a period of time, or areas where biopolymer may aggregate or precipitate or become adsorbed upon or entangled with any surface of the fluidic device including pillars, sidewalls of the nanochannels, or any other linearization structure.

<FIG> depicts an alternate embodiment of a nanofluidic or microfluidic structure <NUM> that may be used for biopolymer analysis. The components of an embodiment of this nanofluidic or microfluidic structure <NUM> are depicted and may be similar to those described in relation to <FIG>. The nanochannel <NUM> is shown adjacent to a sample well <NUM>. In some embodiments, both the nanochannel <NUM> and the sample well <NUM> may be part of the nanofluidic or microfluidic structure <NUM>. In other embodiments, only the nanochannels <NUM> may be part of the nanofluidic or microfluidic structure <NUM>. The sample well <NUM> may be filled with a liquid sample containing a biopolymer or macromolecule, for example DNA molecule <NUM>. The liquid sample can also contain buffer for purposes of electrophoresis and surfactants and other additives for surface modification. The movement of DNA molecules <NUM> through the nanochannel structure <NUM> is described herein as an example, and embodiments of the present disclosure are not limited thereto. While the biopolymer or macromolecule described herein are described as DNA molecules <NUM>, one of skill in the art will understand this is merely an example of a biopolymer and is not limiting.

Coiled or entangled DNA molecule <NUM> is depicted in the sample well <NUM>. Adjacent to the sample well <NUM> are the plurality of nanochannels <NUM>. The plurality of nanochannels runs parallel to each other. The plurality of nanochannels <NUM> receive the linearized DNA molecules and may be sized such that only significantly linearized molecules can fit into and can be transported or moved through the nanochannels <NUM>. The nanochannels <NUM> may advantageously be from about <NUM> to about <NUM> wide, about <NUM> to about <NUM> deep, and from about <NUM> to about <NUM> microns long. In some embodiments, the nanochannels <NUM> are about <NUM> wide, about <NUM> deep, and about <NUM> microns long. As depicted, one or more DNA molecules <NUM> may be located in one of the one or more sample wells <NUM> and/or the plurality of nanochannels <NUM>. In some embodiments, the DNA molecules <NUM> may be located in both a sample well <NUM> and a nanochannel <NUM> at the same time.

The size and the spacing of the nanochannels <NUM> may create a restrictive flow path through which the coiled or tangled DNA molecule <NUM> cannot fit. Thus, as the motive force, such as an electric field, is applied across the nanofluidic or microfluidic structure <NUM>, the coiled or tangled DNA molecule <NUM> is mechanically forced to uncoil as the molecule interacts with the nanochannels <NUM> from the sample well <NUM>.

During use, it is possible for the nanochannel <NUM> to become clogged with the biopolymer molecule <NUM> that is being translocated through the nanochannel <NUM> (see clog <NUM>). Alternatively, the point where the sample well <NUM> and the nanochannels <NUM> meet may become clogged or blocked by coiled DNA molecules <NUM> that do not properly uncoil under the motive force as they should to move into the nanochannel <NUM> (see clog <NUM>).

<FIG> depicts another embodiment of a nanofluidic or microfluidic structure <NUM> that may be used for biopolymer analysis. The components of an embodiment of this nanofluidic or microfluidic structure <NUM> are depicted and may be similar to those described in relation to <FIG>. In some embodiments, the nanofluidic or microfluidic structure <NUM> may comprise a nanochannel <NUM> and a sample well (not shown). In other embodiments, only the nanochannels <NUM> may be part of the nanofluidic or microfluidic structure <NUM>. The sample well may be filled with a liquid sample containing a biopolymer or macromolecule, for example DNA molecule <NUM>. The liquid sample can also contain buffer for purposes of electrophoresis and surfactants and other additives for surface modification. The movement of DNA molecules <NUM> through the nanochannel structure <NUM> is described herein as an example, and embodiments of the present disclosure are not limited thereto. Nanoslits <NUM> may exist between each of the nanochannels <NUM>. As depicted, the nanoslits <NUM> may run diagonally between two nanochannels <NUM>. The nanoslits <NUM> may work to linearize the DNA molecules <NUM> when the nanochannels <NUM> are loaded with the DNA molecules <NUM> and the DNA molecules <NUM> pass through the nanoslits <NUM>. As depicted, one or more DNA molecules <NUM> may be located in one of the one or more nanochannels <NUM> and/or one or more nanoslits <NUM>. In some embodiments, the DNA molecules <NUM> may be located in both a sample well, a nanochannel <NUM>, and a nanoslit <NUM>. While the biopolymer or macromolecule described herein are described as DNA molecules <NUM>, one of skill in the art will understand this is merely an example of a biopolymer and is not limiting.

