Patent Grant
9719935
The present invention relates to nucleic acid sequences, and more specifically, to optical detection of specific nucleic acid sequences.
A nucleic acid sequence is a succession of letters that indicate the order of nucleotides within a deoxyribonucleic acid (DNA) (using G, A, C, and T) or ribonucleic (RNA) (G, A, C and U) molecule. By convention, sequences are usually presented from the 5′ end to the 3′ end.
Deoxyribonucleic acid (DNA) is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms andviruses. Ribonucleic acid (RNA) is a polymeric molecule. It is implicated in various biological roles in coding, decoding, regulation, and expression of genes.
According to one embodiment, a method is provided to determine a presence of a known nucleic acid sequence of a known molecule in a sample in which the sample contains a targeted nucleic acid sequence. The method includes coating a sample surface with a select segment of the known molecule, where the sample surface is configured to hold a liquid medium, and coating a plurality of beads with a first molecule. The method includes attaching the targeted nucleic acid sequence to a second molecule that is configured to bind to the first molecule, such that the targeted nucleic acid sequence is attached to the plurality of beads via the first and second molecules, and placing the sample on the sample surface. The sample includes the liquid medium, the plurality of beads, and the targeted nucleic acid sequence being tested for having the known nucleic acid sequence of the known molecule. The targeted nucleic acid sequence is unknown. Also, the method includes video monitoring a Brownian motion of the plurality of beads with an optical device, and determining whether the Brownian motion of the plurality of beads in the liquid medium is restricted or not restricted over time. In response to determining that the Brownian motion of the plurality of beads is restricted, the presence of the known nucleic acid sequence is recognized to be in the sample, thus indicating that the targeted nucleic acid sequence is the known nucleic acid sequence. In response to determining that the Brownian motion is not restricted, it is recognized that the known nucleic acid sequence is not present in the sample, thus indicating that the targeted nucleic acid sequence is not the known nucleic acid sequence.
According to one embodiment, a system is provided to determine a presence of a known nucleic acid sequence of a known molecule in a sample in which the sample contains a targeted nucleic acid sequence. The system includes a sample surface configured to receive the sample, and the sample surface is coated with a select segment of the known molecule. The sample includes a plurality of beads coated with a first molecule, and the targeted nucleic acid sequence attached to a second molecule that is configured to bind to the first molecule, such that the targeted nucleic acid sequence is attached to the plurality of beads via the first and second molecules. The targeted nucleic acid sequence is being tested for having the known nucleic acid sequence of the known molecule, and the targeted nucleic acid sequence is unknown. The sample also includes a liquid medium. Also, the system includes an electronic communication device configured to video monitor a Brownian motion of the plurality of beads, and determine whether the Brownian motion of the plurality of beads in the liquid medium is restricted or not restricted over time. The electronic communication device is configured to in response to determining that the Brownian motion of the plurality of beads is restricted, recognize the presence of the known nucleic acid sequence in the sample, thus indicating that the targeted nucleic acid sequence is the known nucleic acid sequence. Also, the electronic communication device is configured to in response to determining that the Brownian motion is not restricted, recognize that the known nucleic acid sequence is not present in the sample, thus indicating that the targeted nucleic acid sequence is not the known nucleic acid sequence.
According to one embodiment, an electronic communication device is provided to determine a presence of a known nucleic acid sequence of a known molecule in a sample in which the sample contains a targeted nucleic acid sequence. The electronic communication device includes a processing circuit and a non-transitory storage medium readable by the processing circuit and storing instructions that, when executed by the processing circuit, cause the processing circuit to perform operations. The processing circuit performs operations of video monitoring of a Brownian motion of a plurality of beads attached to the targeted nucleic acid sequence, and determining whether the Brownian motion of the plurality of beads in a liquid medium is restricted or not restricted over time. The processing circuit performs operations of in response to determining that the Brownian motion of the plurality of beads is restricted, recognizing the presence of the known nucleic acid sequence in the sample, thus indicating that the targeted nucleic acid sequence is the known nucleic acid sequence. The processing circuit performs operations of in response to determining that the Brownian motion is not restricted, recognizing that the known nucleic acid sequence is not present in the sample, thus indicating that the targeted nucleic acid sequence is not the known nucleic acid sequence.
