Patent Publication Number: US-2021187503-A1

Title: Apparatus and system for single-molecule nucleic acids detection

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     This application claims the benefit of prior-filed provisional application with application No. 62/950,551, filed Dec. 19, 2019, which is incorporated by reference in its entirety. 
    
    
     BACKGROUND 
     Field of the Invention 
     The present disclosure relates to a bioassay system, in particular, a system including a detection module for single-molecule nucleic acids sequencing. 
     Description of Related Art 
     Continuous single-molecule nucleic acid sequencing method is a promising method to sequencing DNA/RNA/mRNA/modified DNA/modified RNA in high speed and long length. To perform this method needs an optical system to continuously monitor a single polymerase replicating a template DNA/RNA molecule (the molecule to be sequenced) and distinguishing the fluorescent signal associated with the incorporation events, therefore, the order of the nucleic acid bases of that template molecule is read out. Science 2 Jan. 2009: Vol. 323, Issue 5910, pp. 133-138 disclosed a sequencing method, dye determination method is employed for DNA sequencing applications to determine the fluorescently labeled nucleotide (A, T, G, C) sequence of a given DNA fragment at specific reaction sites on a DNA nanostructure arrays. 
     A sequencing site is a location able to affix or hold or confine the polymerase replication complex, i.e. polymerase with a template and primer, in position. Large number of sequencing sites usually arranged into an array format on a substrate, called sequencing chip. 
     A continuous single-molecule sequencing system comprises excitation light source, sequencing chip, fluorescent optical setup, and optical sensors. The excitation light source is to provide excitation light to each sequencing sites. The fluorescent optical setup is configured to collect and guide fluorescent signal emitted from each sequencing sites on the sequencing chip to the optical sensor. The optical sensor used is formed by an array of photodetectors, also called image sensor or area sensor. Each photodetector on the sensor is called a pixel. Since there are four nucleotide bases need to be differentiated, the optical sensor needs to be able to differentiate multi-wavelength bands of labelling fluorophores. 
     The performance of a sequencing system. To make a sequencing system able to catch the fluorescent light emitted from the incorporation event without disturbed by all the labeled dNTPs floating around the polymerase, the replication complex (or sequencing complex, formed by polymerase/template/primer) needs to be fixed in one position (sequencing site). And the system needs to provide a light source that only excites the fluorophore that comes close enough to the polymerase (confined excitation space) and a sensor that only receiving signal coming closing from the polymerase (confined observation space). In order to increase the system efficiency, a system with multiple sequencing sites acting in parallel is preferred. The system performance can be defined as “number of sequencing site/cost of the system”. 
     Lens-based sequencing system. In a laboratory, a high resolution total internal reflection fluorescence (TIRF) microscope is able to be converted to a continuous nucleic acid DNA single-molecule sequencer.  FIG. 1  is a schematic view of an inverted microscope, a typical TIRF microscope. Laser beam launches from a laser launcher  90  through a filter cube  91  into a high NA (typically 1.5 NA) 60× or 100× oil immersion objective lens  92  arranged to create TIRF condition on an upper surface of a coverslip  93  where continuous nucleic acid DNA single-molecule sequencing taking place. The objective lens  92  is infinity collected. The fluorescent light image collected by the objective lens  92  and passing through the filter cube  91  which removes laser wavelengths and reserves only the fluorescent light of interest. With some other optical elements such as mirrors, prisms, and relay lenses (not shown), the beam of image projected onto a sensor device  94  to form an enlarged image by a projection lens  95  (also called field lens or tube lens). Fluorescent image collected by the sensor device  94  is then analyzed and translated into sequencing data. Since the lenses are used in providing excitation light and collecting fluorescent light, this type of system is called lens-based sequencing system. The sequencing sites number of a lens-based system is between several thousands to tens of thousands, depending on the specifications of the lens and sensor. 
     U.S. Pat. Nos. 8,318,094 and 7,170,050 disclosed a sequencing system, more than 100,000 sequencing sites are provided. The reaction sites on the chips of these systems typically featuring micro lenses or micro mirrors to increase the amount of fluorescent light collection efficiency. However, these micro-optical elements prohibited the reduction of the pitch of the reaction sites hence the density cannot be further increased. The micro-optical element increases the chip manufacturing process and cost. Also, such systems typically employ an assortment of different optical elements to direct, modify, and otherwise manipulate light directed to and/or received from a reaction site. The system is bulky and sensitive to the environmental vibration due to its excitation light spots array needs to be precisely aligned with sequencing sites array. These systems employ lens to collect fluorescent light from sequencing chip can be classified as a special case of lens-based sequencing systems. The total number of sequencing sites can be monitored by best-ever commercial lens-based sequencing system is 150,000. In contrast, the sequencing chip in lens-based system is simple and relatively low cost. 
     Regarding the chip-based sequencing system. In another embodiment. U.S. Pat. No. 7,767,441 disclosed a sequencing system, wherein a sequencing sites array, an excitation light distribution waveguide and a sensor are integrated into one chip. This system integrated sequencing chip and optical sensor into one piece can be called as chip-based sequencing systems. The number of sequencing sites is depended upon the size of the chip can be millions or tens of millions. However, the manufacturing cost of the chip is very high and it is designed to be one time used which makes the operation cost not affordable by most applications. 