A coiled or entangled DNA molecule <NUM> is depicted in the one or more nanochannels <NUM>. The plurality of nanochannels runs parallel to each other. The nanochannels <NUM> may be from about <NUM> to about <NUM> wide, about <NUM> to about <NUM> deep, and from about <NUM> to about <NUM> microns long and may receive linearized or coiled DNA molecules <NUM>. In some embodiments, the nanochannels <NUM> are about <NUM> wide, about <NUM> deep, and about <NUM> microns long. In some embodiments, the nanoslits <NUM> are about <NUM> wide, about <NUM> deep, and about <NUM> microns long. In some embodiments, the DNA molecules <NUM> may be located in both a sample well and a nanochannel <NUM> at the same time. A linearized DNA molecule <NUM> is depicted flowing through one nanoslit <NUM>.

The nanofluidic or microfluidic structure <NUM> may be used to translocate at least a portion of a biopolymer molecule from the sample wells through the nanochannel <NUM>. However, during use, it is possible for the nanochannel <NUM> to become clogged with the DNA molecule <NUM> that is being translocated through the nanochannel <NUM> (see clog <NUM>). Alternatively, the region where the sample wells and the nanochannel <NUM> meet may become clogged or blocked by coiled or accumulated DNA molecules <NUM> (see clog <NUM>). Additionally, the nanoslits <NUM> may become clogged or blocked by DNA molecules <NUM> (see clog <NUM>).

Once clogged, the efficiency of the linearization process using the clogged nanofluidic or microfluidic structures may decrease. Also, once clogged it can be difficult to introduce fresh biopolymer molecules into the nanofluidic or microfluidic device and manipulate them therein, seriously limiting throughput and utility. Clogging can further change the optimal electrical conditions required to manipulate biopolymer molecules in the nanofluidic or microfluidic structure, resulting in subpar throughput. Heterogeneous clogging throughout a plurality of nanochannels can give rise to heterogeneous response to electric fields from one portion of the microfluidic or nanofluidic device to the next. The rate of clogging can increase when existing biopolymer molecules are clogged inside the nanofluidic or microfluidic device, creating a snowball effect that accelerates clogging. Given the size of the nanochannels of the nanofluidic or microfluidic structure, clearing the channels through physical or similar means (e.g., cleaning solutions or physical cleaning devices) may be difficult and/or impractical.

Nanofluidic or microfluidic structures, including but not limited to those depicted in <FIG> may initially achieve a high throughput when loading the biopolymer molecules into the nanochannel or microchannel region. As the linearization region and nanochannels are repeatedly used for linearizing more biopolymer molecules, the linearization region and nanochannels may become clogged with tangled or accumulated biopolymer molecules. Similarly, the nanochannels may become clogged by molecules that are not completely linearized when they enter into the nanochannels or when multiple molecules enter a nanochannel at one time. Such tangling and/or clogging can cause reduced throughput as the clogged portions inhibit the ability for the DNA molecules to flow through the desired flow passages, such as nanochannels. For example, over time, when driving DNA through an array of nanochannels, more and more nanochannels will become clogged, so fewer channels can be used to provide information. The reduced number of DNA molecules traveling through the nanochannels results in reduced throughput or reduced information density in the array. Other fluidic devices can similarly become clogged with DNA or other biopolymers, reducing their utility in a related manner.

Accordingly, the clogged portion of the nanofluidic or microfluidic structure may need to be cleaned to restore the throughput of the chips or other structures. As an example, with reference to the structure of <FIG>, one method for clearing out the pillar region and the nanochannels may comprise using a laser or other illumination source to chop the biopolymer molecules that are clogging portions of the nanofluidic or microfluidic structure into fine pieces, after which those pieces of the chopped biopolymer molecules may be flushed from the nanofluidic or microfluidic structure via an appropriate motive force, such as by electrophoretic force or fluid pressure differential. In some embodiments, the biopolymer molecules may be "YoYo-<NUM>" stained or labeled biopolymer molecules. In some other embodiments, the biopolymer molecules being chopped/photocleaved may be stained or labeled with another indicator or exposed to another compound (i.e., YO, TOTO, methylene blue, Cu or Rh, compounds for photodynamic therapy, etc.) that absorb photons to facilitate or aid photocleavage of the biopolymer molecules when exposed to an illumination source. Thus, photocleavage may be achieved with or without a stain, label, indicator, or other photon absorber. Alternate embodiments may utilize non-stained molecules. In some embodiments, the illumination source may be a laser, for example a <NUM> blue laser or a <NUM> laser, or a laser of any other wavelength. Other embodiments may utilize light energy sources of other wavelengths, e.g. UV light, and light energy from other sources, e.g. a light-emitting diode. Thus, laser or other light that matches or overlaps an absorption wavelength of a dye or other absorbing molecule on the biomolecule can be used to cleave a labeled polynucleotide or other biomolecule, and UV or other high-energy illumination sources can be used to cleave even unlabeled polynucleotide or other biomolecule.