Additional features and advantages are realized through the techniques of the present invention. Other embodiments and aspects of the invention are described in detail herein and are considered a part of the claimed invention. For a better understanding of the invention with the advantages and the features, refer to the description and to the drawings.
The subject matter which is regarded as the invention is particularly pointed out and distinctly claimed in the claims at the conclusion of the specification. The forgoing and other features, and advantages of the invention are apparent from the following detailed description taken in conjunction with the accompanying drawings in which:
Embodiments provide techniques to detect the presence or absence of a specific nucleic acid sequence, such as DNA and RNA, in a targeted/unknown molecule being tested.
There are times when one needs to know whether a sample, which may be any item or substance being tested, contains a known nucleic acid sequence. For example, Europe and now the U.S. have begun requiring labelling of genetically modified (GM) food. One may not know whether a shipment of corn was actually from non-GM plants or GM plants. In another scenario, individuals with Celiac disease become sick if they eat gluten. How would a person know if this ‘gluten-free’ product really contains gluten? It is possible that products can be fraudulent or health hazards but individuals may not know.
Embodiments provide techniques to detect the presence or absence of a specific nucleic acid sequence, such as DNA and RNA, in a sample being tested. Accordingly, embodiments can identify the presence of pathogens, viruses, organisms, particular DNA and RNA molecules, etc., using optical detection on a device, such as, e.g., a cellular phone (also referred to as mobile phones, smart phones, mobile devices, etc.).
Embodiments are based on detecting the restricted Brownian motion of microparticles which can be applied to detect the genetic material (DNA/RNA) of flu and other viruses, bacteria, and other organisms. Because embodiments are based on the complementary metal—oxide—semiconductor (CMOS) sensor in a mobile phone (or other device), some embodiments can be fabricated on a silicon chip with integrated optical components to make low-cost, compact, and portable biosensing chips. Due to their portability and compactness, these biosensing chips can have wide applicability in the developing countries where quick and fast diagnosis can be made with these devices while using limited resources.
The current mobile phone user market is huge and the number of mobile phone users has reached 5 billion in 2010. The majority of these users are in the developing countries. Moreover, it is estimated that there will be 8 billion smart phone users with connected health and wellness service by 2018. This scenario offers a tremendous opportunity for developing smart-phone based biosensors delivering health care related information, for example, identifying if a person has the flu or not, performing a cholesterol test, and so on. Smart phones are built with a good complementary metal—oxide—semiconductor (CMOS) sensors having high image capturing and processing capabilities, for example iPhone® 5, 5C, and 6, and this offers a great opportunity for use in embodiments discussed herein. There is a growing need for quick and easy diagnosis of flu-like symptoms with point-of-care diagnostic kits at one's home, away from the doctor's office, or at an epidemic center. This is also highlighted by the recent epidemic associated with the Ebola virus. There have been recent advances made by researchers in developing mobile-phone based sensing devices, for example, for flow cytometry analysis and polymerase chain reaction (PCR) based DNA detection. However, embodiments apply techniques using the Brownian motion of microparticles to detect the presence of DNA or RNA molecules specific to a known DNA sequence such as, for example, the flu type virus.
For ease of understanding, sub-headings are utilized. It is understood that the sub-headings are meant for explanation purposes and not limitation.
Brownian Motion
Colloidal or polymer particles of micron size undergo random motion in a liquid (also referred to as a medium or solution), and this random motion is characteristic of the Brownian motion. Brownian motion can also be observed in air, for example, by watching small pollen grains or dust particles suspended in air shined by a beam of sun light. In both cases, the origin of their random motion can be explained by the random motion of the underlying much smaller molecules that make up either the air or liquid. As these small molecules constantly collide with the bigger particles embedded in them, at any moment there is imbalance in the net force impacted by these small molecules on the bigger particles. This imbalance in the net force results in the movement of the bigger particles and results in the net force being random in direction and magnitude. Therefore, the imbalance in the net force causes random movement of the bigger particles. It follows that in order for this random motion to be detectable macroscopically, for example, either with naked eye or with a simple optical microscope, the size of the bigger particles cannot be too big compared to the size of the small molecules. The Brownian motion of particles in three dimensions is well described by a simple equation for mean-square displacement (MSD):
δx2=6Dt
where t is time. The MSD used in Statistical mechanical description of particle motion is defined as:x(t)−x(0)
2
where x(t) represents the position of the particle at time t, x(0) initial position and the angled brackets represent time average. Supposing one knows the positions of a particle over a time duration at an interval δt, then MSD can be calculated from the equation:
δx2=[(x(t1)−x(0))2+(x(t2)−x(0))2+(x(t3)−x(0))2+ . . . +(x(tn)−x(0))2]/n
Where n is the number of consecutive positions of the particle.