     BRIEF SUMMARY OF THE INVENTION 
     In one exemplary aspect, an apparatus for continuous single molecule nucleic acids sequencing is provided. The apparatus includes a detection module configured to detect fluorescent light generated from a sequencing chip. The detection module includes a sensor device, an objective lens having a first magnification, and a projective lens having a second magnification. The objective lens and the projective lens are configured to transmit the fluorescent light from the sequencing chip to the sensor device. The second magnification is less than unity. 
     In another exemplary aspect, an apparatus for continuous single molecule nucleic acids sequencing is provided. The apparatus includes a sequencing chip having a plurality of sequencing sites arranged by a pitch and a detection module for detecting fluorescent light generated from the sequencing sites. The detection module includes a sensor device having a plurality of pixels, each of the pixels having a pixel size, and a lens set having an objective lens and a projective lens. The objective lens and the projective lens are configured to transmit the fluorescent light from the sequencing sites to the sensor device, and the lens set having an overall magnification. A product of the pitch and the overall magnification is equal to or greater than one pixel size and equal to or smaller than 2 pixel sizes. 
     In yet another exemplary aspect, an apparatus for continuous single molecule nucleic acids sequencing is provided. The apparatus includes a detection module configured to detect fluorescent light generated from a sequencing chip. The detection module includes a sensor device with a plurality of pixels, each of the pixels having a pixel size, and a lens set having an objective lens and a projective lens, the objective lens and the projective lens being configured to transmit the fluorescent light from the sequencing chip to the sensor device. A projected spot size of the fluorescent light on the sensor device is smaller than or equal to 1.5 times of the pixel size. 
     In further another a sequencing chip for continuous single molecule nucleic acids sequencing is provided. The sequencing chip includes a substrate, a waveguide, a light coupler, a sequencing site, and a beam adjusting mechanism. The waveguide is over the substrate. The waveguide includes a core layer and an upper cladding layer over the core layer. The light coupler extends from the upper cladding layer into the core layer. The sequencing site is in the upper cladding layer. The beam adjusting mechanism is configured to adjust a total projection area of a beam from the light coupler when propagating toward the sequencing site. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  illustrates a schematic cross-sectional view of a conventional TIRF microscope. 
         FIG. 2  illustrates a schematic view of a design of lens-based single-molecule sequencing system according to some embodiments of the present disclosure. 
         FIG. 3  illustrates a schematic view of a typical microscope objective lens. 
         FIG. 4  illustrates a schematic view of numerical aperture (NA) of an objective lens according to some embodiments of the present disclosure. 
         FIG. 5  illustrates a field of view (FOV) of a lens system. 
         FIG. 6  illustrates a spatial resolution of an optical system. 
         FIG. 7  illustrates a schematic view of a nanowell according to some embodiments of the present disclosure. 
         FIG. 8A  and  FIG. 8B  illustrate the field strength distribution of epi excitation and evanescent wave excitation. 
         FIG. 9A  and  FIG. 9B  illustrate lens type and prism type TIRF according to some embodiments of the present disclosure. 
         FIG. 10  illustrates that spot size may affect signal strength on a pixel according to some embodiments of the present disclosure. 
         FIG. 11  illustrates a schematic view of an apparatus for continuous single molecule nucleic acids sequencing according to some embodiments of the present disclosure. 
         FIG. 12  illustrates a schematic cross-sectional view of a sequencing chip according to some embodiments of the present disclosure. 
         FIG. 13  illustrates a schematic top view of general circular type nanowells according to some embodiments of the present disclosure. 
         FIG. 14  illustrates a schematic top view of trench type nanowells according to some embodiments of the present disclosure. 
         FIG. 15  illustrates a schematic top view of trench type nanowells according to some embodiments of the present disclosure. 
         FIG. 16  illustrates a schematic top view of general circular type nanowells according to some embodiments of the present disclosure. 
         FIG. 17  illustrates a schematic top view of trench type nanowells according to some embodiments of the present disclosure. 
         FIG. 18  illustrates a schematic top view of trench type nanowells according to some embodiments of the present disclosure. 
         FIG. 19A  illustrate a schematic top view of a waveguide having a beam expanding mechanism according to some embodiments of the present disclosure. 
         FIG. 19B  illustrate a schematic top view of a spacer according to some embodiments of the present disclosure. 
         FIG. 19C  illustrate a schematic top view of a cover according to some embodiments of the present disclosure. 
         FIG. 20  illustrates a pitch of nanowell and a pitch and is also the sizes of the pixels on a sensor device according to some embodiments of the present disclosure. 
         FIG. 21  illustrates the spectral bands of the labeled fluorophores detected by three channels. 
         FIG. 22  illustrates a Philips type prism according to some embodiments of the present disclosure. 
         FIG. 23  illustrates a dispersive device for spectral detection according to some embodiments of the present disclosure. 
         FIG. 24  is a SEM cross sectional image of a sequencing chip with a nanowell according to some embodiments of the present disclosure. 
         FIG. 25A  and  FIG. 25B  illustrate snap shots of frames of sequencing raw data. 
         FIG. 26  illustrates a sequencing time trace from one nanowell of one channel. 
     