By applying a dose of laser or other light energy to the nanofluidic or microfluidic structure at desired times or intervals, clogging biopolymer molecules or stained/labeled biopolymer molecules that can absorb or be cleaved by the light may be fragmented, and more easily flushed from the structure. In one embodiment, specific times in a repetitive fluidic process, such as interleaved loading and imaging cycles in an analysis device, may be defined as the times when clogging biopolymers should be removed. Alternatively, the amount of clogging can be at least partially ascertained by detecting reduction of throughput or channels containing biomolecule beyond a threshold amount. Alternatively, direct imaging of the chip can indicate clogging. Alternatively, cleaning can be initiated during times when the nanofluidic or microfluidic structures are not currently being used for linearization.

For example, with reference to the structure of <FIG>, the device may detect or measure the throughput or loading density of the downstream nanochannels when the pillar regions of the nanofluidic or microfluidic structure are new and entirely unclogged. The system may be configured to detect clogging in the nanofluidic or microfluidic structure. The clog may be detected by identifying a reduced throughput or loading density in the nanochannels. Some embodiments may comprise additional detection methods to determine where the clog is located within a nanofluidic or microfluidic structure. Once the specific location of the clog is determined, the system may focus the illumination source at that location to focus the dosing energy only where needed and not wasting energy by unnecessarily dosing portions of the biopolymer analysis system that are not clogged. Alternatively, the system may direct illumination energy effective to fragment clogging biopolymers at least into any or all regions of the fluidic device that are susceptible to clogging.

In one embodiment, an initial throughput or loading value in a new or unclogged fluidic device may be determined to be a baseline throughput of the nanofluidic or microfluidic structure and may be the basis for determining a threshold level at which point the nanofluidic or microfluidic structures are to be cleaned. In some embodiments, the threshold level may be set as <NUM>% of throughput, such that when the throughput of the downstream nanochannels falls below <NUM>%, the device cleans the pillar regions of the nanofluidic or microfluidic structures. In another embodiment, the threshold level may be set at <NUM>% of throughput or <NUM>% of throughput, or any value in between these values, or at any other desired threshold, dependent on the requirements for the nanochannel throughput and the ability to clean the pillar region with an appropriate dose of biopolymer-cleaving energy (i.e., the device may have an automated ability to apply the photo-energy dose more or less frequently). Alternatively, the nanofluidic or microfluidic structure may be dosed after every loading cycle to ensure the structure is as clear as possible. In any of the embodiments of cleaning described herein, the cleaning process may be implemented in an automatic fashion, including at a predetermined time or at a predetermined clogging, throughput, or loading value.

<FIG> depicts one exemplary embodiment of a control system <NUM> for a biopolymer analysis system that may automatically or manually perform the method disclosed in <FIG>. A control system <NUM> includes a controller <NUM> and a memory <NUM>. The controller <NUM> is in communication with the memory <NUM>. The controller may comprise a processor and an internal memory or cache. The memory <NUM> may contain computer-readable instructions for operating the controller <NUM> and/or the control system <NUM>.

The controller <NUM> is also advantageously in communication with the illumination source(s) <NUM>, one or more x, x-y, or x-y-z translation motors <NUM>, and a motive force generator <NUM>. The controller <NUM> is configured to power on or off the illumination source(s) <NUM> and may also control the intensity of the illumination source(s) <NUM> and/or the duration of illumination. In some embodiments, the illumination source(s) <NUM> may provide control of the wavelength of light to be emitted, or may be selected to have strong or peak emissions at a desired wavelength, such as a wavelength at which a biopolymer or label effectively absorbs photons in a manner sufficient to effect cleavage. The controller <NUM> may be configured to control the direction, focus, or wavelength of the illumination beam by controlling the illumination optics <NUM>. The illumination source(s) <NUM> and the illumination optics <NUM>, individually or in combination, may advantageously comprise, for example, a laser light energy source or an LED light energy source, or any other source of photons effective to photocleave the biopolymer in question.