The only constant in this equation that characterizes the particle is the diffusion constant, D. The diffusion constant D can be calculated from Einstein's relation
D=μkBT
where kB is the Boltzmann constant,μ is the mobility of the diffusing particle, and T is the temperature of the medium (liquid) the particle is diffusing in.
For a spherical particle, the mobility can be calculated from Stokes law for the drag force on the particle and Einstein's relation simplifies to
where ‘r’ is the radius of the particle, η is the dynamic viscosity of the medium (liquid). In addition to the simple equation that can be used to calculate the diffusion co-efficient D of the particle, experimentally measured values are also widely available for polymer micro-beads and DNA molecules. So given the temperature T and the nature of the medium (e.g., the dynamic viscosity η) which the particle is present, the mean-square displacement (δx2) of the particle can be calculated and will be linear in time duration of the observation of the particle.
In the case of experiments tracking particle motion either by cellular-phone based microscopes or research microscopes with high numerical aperture, since the particle position is detected only in a two-dimensional plane, the equation for MSD corresponds to two-dimensional diffusion which is δx2=4Dt. Because of this difference in the coefficients, the diffusion constant for two-dimensional diffusion will be larger than for three-dimensional diffusion.
Detection Of Specific DNA/RNA Sequences
The mean-square displacement (δx2) of a free Brownian particle (such as the bead 30) keeps increasing linearly with time as was just discussed. However, if the particle is tethered at one end to the surface of the sample container, then the particle's motion will be restricted by the tether length according to embodiments, as shown in
In
The DNA molecule 210, having a sequence that needs to be detected, can be attached to the beads 30 at one end by using beads 30 coated with a first molecule 215 represented as diagonal lines. The molecule 215 is chosen to attach to the material of the beads 30. In one implementation to attach the first molecule 215 to the beads 30, the beads 30 may be polystyrene beads and the coated molecule 215 may be the protein (molecule) streptavidin. The protein streptavidin is coated on and binds to the beads 30.
In another implementation, the material of the beads 30 may be poly-methyl-methacrylate (PMMA) beads in the size range of 0.2 to 2.0 microns such as those available from any of these commercial vendors: Bangs Labs, Life Technologies and PolySciences and the first molecule 215 may be streptavidin protein molecules, such that the first molecule 215 binds to the beads 30.
In yet another implementation, the material of the beads 30 may be silica (SiO2) beads in the size range of 0.2 to 2.0 microns such as those available from any of these commercial vendors: Bangs Labs, Life Technologies and PolySciences and the first molecule 215 may be streptavidin protein molecules, such that the first molecule 215 binds to the beads 30.
In order to facilitate the DNA molecule 210 attaching to the bead 30 coated with molecule 215, the end of the DNA molecule 210 is attached with a second molecule 220 that is designed/chosen to attach to the first molecule 215 (e.g., streptavidin). The second molecule 220 has a dual purpose, which is 1) to bind to the unknown DNA molecule 210 and 2) to bind to the first molecule 215. Similarly, the first molecule 215 has a dual purpose, which is 1) to bind to the bead 30 and 2) to bind to the second molecule 220.
In one implementation, the second molecule 220 may be a biotin molecule that will bind to the streptavidin molecules 215 (i.e., first molecules 215) coated on the bead surface of bead 30. Accordingly, this (combination of the first molecule 215 and second molecule 220) forms DNA molecules 210 attached at one end to the bead surface 30.