    
    
     DETAILED DESCRIPTION 
     The following disclosure provides many different embodiments, or examples, for implementing different features of the provided subject matter. Specific examples of elements and arrangements are described below to simplify the present disclosure. These are, of course, merely examples and are not intended to be limiting. For example, the formation of a first feature over or on a second feature in the description that follows may include embodiments in which the first and second features are formed in direct contact, and may also include embodiments in which additional features may be formed between the first and second features, such that the first and second features may not be in direct contact. In addition, the present disclosure may repeat reference numerals and/or letters in the various examples. This repetition is for the purpose of simplicity and clarity and does not in itself dictate a relationship between the various embodiments and or configurations discussed. 
     Further, spatially relative terms, such as “beneath,” “below,” “lower,” “above,” “upper”, “on” and the like, may be used herein for ease of description to describe one element or feature&#39;s relationship to another element(s) or feature(s) as illustrated in the figures. The spatially relative terms are intended to encompass different orientations of the device in use or operation in addition to the orientation depicted in the figures. The apparatus may be otherwise oriented (rotated 90 degrees or at other orientations) and the spatially relative descriptors used herein may likewise be interpreted accordingly. 
     As used herein, the terms such as “first”, “second” and “third” describe various elements, components, regions, layers and/or sections, these elements, components, regions, layers and/or sections should not be limited by these terms. These terms may be only used to distinguish one element, component, region, layer or section from another. The terms such as “first”, “second”, and “third” when used herein do not imply a sequence or order unless clearly indicated by the context. 
       FIG. 2  illustrates a schematic view of a design of lens-based single-molecule sequencing system which mostly follows the design principle for single-molecule detection. An infinity corrected objective lens is used to collect fluorescent light from sequencing sites  10  and a projection lens  11  projects the signal of sequencing sites  10  to an optical sensor set  12 . Generally. the objective lens is used to collect fluorescent light from the sequencing sites and the projection lens (also called as field lens or tube lens) is used to project the signal of sequencing sites to the optical sensor set. In some embodiments, the sequencing system further includes a microfluidic structure coupled to the nanowells, and the samples are loaded onto the sequencing chip  13  through the microfluidic structure. The microfluidic structure may spread the samples on the sequencing chip  13  evenly or distribute the samples to the designated nanowells. 
       FIG. 3  illustrates a schematic view of a typical microscope objective lens  14 . Usually, the magnification of the objective lens  14  is marked on the body thereof, such as “100×” as shown in the figure. In an ordinary microscope, a 100× objective lens is working with a default or preset 1× projection lens as shown in  FIG. 1 , and the lens set may result an overall 100× magnification. Since a microscope is utilized to enlarge the detailed structures of the specimen, the magnification of projection lens is always equal to or greater than unity. Accordingly, the most common magnification of the projection lens is 1× in order to render the magnification marked on the objective lens body, while 2× or greater magnification is also available. 
       FIG. 4  illustrates a schematic view of numerical aperture (NA) of the objective lens  14 . The NA of the objective lens  14  is a dimensionless number that characterizes a range of angles over which the emitted fluorescent light can be collected by the objective lens  14 , while an objective lens with a higher NA may collect more light. Usually, the NA of the objective lens  14  is also marked on the body thereof, such as “1.5” as shown in the figure. The governing formula may be illustrated as NA=n×sin θ, wherein n is the refractive index of the immersed medium and θ is the collection angle of the objective lens. To reach high single-molecule sensitivity, the NA of the objective lens  14  must be higher than a certain level. Generally, the minimum NA is affected by the sensor performance specifications and optical lens arrangement. 
     In a lens-based single-molecule sequencing system, the NA of the objective lens  14  is smaller than 1, 0.9, 0.8, or 0.7. 
     The field of view (FOV) of the lens-based optical module is the diameter of the circular area that can be imaged by the system as shown in  FIG. 5 . Since a sensor  120  is used to receive the image projected from the optical module, an effective FOV  151  may be determined by the overlap between a lens FOV  150  and a corresponding area at the sensor  120 . If the size of the sensor  120  is larger than the lens FOV  150  projected thereon, the effective FOV  151  is thus dominated by the lens. Otherwise, the effective FOV  151  is restricted by the size of the sensor  120   
     An effective chip area is the area on the sequencing chip  13  that corresponded to the effective FOV  151  of the optical module. To achieve high performance, the sequencing sites  10  need to be arranged within the effective chip area as much as possible to ensure the accommodation of the sequencing sites  10 . A pitch may be defined as the distance between each two adjacent sequencing sites  10 . There are several factors that may prohibit the sequencing sites  10  getting too close. 
     For example, the optical spatial resolution is the minimum pitch that the optical module be able to distinguish signals from two neighboring sequencing sites  10 . Due to the nature of light, signals from different sequencing sites  10  are normally distributed as a Gaussian distribution. As shown in  FIG. 6 , the fluorescent light signals from single molecule sequencing site A and site B are projected onto the sensor plane. There is no distinct boundary of each signal beam spot and they are always partially overlapped and cannot be completely separated. Whenever the locations of site A and site B are distant enough and the overlap of the signal beam spot thereof does not beyond the resolvable level, the signals from these two sites are distinguishable. Accordingly, the minimum distance between the signals from site A and site B is called as the spatial resolution of an optical system. 
     Usually, high numerical aperture (NA) of an objective lens may provide high spatial resolution due to the governing equation that the resolution (r)=0.61×wavelength (λ)/NA, and hence the sequencing sites  10  can be arranged closer or denser with small pitch for resolving smaller features. That means more sequencing sites  10  can be arranged within the same area. Therefore, the design of the optical system is to provide a combination of lens module and sensors that may be used to identify more sequencing sites and so that ultimately a best performance may be provided. 
     An example is given bellow to explain the traditional lens-based single-molecule system design. In such example, a sensor has an array of 2000×1500 pixels, and each the pixel size is 3.45 μm squared. Table 1 is the spatial resolution of lenses with different magnifications and NA values. 
     The 60× oil immersion lens with NA 1.5 has a spatial resolution of 0.24 μm, i.e. the minimum pitch of sequencing sites is 0.24 μm. The 60× objective lens with 1× projection lens will magnify the 0.24 μm pitch to 14.4 μm pitch on sensor plane. The maximum total number of sequencing sites can be imaged is (3.45×2000)/14.4×(3.45×1500)/14.4=479×359=171,961 (sequencing sites). 
     