The controller <NUM> is configured to send control signals to one or more x, x-y, x-y-z translation motors <NUM>, such as are described herein. For example, the controller <NUM> may be configured to control operation of the x, x-y, or x-y-z translation motor <NUM> in order to move the nanofluidic or microfluidic structures discussed above to bring portions of the nanofluidic or microfluidic structure into range/view of the illumination optics <NUM> and illumination source(s) <NUM>, as needed or desired. Alternatively, the x, x-y, or x-y-z translation motor <NUM> may move the illumination optics <NUM> and/or the illumination source(s) <NUM> to direct light energy to a specific region or portion of the nanofluidic or microfluidic structure that is clogged or is otherwise is desired to be cleaned. It should be noted that prophylactic or preventative cleaning is also contemplated, so that accumulated biopolymer can be removed even if no decrease or only minor decrease in performance has occurred. In some embodiments, the photocleaving cleaning method described herein may be used prophylactically to prevent clogging, or may be used in conjunction with other prophylactic cleaning methods. In some embodiments, the translation motor <NUM> may be replaced with the positioning system described above. The controller <NUM> can be configured to operate or supply control signals to the motive force generator <NUM>. The motive force generator may comprise electrodes, pressure generating elements, or other components configured to generate a motive force as described herein. The motive force, as described above, may be configured to move the biopolymer molecules through the fluidic device and into the detection region.

In some embodiments, the controller <NUM> operates by automatically controlling and coordinating the timing of operating the illumination source(s) <NUM>, the motive force generator <NUM>, the illumination optics <NUM>, and the other portions of the control system <NUM>. For example, in some embodiments, the controller <NUM> can supply a signal to the motive force generator <NUM> to induce movement of biopolymers or macromolecules in a fluidic system. After an amount of time has passed, the controller <NUM> may remove the signal, or may provide an interrupt signal to stop application of the motive force from the motive force generator <NUM>. After the motive force is removed, the controller <NUM> may provide a signal to the illumination source(s) <NUM> to illuminate a portion of the nanofluidic or microfluidic structure which may be clogged with biopolymers or macromolecules or may otherwise be desired to be cleaned. In some embodiments, the controller <NUM> may determine that the nanofluidic or microfluidic structure of the biopolymer analysis system needs to be cleaned. As discussed above, this determination may be based on the flow rate of the biopolymers through the nanofluidic or microfluidic structure. In other embodiments, the controller <NUM> may clean the nanofluidic or microfluidic structure after every sample of biopolymers is analyzed by the biopolymer analysis system. Note that while automated systems are disclosed, a manual or partially manual system may also be used, if desired. For example, a cleaning cycle could be initiated when a user hits a button, makes a menu selection, manually translates the x, x-y, or x-y-z motor to irradiate specific portions of the fluidic device, or otherwise initiates a cleaning cycle. This could occur whenever a user desires, or can occur, for example, in response to a notification provided by the controller to a user requesting input if the user agrees to initiate cleaning.

Cleaning the nanofluidic or microfluidic structure may comprise dosing the region or portion of the nanofluidic or microfluidic structure to be cleared. In one exemplary embodiment, such as when biopolymer molecules such as DNA is labeled with a dye or other molecule that absorbs at <NUM>, the laser dosing process may involve dosing each biopolymer molecule with between <NUM> and <NUM> MJ/m^<NUM> of <NUM> laser energy density per cycle depending on the biopolymer molecules that are being analyzed with the biopolymer analysis system. For example, in one embodiment, the most common energy density per cycle may be <NUM> MJ/m^<NUM> of <NUM> laser. Additionally, in other embodiments, different wavelengths of laser may be used, such as when DNA is labeled with a different dye or other absorber. A designer can readily determine an appropriate energy density per cycle that is effective to photocleave the biopolymer molecules. In this manner, biopolymer molecules that previously clogged a portion of the nanofluidic or microfluidic structure or otherwise clogged, reduced, or inhibited the flow of biopolymer molecules through the fluidic structure may be cleaved or "chopped" into smaller pieces that can pass from the regions in which such biopolymer molecules have accumulated.

The controller <NUM> may control the dosing energy of the laser dosing process described above by turning on and off the illumination source(s) <NUM> and directing the illumination to the appropriate location using the illumination optics <NUM>. The controller <NUM> may determine what energy density should be used based on the biopolymer molecule in each sample and based on the light energy source being used to photocleave the biopolymer molecules. For example, as mentioned above, DNA molecules being photocleaved by a <NUM> laser may require <NUM> MJ/m^<NUM> to photocleave when the DNA molecules have been stained with a YoYo-<NUM> fluorescent label. Alternatively, photocleaving DNA molecules using UV light may not require staining but may require more energy during dosing than that of the <NUM> laser. The controller <NUM> may thus determine the amount of time to expose the portion of the nanofluidic or microfluidic structure being cleaned to the illumination source(s) <NUM> and the illumination optics <NUM> and may provide the desired energy level to the device. Control of the energy level may be achieved by any appropriate means, such as by pulse width modulation, control of energy input into the illumination source <NUM>, filtering, or changing the illumination time.