In
As the DNA-attached bead 30 comes in contact with this short probe DNA molecule 205, the unknown DNA molecules 210 form the tether thereby restricting the Brownian motion of the DNA-attached bead 30. Therefore, the presence of a specific DNA sequence (in the unknown DNA molecule 210) of the DNA-attached bead 30 can be detected (indirectly).
The short probe DNA molecules 205 are known and may be the DNA molecules of the virus, pathogen, food product, etc., that is being tested for. Since the short probe DNA molecules 205 are the complementary sequence of what the unknown DNA molecule 210 should be, the short probe DNA molecules 205 are designed to bind to the expected (but unknown) sequence of the DNA molecule 210. When the DNA molecules 210 are the complementary sequence to the short probe DNA molecules 205, the two DNA molecules 205 and 210 bind to form a double strand DNA molecule. In a DNA double helix, each type of nucleobase on one strand binds with just one type of nucleobase on the other strand. This is called Watson-Crick or complementary base pairing. The short probe DNA molecules 205 are single strand DNA molecules, while the tested DNA molecules 210 are single strand DNA molecules. One skilled in the art understands how to prepare complementary DNA sequences, single strand DNA, and short DNA probes.
In one embodiment, single-stranded DNA molecules 210 made of the same type of bases (A, T, G or C) can be used for detecting their binding to the beads 30 and the resulting restricted Brownian motion. These homopolymer DNA molecules can be custom-made with a pre-attached Digoxigenin molecule at one end and the biotin molecule at the other end. Here is one example of such a DNA molecule: Digoxigenin-C6-amino-(TTTTTTTTTT)15-3′-biotin (SEQ ID NO. 1). These molecules consisting of 150 Thymine bases can be obtained from commercial vendors (Midland Certified Reagent Company Inc™, Midland, Texas and Integrated DNA Technologies, Inc™, Coralville, Iowa). These DNA molecules 210 can be attached to the beads 30 coated with streptavidin molecules through biotin molecules 220 in one end of them. The DNA-attached beads will be filled in the sample chamber to test their binding to the antibody molecules coated on the glass surface of the sample cell through the Digoxigenin molecules at the other end of the DNA molecules.
In another embodiment, long double-stranded DNA molecule from bacteriophage viruses can be used as DNA molecules 210. The linear lambda-DNA (SEQ ID NO. 2) extracted which has 48,502 bases can be used (available from New England Biolabs, Inc™, Ipswich, MA). It has two cohesive or sticky overhangs each 12 bases long at each end. Their sequences are: 5′-GGGC GGCG ACCT-3′ (SEQ ID NO. 3) and 5′-AGGT CGCC GCCC-3′. (SEQ ID NO. 4) The short DNA oligomers SEQ ID NO. 3-biotin and SEQ ID NO. 4-Digoxigenin (SEQ ID NO. 3) can be mixed with Lamda DNA one at a time so that one of these DNA oligomers will bind to their sticky ends (can be purchased from Integrated DNA Technologies, Inc™). After attaching one of them they will be ligated to chemically link to the long strands of Lamda DNA to which they attach by complementary pairing. After ligation, for example, the oligomer with the biotin on one end can be mixed with streptavidin coated beads in solution. The DNA attached beads can be isolated by sedimenting the beads by centrifugation and extracting the supernatant solution. These isolated DNA attached beads can be mixed with the Digoxigenin attached oligomers to bind to the other overhang in the Lamda DNA and ligated. At the end, one will have Lamda DNA with Digoxigenin ends that are free to bind to the antibody coated surface.