       
         
           
               
               
               
               
               
             
               
                 TABLE 1 
               
               
                   
               
               
                 Lens 
                 100X oil 
                 60X oil 
                 40X oil 
                 20X air 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 Magnification 
                 100 
                 60 
                 40 
                 20 
               
               
                 NA 
                 1.5 
                 1.5 
                 1.3 
                 0.7 
               
               
                 FOV (D, μm) 
                 220 
                 366 
                 550 
                 1100 
               
               
                 SR (μm) 
                 0.24 
                 0.24 
                 0.28 
                 0.5 
               
               
                 Number of Sites1 
                 61,705 
                 171,961 
                 284,592 
                 356,730 
               
               
                 Number of Sites2 
                 61,705 
                 136,354 
                 100,178 
                 31,416 
               
               
                 Number of Pixel per Site 
                 48 
                 17 
                 11 
                 8.4 
               
               
                   
               
            
           
         
       
     
     In Table 1, the row titled “Number of Sites  1 ” is the results that optical spatial resolution of the lens module is the only major factor taken into consideration. 
     The continuous single-molecule sequencing requires a certain substrate concentration level to maintain polymerase incorporation in a reasonable speed. As shown in  FIG. 7 , even though some labeled triphosphate nucleotide  21  are not incorporated as the molecule being sequenced  20 , the fluorophore or fluorescent dye attached on those triphosphate nucleotides may emit unwanted fluorescent light that have the same wavelength once they are excited. That is, all of the fluorescent dyes entering observation space, i.e., the sequencing nanowell, may generate fluorescent light and thus become unwanted “fluorescent background”. The details of the nanowell will be described later. A resolvable detected incorporation event should have a high ratio of “(incorporating signal+fluorescent background)/(fluorescent background)”, where, the fluorescent background can be estimated from substrate concentration, excitation field distribution and observation volume of corresponded pixel. 
     A meaningful observation volume for this situation is the space that fluorescent light can go through lenses to reach the corresponded pixel. If epi-excitation is used as shown in  FIG. 8A , none of the lenses listed in above Table 1 is able to detect single-molecule events at 1 μm substrate level since quite a lot of background molecules would be excited and overwhelming the single-molecule signal. To overcome this interference issue, the single-molecule sequencing system may deploy evanescent wave as shown in  FIG. 8B  to provide excitation energy to the sequencing sites  10  without increasing the background fluorescent signal. The evanescent wave may decay in an exponential manner and quickly fading away beyond 100 nm range. 
     The lens-based total internal reflection (TIRF) as shown in  FIG. 9A  or the prism-based TIRF as shown in  FIG. 9B  can confine the effective excitation energy within 100 nm range from the reflective surface. Due to the limitation of laser power, the lens-based TIRF or the prism-based TIRF can only excite a small area, for example, about 100 micro-meters in diameters. The row “Number of Sites  1 ” in Table 1 is only the effective FOV is considered. The row “Number of Sites  2 ” in Table 1 is the results of assuming an excitation area around 100 μm in dimension. It is shown in Table 1 that the available sequencing sites of a lens-based system based upon traditional design (i.e., by using 60× oil immersion lens) is around 150,000. The effective FOV can be increased by applying a large area sensor, but the system limitation will be the area of evanescent wave excitation field. In the present disclosure, the laser power is guided by a 250 nm waveguide core and within 100 nm evanescent wave range rather than 100 μm beam size hence resulting strong field intensity across the whole sequencing chip so that extending 2 mm area wide rather than 100 μm. Therefore, there are more sequencing sites  10  can be arranged in the excitation area. In some embodiments, there are more than 1 million sequencing sites  10  may be arranged and observed in a 2 mm×2 mm area. 
     Regarding to the sensitivity of sensor, due to the magnification nature of a microscope, a sequencing site emission may spread out onto several pixels  24 , such as the “big spot”  22  illustrated in  FIG. 10 . Accordingly, the signal intensity may be divided by these pixels which make the signal too weak to be detected by each of the pixels  24  of the CMOS image sensors. Even though some scientific grade CCD, ICCD, EMCCD, or special designed scientific grade CMOS sensor may be applied to detect weak signals, they are usually bulky and expensive components which may significantly increase the size, weight, and overall cost of the system. Ideally, while a sequencing site emission is projected onto just one or two or at most four pixels  24 , as the “small spots”  23  illustrated in  FIG. 10 , the signal is comparatively concentrated and may drastically increase the detected signal intensity. As a result, a reasonable priced modern CMOS sensor is sensitive enough to detect the signal. Nowadays a quality CMOS sensor is achieving 60% of peak quantum efficiency which is not far from scientific grade one at 90%. This disclosure may employ modern industrial or surveillance grade CMOS sensor and avoid using the luxury scientific grade sensors by arranging the sequencing chips and optical elements appropriately. Indeed, though the projected spot size can be as small as or smaller than the pixel  24 , the projection may overlap the boundary of pixels  24  and resulting two or the worst four adjacent pixels  24  sharing the same signal from a sequencing site. However, in the scenario that the signal divided by four, the signal strength scattered on each of the four pixels is still strong enough to be detected. 
     The present disclosure provides a design rule of lens-based continuous single-molecule sequencing apparatus. Based upon the disclosed design rule, a lens-based continuous single-molecule sequencing system can have more than 150,000, 300,000, 500,000 or 1,000,000 sequencing sites. According to Nyquist sampling theorem 1 sequencing well can be resolved by 2×2 pixels of the sensor. Hence a 5 million pixels sensor is able to resolve more than one million sequencing wells. 
     As shown in  FIG. 11 , in some embodiments, that includes a sequencing chip  31  and a detection module  32 . In some embodiments, the detection module  32  includes a sensor device  321 , an objective lens  322  having a first magnification, and a projective lens  323  having a second magnification. In some embodiments, the objective lens  322  and the projective lens  323  are configured to transmit the fluorescent light from the sequencing chip  31  to the sensor device  321 . In some embodiments, the second magnification is less than unity. In some embodiments, a laser source  33  may be coupled to the sequencing chip  31  via a laser coupler  34  and thus a laser light is guided to the sequencing sites  10  by a waveguide  35  of the sequencing chip  31 . Laser source  33  is as close as possible to the sequencing chip  31  to avoid unwanted scattering light to the enclosed space. The distance between them is smaller than 1 mm, is smaller than 0.5 mm or is smaller than 0.3 mm. In some embodiments, the sequencing signal is collected by the objective lens  322  and passed through a filter  36  to block the wavelength of the laser light before the sequencing signal is projected onto the sensor device  321  by the projection lens  322 . 