During, or after at least a portion of the fluidic system is illuminated, the controller <NUM> may signal the motive force generator <NUM> to activate. Activating the motive force generator <NUM> after the photocleaving process may flush out the photocleaved fragments of the biopolymer. After the motive force generator <NUM> is deactivated, the controller <NUM> may signal the x, x-y, or x-y-z translation motor <NUM> to move the nanofluidic or microfluidic structure a specified amount to position the next portion to be cleaned within range of the illumination source(s) <NUM> and illumination optics <NUM>, or may move the illumination source(s) <NUM> and illumination optics <NUM> to the appropriate location to clean the next portion of the nanofluidic or microfluidic structure that needs to be cleaned. After the nanofluidic or microfluidic structure or the illumination source(s) <NUM> and optics <NUM> have been moved, the controller <NUM> may re-energize the illumination source(s) <NUM> and optics <NUM> to properly dose the new portion of the nanofluidic or microfluidic structure and flush the chopped portions of biopolymer molecules to clear the next region of the nanofluidic or microfluidic structure. This process may repeat as many times as needed to fully clean and clear all clogged portions of the nanofluidic or microfluidic structure, or as desired. Alternatively some or all of the areas to be cleaned may be scanned with laser or other optical energy one or more times in a repetitive manner until sufficient cleaving energy has been administered. This process will be described in more detail with respect to <FIG>.

<FIG> is a flow diagram of an exemplary process for cleaning a nanofluidic or microfluidic structure after being used to linearize biopolymer molecules. A process <NUM> for cleaning a nanofluidic or microfluidic structure may begin at block <NUM>, wherein a sample containing an optionally marked, tagged, or stained biopolymer, such as DNA is added to a first reservoir or sample well. In some embodiments, a buffer solution or identical or other liquid or fluid may be added to a second reservoir or sample well, in order to facilitate the electrophoresis of the biopolymer or macromolecule. Following addition of the sample, the biopolymer analysis system may form a seal around the reservoir or the nanofluidic or microfluidic structure to prevent evaporation of the sample. In some embodiments, the biopolymer analysis system may include negative and positive electrodes. The negative and positive electrodes, or portions thereof, may be brought into contact with the sample in the first reservoir or sample well and the buffer solution or liquid in the second reservoir or sample well, respectively, to provide an electrostatic force to move the biopolymer molecules. In other embodiments, the motive force may comprise the pressure force generated by the pressure generation element as described above, which is brought into position after the sample is placed in the reservoir or sample well.

The process moves to block <NUM>, wherein the motive force is applied to the reservoirs or sample wells. As described above, in some embodiments, this is accomplished by applying an electric field to the sample wells by using, for example, the negative and positive electrodes, and/or the electrode portions of the substrate. In some embodiments, this is accomplished by applying a pressure gradient sufficient to drive molecules from the first reservoir to the second reservoir through the microchannels or nanochannels.

The process <NUM> moves to block <NUM>, wherein the motive force is removed after a predetermined amount of time. In some embodiments, block <NUM> may comprise removing the motive force when the flow through the nanofluidic or microfluidic structure drops below a threshold value, indicating the flow through the nanochannels is complete. Alternatively, the block <NUM> may be timed to allow biopolymers in the nanochannels to move out of the nanochannels and other biopolymers to move into the nanochannels for imaging or other analysis. Upon removal of the motive force in block <NUM>, the movement, driving, or migration of molecules through the nanofluidic or microfluidic structure, and, specifically, the nanochannels stops, and the molecules maintain their current positions, either within the nanochannels or in the second reservoir or sample well. The predetermined amount of time may be determined based on the biopolymer or macromolecule of interest. In some embodiments, the predetermined amount of time may be determined based on the quantity of biopolymer molecules being linearized and transported by the system. The time the motive force is applied may be <NUM> microsecond, <NUM> microseconds, <NUM> microseconds, <NUM> microseconds, <NUM> microseconds, <NUM> seconds, <NUM> seconds, <NUM> second, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> seconds, <NUM> minutes, <NUM> minutes, <NUM> minutes, <NUM> minutes, <NUM> minutes, or more, or any amount of time therebetween.