In yet another embodiment, a single-stranded DNA molecule M13mp18 (SEQ ID NO. 5) from a virus can be utilized as DNA molecules 210. This DNA has 7249 bases and its contour length is about 5 microns which is a sufficiently long tether for the bead. The DNA sequence CTC GCG CCC CAA (SEQ ID NO. 6) occurs near the 5′ end of this DNA molecule and has a melting temperature of 51.9 C. which is much higher than normal operating temperature. The DNA sequence ATG CTC TGA GGC TTT TA (SEQ ID NO. 7) occurs near the 3′ end and has a melting temperature of 47.3 C. much higher than normal operating temperature. Therefore these two sequences can be utilized to design short DNA oligomers attached with biotin and Digoxigenin molecules. The DNA oligomer, Biotin-3′-GAG CGC GGG GTT-5′ SEQ ID NO. 8 will form complementary base pairing with the sequence near the 5′ end, namely, CTC GCG CCC CAA (SEQ ID NO. 6). The biotin attached to the 3′ end will bind to the Streptavidin molecules coated on the beads 30 when mixed with them in solution. In order to break any unwanted hair pin formation in these DNA oligomers the mixture with the beads can be heated above their complementary base pair melting temperature and slowly cooled across their melting zone and then cooled rapidly to either room temperature or quenched in an ice-bath. The other short oligomer 3′-TAC GAG ACT CCG AAA AT-5′-Digoxigenin (SEQ ID NO. 9) can be mixed with the DNA attached beads and will bind to the antibody coated on the sample cell surface thereby forming DNA tethers for the beads 30. The dynamics of binding of either biotin to streptavidin beads or the Digoxigenin to antibody molecules coated on the sample cell surface can be made faster by using a homopolymer spacer between biotin or Digoxigenin and the short oligomer DNA sequence. The length of such homopolymers can be in the range of 20 to 200 bases long. By having the single-strand DNA being much more flexible than double-stranded DNA (persistence length for dsDNA is 50 nm and for ssDNA is ˜2 nm which is twenty five times shorter), these homopolymers will let the binding molecules Biotin or Digoxigenin to explore different configurations before they bind to their counterparts (Streptavidin or Antibody molecules as discussed before) accelerating their time for binding.
This limited/restricted Brownian motion of the tethered beads 30 can be optically recognized and traced via a cellular phone 401, a charge coupled device (CCD), and/or a microscope. When the limited/restricted Brownian motion of the tethered beads 30 is recognized, it is determined that the tested DNA molecule 210 is the same molecule as the short probe DNA molecule 205. The identification of the short probe DNA molecules 205 are known in advance.
For the sake of clarity and simplicity, the small molecules 40 of the liquid 20, the short probe DNA molecules 205, and the DNA molecules 210 are omitted in
In the case when the unknown DNA molecules 210 do not bind with the short probe DNA molecules 205, this means that the sequence of the unknown DNA molecule 210 is not the complementary sequence to the short probe DNA molecules 205. Therefore, the unknown DNA molecules 210 are not the same molecule as the known short probe DNA molecules 205, and the unknown DNA molecules 210 can be ruled out as being the same molecule as the known molecule (e.g., a particular virus).
In contrast, plot 309 illustrate that, when tethering is formed by the targeted nucleic acid sequence, the tethered beads' motion will be slowed down for smaller displacements resulting in smaller diffusion constant over a shorter time duration. The tethered beads may also exhibit non-linear behavior arising from the polymer elasticity of the tether. Plot 310 illustrates that, on a longer time duration as the beads try to move beyond the length of the tether, they become confined to a circle. This results in the flattening of their mean-squared displacement.
According to another embodiment,
According to another embodiment,
Optical Detection Of Bead Motion With A Cellular Phone
Many smart phones (and tablets) available today in the market like iPhones® (4S, 5, 5C and 6), Samsung® Galaxy, HTC™ and other Android™ phones have a good camera with video recording capabilities. However, their current minimum-focusable distance and the magnification achievable at that distance are not adequate to detect the presence of micron to submicron (10−6 to 10−5 meter) beads 30 in the solution. For iPhone® 5, the minimum-focusable distance is about 5 centimeters (cm) from the front of the camera, and the magnification achieved is about few times which directly impacts the resolution. Therefore, a special lens adapter is needed for current camera phones not having adequate magnification and resolution, and the special lens adapter (e.g., ball lens holder assembly 400 shown in
The special lens adapter has special characteristics like a short focal length and high numerical aperture that can result in magnification in the range of 100-200 times (100-200×) and a spatial resolution of 1 to 2 micrometers. Such characteristics can be achieved by a ball-lens based adapter (e.g., ball lens holder assembly 400 shown in FIGS. 4 and 5), and it can be attached to and/or placed in front of the camera of these cellular phones in a special holder (e.g., micropositioner 418 in
A cellular phone 401 includes a camera 450 with an electronic image sensor 402 (can also be other imaging sensors (including CCDs) with focusing optics). The electronic image sensing surface 402 is positioned behind a camera focusing lens assembly 403. The cellular phone 401 includes a processor, memory (including removable memory), camera computer-executable instructions stored in memory, video recording computer-executable instructions stored in memory, antenna, transceiver, power source (e.g., battery), user interface (touch screen, key pad, voice activation) etc., as understood by one skilled in the art.