     In some embodiments, the first magnification of the objective lens  322  is configured to collect the fluorescent light. In some embodiments, the second magnification of the projective lens  323  is configured to project the fluorescent light from the objective lens to the sensor device. In some embodiments, the second magnification of the projective lens  323  is less than unity, less than 0.5× or less than 0.25×. 
     As shown in  FIG. 12 , in some embodiments, the sequencing chip  31  includes a substrate  310 , a thin-film or a channel waveguide  312  over the substrate  310 , a light coupler  311  formed at the waveguide  312 . In some embodiments, the waveguide  312  includes an upper cladding layer  313 , a lower cladding layer  314 , and a nanowell sequencing site array  315 . In some embodiments, the nanowell sequencing site array  315  includes a plurality of nanowells  316 . In some embodiments, a core layer  317  having a bottom surface and a top surface opposite to the bottom surface may be sandwiched by the upper cladding layer  313  and the lower cladding layer  314 . In some embodiments, the light coupler  311  is configured to couple an excitation light into the waveguide  312 , and the waveguide  312  may confine and guide the excitation light to the nanowell sequencing site array  315  and forming an evanescent wave excitation field as previously shown in  FIG. 8B  from a bottom of each of the nanowells  316 . That is, the light field intensity is stronger at the bottom and weaker away from the bottom in a manner of exponential decay as shown in  FIG. 8B . In a preferred scenario, the field intensity on a top of the upper cladding layer  313  is weak and neglectable or close to zero. So that the floated or non-incorporated fluorophore over an upper surface of the upper cladding layer  313  may not generate unwanted fluorescent background signal. In some embodiments, the nanowell sequencing site array  315  is fabricated in the upper cladding layer  313  with an upper opening  315 A and a cylindrical wall  315 B, and a bottom of the nanowell sequencing site array  315  is at or close to an upper surface of the core layer  317 . In some embodiments, the cylindrical wall  315 B is formed in the upper cladding layer  313  of the waveguide  312 . In some embodiments, the bottoms of each of the nanowells  316  may be coplanar to an upper surface of core layer  317  or has a thin-bottom layer (not shown in the figure) covering the upper surface of core layer  317 . The thin-bottom layer of the nanowells  316  may be made by a material identical to or different to that of the upper cladding layer  313 . 
     In some embodiments, the shapes of the nanowells  316  are in general circular as shown in  FIG. 13 . In some embodiments, the nanowells  316  may be formed as other shapes such as square, hexagonal etc., from a top view perspective. In some embodiments, the nanowell  316  maybe also laterally elongated to form a long trench rather than an ordinary well. For example, the sequencing site array may include numerous nanotrenches  318  arranged in parallel as shown in  FIG. 14  and  FIG. 15 . 
       FIG. 16  illustrates a schematic top view of general circular type nanowells according to some embodiments of the present disclosure. As shown in the figure, a beam adjusting mechanism  41  of the sequencing chip may be located between a spot type light coupler  311  and a first side of a nanowell sequencing site array  315  to adjust a total projection area of each of the beams from the light couplers  311  when propagating toward the sequencing site  10 . For example, the beam adjusting mechanisms  41  may transform a narrower beam (e.g., the injected laser light) from the light coupler  311  to a wider beam entering the sequencing sites therein, while a bar type light coupler  311  is located in proximity to a second side of the sequencing site array  315 . In some embodiments, the second side is opposite to the first side and thus the sequencing site array  315  is substantially between different types of the light couplers  311 . 
       FIG. 17  illustrates a schematic top view of trench type nanowells according to some embodiments of the present disclosure. As shown in the figure, a beam adjusting mechanism  41  may be located between a spot type light coupler  311  and a sidewall of a nanotrench  318 , while a bar type light coupler  311  is located in proximity to a sidewall of another nanotrench  318 . In some embodiments, numerous nanotrenches  318  are arranged in parallel and they are parallel to the bar type light coupler  311  as well. 
       FIG. 18  illustrates a schematic top view of trench type nanowells according to some embodiments of the present disclosure. Similar with the embodiment shown in  FIG. 17 , a beam adjusting mechanism  41  may be located between a spot type light coupler  311  and numerous nanotrenches  318 , while the nanotrenches  318  are arranged in parallel but perpendicular to a bar type light coupler  311 . The spot type light coupler  311  and the beam adjusting mechanism  41  are located at a first side of the array of the nanotrenches  318  while the bar type light coupler  311  is located at a second side of the array of the nanotrenches  318  opposite to the first side. In such embodiments, the beam adjusting mechanism  41  is in proximity to each end of the nanotrenches  318 . 
     Referring to  FIG. 19A , in some embodiments, there are more than one beam adjusting mechanism  41  may be employed. For example, the beam adjusting mechanisms  41  may be located between each of the light couplers  311  and the nanowell sequencing site array  315  to adjust a total projection area of each of the beams from the light couplers  311  when propagating toward the sequencing site  10 . For example, the beam adjusting mechanisms  41  may transform narrower beams (e.g., the injected laser lights) from the light couplers  311  to wider beams entering the sequencing sites  10 . In some embodiments, the light coupler  311  includes a nano size grating structure. In some embodiments, the light coupler  311  is a bar type. In some embodiments, the light coupler  311  is a spot type. In some embodiments, the waveguide  312  is a thin-film type. In some embodiments, the waveguide  312  is a channel type. In some embodiments, the sequencing sites  10  forms the sequencing site array  315 , and the wider beam has a beam width substantially covering the sequencing site array  315 . In some embodiments, the beam adjusting mechanism  41  includes a nanostructure beam expander between the light coupler  311  and the sequencing sites  10 . In some embodiments, the nanostructure beam expander is at least a portion of the waveguide  312  and thus being a thin film waveguide or a channel waveguide. In some embodiments, the sequencing site array  315  includes 2000×2000 pixels, while the light coupler  311  with a diameter of about 50 μm. In some embodiments, the sequencing chip includes a pair of holes  42  for the input and output of the fluid that conveying samples. 