The process <NUM> moves to block <NUM> wherein either the illumination optics or the nanofluidic or microfluidic structure is moved so as to direct illumination for cleaning by a light energy source to be directed onto a desired region of the fluidic structure. For example, if the fluidic structure is to be moved, an assembly or a platform on which the nanofluidic or microfluidic structure is attached may be moved to bring the nanofluidic or microfluidic structure into position for cleaning. In some embodiments, for example, a first portion to be cleaned may include the point where the nanochannels meet the sample well, while a second portion may include the nanochannels themselves. In some embodiments, the second portion cleaned may include an array of pillars or a subset of nanochannels, other than those previously cleaned. A person of skill in the art will understand that the second portion of the nanofluidic or microfluidic structure cleaned may vary without departing from the scope of this application.

Alternatively, at block <NUM>, the illumination optics may be moved so as to position the illumination optics to clean a portion of the nanofluidic or microfluidic structure or biopolymer analysis system. In some of embodiments, the illumination optics may be moved to clean a portion of the nanofluidic or microfluidic structure or biopolymer analysis system that is immovable. Similarly as described above, the illumination optics may be operated to direct the illumination beam at a different portion of the nanofluidic or microfluidic structure or the biopolymer analysis system, or to scan an area, which can then be cleaned using the illumination beam. In some embodiments, for example, a first portion of the biopolymer analysis system to be cleaned may include nanofluidic or microfluidic structure comprising the nanochannels or an area adjacent to or upstream from an entrance into the nanochannels. Furthermore, a person of skill in the art will understand that any portion of a fluidic system using biopolymers that can be exposed to the illumination beam may be cleaned using a similar process, adapted as necessary to the particular system in question. Alternatively, an appropriate source of photon energy, such as a UV LED or visible light LED, or an array or arrangement of such LEDs, may be permanently positioned to direct photo-cleavage light energy when actuated onto appropriate portions of a fluidic device.

At block <NUM>, a portion of the nanofluidic or microfluidic structure (or biopolymer fluidic system) is cleaned. This block may comprise exposing a portion of the fluidic structure to an illumination beam such that any biopolymer molecules that are remaining in that portion are dosed with energy from the illumination beam that may react with the biopolymer molecules and photocleave the biopolymer molecules that are appropriately dosed such that the biopolymer is chopped into smaller pieces. As discussed above, the dosing requirements may vary according to at least one of the biopolymer molecule, the staining or labeling element used, or the illumination source being used. In some embodiments, block <NUM> may be directed to specific locations that are determined to need to be cleaned. In some embodiments, block <NUM> may be directed to all location of the chip. After photocleaving the selected region of the nanofluidic or microfluidic structure, the process proceeds to block <NUM>.

Block <NUM> may represent an optional dedicated cleaning block that may be inserted after block <NUM>, where the nanofluidic or microfluidic structure region(s) or the portion of the biopolymer analysis system was previously cleaned. The optional block <NUM> may provide for the application of a dedicated motive force to the nanofluidic or microfluidic structure or the portion of the biopolymer analysis system that has been cleaned by a previous step. The dedicated motive force may be dedicated to flushing out the chopped pieces of the biopolymer molecules and leaving the area clear of elements that may inhibit the flow of biopolymers through the system. In some embodiments, the processes of optional block <NUM> may be performed after the optional decision block <NUM>. In some embodiments, a non-dedicated motive force, such as a motive force used to load the DNA into the chip after a photocleavage step (e.g., the motive force of Block <NUM>) may be used to clear the chopped pieces of the biopolymer molecules concurrently with the loading of the next DNA sample.

The process <NUM> moves to an optional decision state <NUM> wherein it is determined if each portion of the nanofluidic or microfluidic structure or biopolymer analysis system that needed to be cleaned or was scheduled to be cleaned has been cleaned. The portion to be cleaned can include a specific nanochannel or the full array of nanochannels, or the pillar array (if one exists), or any desired portion of a nanochannel or fluidic device. If the nanofluidic or microfluidic structure or biopolymer analysis system has not been fully cleaned, the process returns to step <NUM>, wherein the cleaning of portions of the fluidic structure or biopolymer analysis system continues.

The process <NUM> described above may provide an increase in biopolymer molecule loading or throughput through the fluidic system. This increase in loading and throughput may be accomplished without observed side effects, such as decreased DNA size, photobleached labels or other related metrics. Additionally, in systems where the cleaning method may be utilized after every loading instance, the biopolymer analysis system may be more aggressively loaded than in a biopolymer analysis system that is not cleaned, leading to higher throughput.

A person of skill in the art will understand that the steps of process <NUM> need not be performed in the order specified, nor must all steps be performed. Furthermore, a person of skill in the art will understand that the processes may be performed in parallel, and no steps in one process necessarily preclude the performance of steps in another process. In some embodiments, the processes occur in an overlapping fashion, with steps from one process giving rise to or, initiating steps from another process, or steps from one process being triggered by steps from another process. The process may be fully automatic, may be partially automated while requiring one or more user inputs, or may be manually implemented.