The ball lens holder assembly 400 includes a resolution limiting aperture 404. An emission filter (not shown), that blocks the excitation light in the case of imaging fluorescent beads or fluorescent biomolecules like DNA and proteins, can be placed over resolution limiting aperture 404 in one implementation.
The ball lens holder assembly 400 includes the spherical ball lens 405 made from glass, e.g., with a diameter 3.0 millimeters (mm) positioned in a lens holder 430. In another implementation, other smaller or larger diameters such as, e.g., 2.5, 4.0, and 5.0 mm may also be used as the spherical ball lens 405 with the appropriate lens holder assembly. The lens holder 430 may have a tapered opening 406 to accept a light cone of large angle from the sample plane formed by the solution 20 of beads 30. Spacers 407 and 413 keep the required separation between the ball lens holder assembly 400 and the glass slide 10 that contains the bead solution 20. Double-sided tape or adhesive may act as spacers 408 and 411 for the sealed sample chamber 435. In another implementation, a sample cell may also consist of a glass or transparent polymer-based microfluidic cells. A glass cover slip 409 acts as the lid for the sample chamber 435. The sealed sample chamber 435 comprises the glass slide 10 and glass cover slip 409. The bead solution 20 (containing the beads 30) that is being imaged (via camera 450 of the cellular phone 401) is placed on the glass slide 10. The glass slide 10 forms the bottom surface of sample chamber 435 enabling different kinds of functionalization such as with antibody and protein coatings to bind to either the DNA molecule 210 or other small molecules 220 like biotin.
The ball lens holder assembly 400 works with light limiting apertures 414 and 416. An excitation filter (not shown) can be placed over the aperture 414 for imaging fluorescent beads and fluorescent DNA and RNA biomolecules. A mirror 415 is utilized for reflecting light towards the sample chamber 435 and the ball lens holder assembly 400.
A battery-operated LED flash lamp, with white light or colored light, may be utilized as a light source 417. As another option, the light source 417 may be a single LED suitably wired for electrical power. The light source 417 may be a small laser diode suitably powered. In the case of a single LED or laser diode, the light source 417 can be placed directly under the aperture 414 without the need for the mirror 415 and the light limiting aperture 416. The light source 417 may also be formed with a flat LED chip mounted on a suitable holder, wired for electrical power, and placed under the aperture 414. A micropositioner 418 holds the cellular phone 401 and can move in three orthogonal x, y, and z directions. The micropositioner 418 is used for positioning the cellular phone camera 450 directly over the lens holder assembly 400 centered at the resolution limiting aperture 414 and for adjusting the vertical distance from this aperture 414 to get a good focus of the beads in the solution.