     In other embodiments, the beam adjusting mechanism may include a plurality of beam splitters to multiply the number of beam coming out from the light coupler  311  so as to allow the multiplied number of beams simultaneously propagate toward the sequencing site  10 . The multiplied number of beams may provide a greater coverage to the plurality of sequencing sites than a single beam does. 
     As shown in  FIG. 19B , in some embodiments, a spacer  43  may be disposed over the sequencing chip. The spacer  43  may include a plurality of first openings  44  aligning to the light couplers  311  previously shown in  FIG. 19A  for the pass of the laser light. The spacer  43  may include a fluidic channel  45  at a center thereof and over the sequencing site array  315  previously shown in  FIG. 19A  for storing the fluid that including samples. In some embodiments, the diameter of the opening  44  is larger than that of the light coupler  311 . As shown in  FIG. 19C , in some embodiments, a cover  46  may be disposed over the spacer  43 . The cover  46  may include a plurality of second openings  47  aligning to the first openings  44  of the spacer  43 . In some embodiments, the spacer  43  is sandwiched by the cover  46  and the sequencing chip. 
     In some embodiments, the polymerase replication complex can be affixed at the bottom of the nanowell  316  by linker sites as previously shown in  FIG. 7 . In some embodiments, the polymerase replication complex may be affixed to the linkers by biotin-streptavidin like conjugation or covalent bonding, or by charged attraction or physically confinement. 
     In the case of the sequencing site array includes numerous nanotrenches  318  arranged in parallel, the linker sites in different nanotrenches  318  may be disposed with substantially identical intervals there between. In some embodiments, the interval is determined based on the consideration that such arrangement may prevent the fluorescent lights generated from each of the linker sites interfere to one another, and thus a preferred optical spatial resolution may be ensured. 
     In some embodiments, an interval between adjacent nanowells  316  is in a range of from smaller than 1 μm to about 5 μm. In some embodiments, an interval between the linker sites is about 3 μm. Although not being illustrated in the present disclosure, in some embodiments, there is no nanowell formed on the sequencing chip  31 . In such embodiments, the plurality of linker sites are distributed with suitable intervals on a flat surface of the sequencing chip  31 . 
     In some embodiments, as previously shown in  FIG. 7 , each of the nanowells  316  may have a width (along Y-axis) in a range of from about 50 nm to about 650 nm. Each of the nanowells may have a height (along Z-axis) in a range of from about 20 nm to about 600 nm. In some embodiments, the pitch (along Y-axis) between two adjacent nanowells is in a range of from smaller than 1 μm to about 5 μm. Under the circumstances that the width of the nanowell  316  is smaller than about 50 nm or the height of the nanowell  316  is larger than about 600 nm, the sample may be difficult to load into the nanowell  316  and reach the bottom thereof due to capillary force. On the other hand, under the circumstances that the width of the nanowell  316  is larger than about 650 nm, the nanowell  316  may have insufficient spatial confinement to the sample. In one embodiment, the pitch of the two adjacent nanowells  316  is smaller than about 1 μm. Under some circumstances that the pitch of the two adjacent nanowells is larger than about 5 μm, the density of the nanowells  316  is too small to maintain the detection throughput. In some embodiments, the nanowells  316  may have a width of about 80 nm and a height of about 100 nm, and the pitch between two adjacent nanowells  316  is about 1.3 μm. 
     In some embodiments, in order to improve the stability of the sequencing complex (e.g., polymerase replication complex) in the nanowells  316  of the sequencing chip  31 , a bottom surface or a sidewall of the nanowells  316  are chemically modified to improve the adhesion to the sequencing complex at the linker sites. For example, a hydrophilic treatment may be performed at the bottom surfaces and/or the sidewalls of the nanowells  316 . Optionally, a hydrophobic treatment may be performed at the top surface of a cover layer (e.g., the upper cladding layer  313 ) defining the nanowells  316 , thereby to avoid non-corporation fluorophore labels and hence reducing the unwanted background fluorescent signal. Furthermore, the hydrophobic treatment may prevent the fluids including the non-incorporated fluorophore labels flowing through the non-reaction area and hence reducing the unwanted background fluorescent signal. 
     In some embodiments, the substrate  310  as shown in  FIG. 12  can be opaque silicon wafer, transparent glass, quartz, fused silica, sapphire, etc. 
     In some embodiments, the space of the nanowells  316  may be defined by patterning the upper cladding layer  313 . In other words, two adjacent nanowells on the sequencing chip  31  are separated by the patterned upper cladding layer  313 . The upper cladding layer  313  is configured to reduce the background signal such as the scatter light comes from no-formation space (i.e., the space between adjacent linker sites). In some embodiments, the upper cladding layer  313  can be transparent but physically prevent the fluorescent dye-labeled substrates reaching excitation field other than the sequencing site  10  (i.e., the linker site). The patterned cover layer can be non-transparent that partially or totally blocking the light comes from no-information space. In some embodiments, the upper cladding layer  313  is a metal sheet. In some embodiments, the upper cladding layer  313  is a chemically modified surface which reduces the chance of fluorescent dye-labeled substrate coming closer to the excitation field. In some embodiments, the upper cladding layer  313  can be a plastic film. In some embodiments, the upper cladding layer  313  can be SiO 2  or other inorganic oxide that having low refractive index comparing to the core layer  317 . 
       FIG. 20  illustrates the pitch of the nanowell  316  and the pitch of the pixels on the sensor device  321 . In some embodiments, the pitch of sequencing sites (S) may be designed as: 
       2 P&gt;=S×F&gt;= 1 P    
     That is, a product of the pitch and the overall magnification is equal to or greater than one pitch and equal to or smaller than 2 pitches, wherein (F) is the overall magnification of the detection module  32 ′. (P) is the pitch of pixels of the sensor device  321  that equal to the pixel size. In some embodiments, the pixel size is smaller than or equal to about 10 μm, about 5 μm, or about 3 μm. In some embodiments, the pitch of two adjacent sequencing sites is smaller than or equal to about 5 μm, about 3 μm, or about 1 μm. 
     In some embodiments, the fluorescent signal from a sequencing site may firstly be collected by the objective lens  323  and then be projected onto the sensor device  321  in a size of less than 1.5 or one time of pixel size P. The fluorescent signal may be well concentrated onto one or at most four pixels while overlapping the boundaries and thus resulting a well-detected signal strength as the “small spots”  23  previously shown in  FIG. 10 . 
     One embodiment of the apparatus following the design rule as aforementioned includes a sensor device  321  having 2000×1500 pixels, and each of the pixels has a pixel size and pitch of 3.45 μm, an objective lens  322  with NA 0.7 and 20× magnification, a projection lens  323  of 0.25× magnification, and a sequencing chip  31  with nanowell sequencing sites pitch 1.38 μm, 
       wherein  X 1* X 2=5 
       (2×3.45 μm)/5=1.38 μm.
 