<FIG> is a flowchart of one exemplary method of enhancing fluid flow. In some aspects, the process <NUM> may be performed by the control system <NUM>. In some aspects, the process <NUM> may be performed by a standalone photocleaving system (not shown). Process <NUM> may demonstrate the process of cleaning a nanofluidic or microfluidic structure after being used to linearize biopolymer molecules, for example the process <NUM> shown in <FIG>.

At block <NUM>, biopolymer molecules may be moved into contact with at least one fluidic channel in or on a device, whereby clogging occurs in the device due to coiling or aggregation of the biopolymer molecules or adsorbtion to or tangling around the channels or other nano- or micro-patterned features inside the channel or fluidic device. In some aspects, the biopolymer molecules may be moved using a motive force to flush photocleaved biopolymer molecules from the cleaned region. In some aspects, the motive force may comprise an electrostatic, a pneumatic force, a capillary force, or any combination thereof.

At block <NUM>, the process <NUM> may direct a light source at a region of the device in which said clogging has occurred so as to photocleave any biopolymer molecules that contribute to said clogging and facilitate removal or reduction of said clogging. In some embodiments, the light source may emit a light having a wavelength of <NUM> or <NUM>. In some aspects, the process <NUM> may further include labeling the biopolymer molecules with an indicator to facilitate photocleaving of the biopolymer molecules when exposed to the light source. In some aspects, the block <NUM> or another block of process <NUM> (not shown in this figure) may configure the light source to generate light that matches the indicator or photon absorber used to label the biopolymer molecules to maximize the photocleaving capabilities of the process. Generating light that matches the indicator or photon absorber may comprise determining what characteristics of the light (i.e., wavelength, intensity, etc.) would maximize photocleaving of the biopolymer molecules labeled with particular indicators or photon absorbers. Each indicator or photon absorber may have a different light (i.e., light with a different wavelength, intensity, etc.) that maximizes photocleavage of the biopolymer molecules to which the indicator or photon absorber is applied. In some aspects, the process <NUM> may further include detecting a clogged or reduced flow condition prior to or concurrent with or after the block <NUM>. In some aspects, the process <NUM> may be implemented automatically by system <NUM> at one of a predetermined time or predetermined transport threshold. Any of the blocks described above in relation to process <NUM> may be performed by one or more of the components of system <NUM>, including the controller <NUM>, the illumination source(s) <NUM> and optics <NUM>, motive force generate <NUM>, and x, x-y, or x-y-z translation motor <NUM>. In some embodiments, one or more of the blocks described above may be performed by components of similar structure and function as those depicted in <FIG>.

The technology is operational with numerous other general purpose or special purpose computing system environments or configurations. Examples of well-known computing systems, environments, and/or configurations that may be suitable for use with the invention include, but are not limited to, personal computers, server computers, hand-held or laptop devices, multiprocessor systems, processor-based systems, programmable consumer electronics, network PCs, minicomputers, controllers, microcontrollers, mainframe computers, multiple processors directly or indirectly linked, distributed computing environments that include any of the above systems or devices, and the like. Combinations of these devices can be used together.

As used herein, instructions refer to computer-implemented steps for processing information in the system. Instructions can be implemented in software, firmware or hardware and include any type of programmed step undertaken by components of the system.

As used herein, a processor may be any conventional general purpose single- or multichip processor such as a Pentium® processor, a Core I3, I5, or I7 processor, a <NUM> processor, an AMD FX series processor, a MIPS® processor, an Atom processor, an Alpha® processor, or any other desired or suitable processor or combination of processors. In addition, the processor may be any conventional special purpose processor such as a digital signal processor a graphics processor or an embedded microcontroller. The processor typically has conventional address lines, conventional data lines, and one or more conventional control lines.

The system is comprised of various modules as discussed in detail. As can be appreciated by one of ordinary skill in the art, each of the modules comprises various subroutines, procedures, definitional statements and macros. Each of the modules are typically separately compiled and linked into a single executable program. Therefore, the description of each of the modules is used for convenience to describe the functionality of the preferred system. Thus, the processes that are undergone by each of the modules may be arbitrarily redistributed to one of the other modules, combined together in a single module, or made available in, for example, a shareable dynamic link library.

The system may be used in connection with various operating systems such as Linux®, UNIX® or Microsoft Windows®.