In the experimental setups described in
Before detecting Brownian motion of the beads 30, experiments were carried out imaging beads that are stuck to a glass surface or frozen in a gel matrix coated on a glass slide in order to compare with the recordings of moving beads 30. Images recorded with 1.2 micron sized beads 30 are shown in a raw image 750 and processed image 755 in
For comparison, the bead positions detected with a MATLAB® function called imfindcircles function is shown in
It is noted that the displacement of a bead is the length/distance that a bead moves in a particular direction, along the x-axis or y-axis. Since the microscope images the motion in a plane which is two dimensional, in general, the bead displacement will be in an arbitrary direction in the plane. For simplification of the analysis, only x- or y-component of the bead motion was analyzed which corresponds to diffusion in one dimension. However, from the x- and y-positions of the beads obtained in the analysis their total displacement,={right arrow over (r2)}−{right arrow over (r1)}=({right arrow over (x2)}−{right arrow over (x1)})+({right arrow over (y2)}−{right arrow over (y1)})=δx.{circumflex over (x)}+δy.{circumflex over (y)}
Where {right arrow over (r2)} and {right arrow over (r1)} denote the 2D position vector of the bead displacements, {circumflex over (x)}, ŷ represent the unit vectors along x- and y-directions respectively. Therefore, square of radial displacement can be calculated as:2=δx2+δy2
and the mean-squared displacement δr2 can be calculated from the successive x- and y-positions of the beads and it obeys the following equation:
δr2=4Dt
On the other hand, the bead displacements between first and third frames spanning 0.5 pixels are still smaller than a single pixel as shown in
An example algorithm for detecting and tracking the movement (i.e., bead positions) of the individual beads 30 is provided below according to an embodiment. For a video clip/recording of the motion of the beads 30 (e.g., captured with the cellular phone 401), the example algorithm may be utilized to detect and track beads from one video frame to the next (consecutive video frame). The algorithm may be executed by and stored in memory of the cellular phone 401 and/or the cellular phone 401 may send the recorded video clip/recording to a computer system (such as the computer system 1200) for analysis; the computer system has memory to store the algorithm. The example algorithm is configured to identify each circular bead and store each bead's pixel location in a video frame, such that the algorithm identifies and stores each bead's pixel location throughout consecutive video frames. For example, the algorithm is configured to track and identify each bead's pixel location over video frames (e.g., over consecutive video frames). The algorithm is configured to measure the x-displacement and y-displacement of each bead 30 from one video frame to the next video frame, such that the algorithm stores the change in pixel location for each bead. The algorithm determines an x-displacement and y-displacement for each bead 30 in the x-axis and y-axis, over a predefined number of video frames (i.e., a particular time, such as, e.g., 1, 3, 5, 10, 15, 20, 25 . . . 60 seconds). For the particular sample having the unknown DNA molecule 210 being tested, the algorithm determines the total x-displacement for all of the individual beads 30 and the total y-displacement for all of the individual beads 30. The algorithm is configured to compare the total x-displacement and y-displacement for the beads 30 being tested with the unknown DNA molecule 210 attached (i.e., corresponding to the Brownian motion of the tested DNA molecule 210) to the previously stored total x-displacement and y-displacement for the same size beads without the unknown DNA molecules 210 attached (i.e., corresponding to free Brownian motion). When the total x-displacement and y-displacement for the beads 30 being tested with the unknown DNA molecule 210 attached (i.e., corresponding to the Brownian motion of the tested DNA molecule 210) is less than (by a predetermined amount) the previously stored total x-displacement and y-displacement for the same size beads without the unknown DNA molecules 210 attached (i.e., corresponding to free Brownian motion), the algorithm determines that the Brownian motion is restricted (i.e., the beads 30 are tethered to the sample surface 10 via the DNA molecule 210) and the unknown DNA molecule 210 contains the known specific nucleic acid sequence being tested for.
However, when the total x-displacement and y-displacement for the beads 30 being tested with the unknown DNA molecule 210 attached (i.e., corresponding to the Brownian motion of the tested DNA molecule 210) is about equal to (within a predetermined margin) the previously stored total x-displacement and y-displacement for the same size beads without the unknown DNA molecules 210 attached (i.e., corresponding to free Brownian motion), the algorithm determines that the Brownian motion is not restricted (i.e., the beads 30 are not tethered to the sample surface 10 via the DNA molecule 210) and the unknown DNA molecule 210 does not contain the known specific nucleic acid sequence being tested for.
Referring to
In
Analysis of the displacement of beads in two consecutive frames shows that the displacement less than 0.01 pixels dominates the distribution in
Now, turning to another experiment, dilute solutions of polystyrene beads of 1.2 micron size were used to record the motion of the beads. An image 905 of a frame from the video clip recording the bead motion is shown in
The band-pass filtered image and the identified bead positions in a single frame are shown in
At block 1002, the glass surface or polymer surface of sample cell 10 is coated with antibody molecules 202. After most of the antibody molecules 202 bind to the surface, the sample cell surface 10 may optionally be flushed with buffer solution to remove unbound antibody molecules 202 from the solution in sample cell 10.
At block 1005, the sample cell surface 10 is coated with short probe DNA oligomers 205 in which the short probe DNA oligomers 205 are attached with anti-digoxigenin molecules 203 on one end which will bind to the antibody molecules 202 coated on the sample cell interior surface 10.