     That is, the pitch of sequencing site is 1.38 μm, which is conformed to the design rule as aforementioned. In some embodiments, the number of effective sequencing sites is 750,000. 
     One embodiment of the apparatus follow the design rule as aforementioned includes a sensor device  321  having 2000×1500 pixels, and each of the pixels has a pixel size and pitch of 3.45 μm, an objective lens  322  with NA 0.7 and 20× magnification, a projection lens  323  of 0.25× magnification, and a sequencing chip  31  with nanowell sequencing sites pitch 1.04 μm, 
       wherein  X 1* X 2=5 
       (2×3.45 μm)/5=1.38 μm
 
       (1×3.45 μm)/5=0.69 μm
 
     That is, the pitch of sequencing sites is 1.04 μm while 1.04 μm&gt;0.69 μm and &lt;1.38 μm, which is conformed to the design rule as aforementioned. In some embodiments, the number of effective sequencing sites is 1,333,333. 
     One embodiment of the apparatus follow the design rule as aforementioned includes a sensor device  321  having 2000×1500 pixels, aid each of the pixels has a pixel size and pitch of 3.45 μm, an objective lens  322  with NA 0.7 and 20× magnification, and a projection lens  323  of 0.25× magnification, and a sequencing chip  31  with nanowell sequencing sites pitch 0.7 μm, 
       wherein  X 1× X 2=5
 