The system may be written in any conventional programming language such as C, C++, C#, BASIC, Pascal, or Java, and run under a conventional operating system. C, C++, BASIC, Pascal, Java, and FORTRAN are industry standard programming languages for which many commercial compilers can be used to create executable code. The system may also be written using interpreted languages such as Perl, Python or Ruby.

Those of skill will further appreciate that the various illustrative logical blocks, modules, circuits, and algorithm steps described in connection with the embodiments disclosed herein may be implemented as electronic hardware, computer software, or combinations of both.

One of skill will further appreciate that the methods and apparatus described herein may be applied to any fluidic system making use of biopolymer molecules in situations where clogs may develop.

In one or more example embodiments, the functions and methods described may be implemented in hardware, software, or firmware executed on a processor, or any combination thereof. A storage medium may be any available media that can be accessed by a computer. By way of example, and not limitation, such computer-readable media can comprise RAM, ROM, EEPROM, CD-ROM or other optical disk storage, magnetic disk storage or other magnetic storage devices, or any other medium that can be used to carry or store desired program code in the form of instructions or data structures and that can be accessed by a computer. Disk and disc, as used herein, includes compact disc (CD), laser disc, optical disc, digital versatile disc (DVD), floppy disk and Blu-ray disc where disks usually reproduce data magnetically, while discs reproduce data optically with lasers.

The foregoing description details certain embodiments of the systems, devices, and methods disclosed herein. It will be appreciated, however, that no matter how detailed the foregoing appears in text, the systems, devices, and methods can be practiced in many ways. As is also stated above, it should be noted that the use of particular terminology when describing certain features or aspects of the invention should not be taken to imply that the terminology is being re-defined herein to be restricted to including any specific characteristics of the features or aspects of the technology with which that terminology is associated.

It will be appreciated by those skilled in the art that various modifications and changes may be made without departing from the scope of the described technology. Such modifications and changes are intended to fall within the scope of the embodiments.

It will be understood by those within the art that, in general, terms used herein are generally intended as "open" terms (e.g., the term "including" should be interpreted as "including but not limited to," the term "having" should be interpreted as "having at least," the term "includes" should be interpreted as "includes but is not limited to," etc.). It will be further understood by those within the art that if a specific number of an introduced claim recitation is intended, such an intent will be explicitly recited in the claim, and in the absence of such recitation no such intent is present. However, the use of such phrases should not be construed to imply that the introduction of a claim recitation by the indefinite articles "a" or "an" limits any particular claim containing such introduced claim recitation to embodiments containing only one such recitation, even when the same claim includes the introductory phrases "one or more" or "at least one" and indefinite articles such as "a" or "an" (e.g., "a" and/or "an" should typically be interpreted to mean "at least one" or "one or more"); the same holds true for the use of definite articles used to introduce claim recitations. In addition, even if a specific number of an introduced claim recitation is explicitly recited, those skilled in the art will recognize that such recitation should typically be interpreted to mean at least the recited number (e.g., the bare recitation of "two recitations," without other modifiers, typically means at least two recitations, or two or more recitations). Furthermore, in those instances where a convention analogous to "at least one of A, B, and C, etc." is used, in general such a construction is intended in the sense one having skill in the art would understand the convention (e.g., "a system having at least one of A, B, and C" would include but not be limited to systems that have A alone, B alone, C alone, A and B together, A and C together, B and C together, and/or A, B, and C together, etc.). In those instances where a convention analogous to "at least one of A, B, or C, etc." is used, in general such a construction is intended in the sense one having skill in the art would understand the convention (e.g., "a system having at least one of A, B, or C" would include but not be limited to systems that have A alone, B alone, C alone, A and B together, A and C together, B and C together, and/or A, B, and C together, etc.). It will be further understood by those within the art that virtually any disjunctive word and/or phrase presenting two or more alternative terms, whether in the description, claims, or drawings, should be understood to contemplate the possibilities of including one of the terms, either of the terms, or both terms.

Claim 1:
A method for enhancing fluid flow, the method comprising:
moving biopolymer molecules into a detection region of a device and into contact with at least one fluidic channel in or on the device, whereby clogging occurs in the device due to coiling or aggregation of the biopolymer molecules or adsorption to or tangling around the channels or any other nano- or micro- features inside the channel or fluidic device;
detecting a clogged or reduced flow condition;
directing a light source at a region of the device in which said clogging has occurred in a manner effective to photocleave biopolymer molecules that contribute to said clogging, thereby facilitating removal or reduction of said clogging;
after directing the light source to the region, applying a motive force to fluid in the region of the device in a manner effective to flush the photocleaved biopolymer molecules from the region of the device comprising said clogging, and
applying a motive force to flow additional biopolymer molecules into the detection region of the device for characterization.