       (1×3.45 μm)/5=0.69 μm
 
     That is, the pitch of sequencing sites 0.7 μm while 0.7 μm&gt;0.69 μm, which is conformed to design rule as aforementioned. In some embodiments, the number of effective sequencing sites is 3,000,000. 
     The present apparatus and system are able to detect single-molecule nucleic acids with higher performance, i.e. higher sequencing sites number by using lens-based optical module. Furthermore, the cost of the detection is also reduced by utilizing a simplified and replaceable sequencing chip. The sequencing signal from a site is projected onto less than 1.5 pixels or even less than 1 pixel in size on the sensor device to concentrate the signal intensity thereon and drastically improves the detection signal strength. As a result, bulky high sensitivity and expensive scientific grade CCD or CMOS sensor is not necessary and thus the cost of detection module may be reduced. 
       FIG. 21  illustrates the spectral bands of the labeled fluorophores. In some embodiments, each of the nucleotide sequences of a sequencing four d-NTPs ATCG are labeled with different fluorophores (fluorescent dyes) that may emit distinct wavelengths. As shown in the figure, there are three channels of spectral range may be used to resolve these different fluorophores by calculating the weightings of different channels and can be analyzed and translated into sequencing data. For example, when lasers are utilized as the excitation energy and thus are coupled into the waveguide and are guided to the sequencing sites, dye  1 , which is located at a specific sequencing site in the array, will be evanescently excited and the light emitted thereby can be collected by channel  1  and channel  2 . Based on the emission spectra information, for example, only channel  1  will show pixel signal values above a threshold, therefore weightings (1, 0, 0) is equivalent to the specific incorporated nucleotide labeled with dye  1  at that reaction site. However, if the dye is changed to dye  2 , the result will show weightings (1, 1, 0) which means channel  1  and  2  shows pixel value above a threshold, therefore weightings (1, 1, 0) is equivalent to the specific incorporated nucleotide labeled with dye  2 . Dye  3  will be evanescently excited by lasers as well and the result will show weightings (0, 1, 1). However, if the dye is changed to dye  4 , the result of weightings (0, 0, 1) will appeals. Note these weightings (1, 0, 0), (1, 1, 0), (0, 1, 1) and (0, 0, 1) are for illustrating purpose rather than exact number of the measurements. 
     In one embodiment, the trichroic prisms are designed such that channel  1  will receives wavelengths ranging from 530 nm to 610 nm, channel  2  will receive wavelengths ranging from 610 nm to 675 nm, and channel  3  will receive wavelengths ranging from 675 nm to 800 nm, for example. The collected light intensity and therefore signal values of each pixel of these three optical sensors can be adjusted by changing the type of dyes or modify the spectral range of each channel on the trichroic beam splitter prism. 
       FIG. 22  illustrates a Philips type prism according to some embodiments of the present disclosure. In some embodiments, a wavelength splitter is used to direct the fluorescent light with different wavelength spectral ranges to the at least two sensor devices. In some embodiments, a Philips type prism  50  is employed to separate the sequencing signals into three channels. The sensor devices  321  are glued (glue is not shown in the figure) firmly onto the prism and hence have a profound mechanical stability of the working environment. By glued the components into one piece, therefore, the device is more tolerable to vibration and by which the pixel correlation in three sensors are fixed. Philips prism  50  is commercially available and practical but other types of color separators are also viable such as a cross dichroic prism or more conventionally, the cube dichroic beam splitters. In contrast to Byer filters that employed in common color sensors, Philips prism  50  may separate colors rather than filter and hence it may absorb unwanted colors and provide much higher overall transmission efficiency. Virtually, no photon is wasted by using prism trichroic beam splitters. 
       FIG. 23  illustrates a dispersive device for spectral detection according to some embodiments of the present disclosure. In some embodiments, instead of using multi-channel sensor devices, a dispersive device  51  such as a wedge prism or an optical grating can be deployed to spread out different spectral range into different pixels in an array. For example, to spread out different spectral range into 4, 5, or 6 pixels in an array. 
       FIG. 24  is a SEM cross sectional image of the sequencing chip with a nanowell  316  according to some embodiments of the present disclosure. The nanowell  316  is built in the cladding layer  313  and nanowell bottom is close to the upper surface of the core layer  317 . 
       FIG. 25A  and  FIG. 25B  illustrate snap shots of frames of sequencing raw data according to some embodiments of the present disclosure.  FIG. 25A  is part of a snap shot of one frame from the dye-touched down data. One can see the fluorophores signals catches by the sensor device. As this optical arrangement, the signals are at most overlapping four adjacent pixels and solid signal strength may be ensured.  FIG. 25B  illustrates one typical pixel. One can see that most of the light is projected on one pixel and only a little portion spreads onto the adjacent pixel. Overall, the sequencing site signals are quite concentrated. 
       FIG. 26  illustrates a sequencing time trace from one nanowell of one channel. One can see the rise and fall of the fluorescent signal are accompanied with the happening of the dye touched-down events. By the arrangement of the optical components provided in the present disclosure, the signal to noise ratio (SNR) is quite good (e.g., signal/noise=54976/2441=22.52) and is commercially available through using reasonable priced industrial CMOS cameras. 
     The foregoing outlines features of several embodiments so that those skilled in the art may better understand various aspects of the present disclosure. Those skilled in the art should appreciate that they may readily use the present disclosure as a basis for designing or modifying other processes and structures for carrying out the same purposes and/or achieving the same advantages of the embodiments introduced herein. Those skilled in the art should also realize that such equivalent embodiments still fall within the spirit and scope of the present disclosure, and they may make various changes, substitutions, and alterations thereto without departing from the spirit and scope of the present disclosure.