At block 1010, the unknown DNA molecule 210 being tested is biotinylated on one end (with the second molecule 220) so that the biotinylated end of the DNA molecule 210 can then be attached to the micron size polymer beads 30 coated with the first molecule 215 (e.g., streptavidin protein molecules).
At block 1015, a small amount (e.g., 10-20 microliters (μL) in one implementation) of DNA-attached beads 30 is added to the sample cell surface 10 coated with the short probe DNA oligomers 205.
At block 1020, the Brownian motion of the DNA-attached beads 30 is video monitored with, e.g., a CCD camera, other detector, and/or the cellular phone 401 in the camera setup in
At block 1025, the cellular phone 401 and/or a computer system 1200 is configured to detect the bead positions and follow their track over time.
At block 1030, the cellular phone 401 and/or a computer system 1200 is configured to analyze the tracked bead positions (over a predetermined number of consecutive video frames) for restricted Brownian motion by comparing the tracked bead positions to free Brownian motion behavior (for the same type of beads 30 in the liquid 20 without the unknown DNA molecule 210 attached and/or for the same type of beads 30 in the liquid 20 without the short probe DNA oligomers 205 coated on the sample surface.
At block 1035, when the cellular phone 401 and/or a computer system 1200 recognizes that there is restricted Brownian motion for the tracked beads 30, the cellular phone 401 and/or a computer system 1200 determines that a specific known nucleic acid sequence is present in the unknown DNA molecule 210 being tested which directly corresponds to DNA tethering of the tracked beads 30.
At block 1040, when the cellular phone 401 and/or a computer system 1200 recognizes that there is no restricted Brownian motion for the tracked beads 30, the cellular phone 401 and/or a computer system 1200 determines the absence of a specific known nucleic acid sequence from the unknown DNA molecule 210 being tested because of no DNA tethering of the tracked beads 30.
In one implementation, in performing block 1030, the cellular phone 401 and/or a computer system 1200 is configured to calculate the diffusion coefficient of the bead motion for the tracked beads 30, and then compare the calculated diffusion coefficient (of the tracked beads 30 having the DNA molecule 210 attached) to that of the known diffusion coefficient (i.e., baseline) for free particle motion (of particles/beads having the same or similar size as the tracked beads 30) to determine if there is a statistically significant restricted Brownian for the tracked beads 30.
When there is no statistically significant restricted Brownian motion for the tracked beads 30 (as compared to the known diffusion coefficient for free particle motion), then the cellular phone 401 and/or a computer system 1200 is configured to determine that there is the absence of a specific nucleic acid sequence from the unknown DNA molecule 210 being tested because of no DNA tethering of the tracked beads 30.
However, when there is statistically significant restricted Brownian motion for the tracked beads 30 (as compared to the known diffusion coefficient for free particle motion), then the cellular phone 401 and/or a computer system 1200 is configured to determine that there is the specific nucleic acid sequence present in the unknown DNA molecule 210 being tested which directly corresponds to DNA tethering of the tracked beads 30.
Now turning to
At block 1102, the glass surface or polymer surface of sample cell 10 is coated with antibody molecules 202.
At block 1103, the sample cell surface 10 is coated with first short probe DNA oligomeric molecules 205 attached with anti-digoxigenin molecules 203 on one end which will bind to the antibody molecules 202 coated on sample cell interior surface 10.
At block 1104, a plurality of beads are coated with second short probe DNA oligomeric molecules 1405.
At block 1105, a plurality of beads 30 coated with second short probe DNA molecules 1405 are mixed with the targeted nucleic acid sequence molecule 210 (e.g., the DNA/RNA molecule of virus, bacteria, pathogen, plant, human, animal, etc.), and the sample surface 10 is configured to hold a liquid medium 20.
At block 1110, the sample is placed on the sample surface 10, and the sample comprises the liquid medium 20, the plurality of beads 30, and the targeted nucleic acid sequence molecule 210 being tested for having the known nucleic acid sequence of the known molecule, where the targeted nucleic acid sequence is unknown (at this point).
At block 1115, this mixture is left for sufficient time (e.g., which may be 30, 30, 90 minutes in one case) enable binding of the targeted nucleic acid sequence 210 to the first and second oligomeric DNA molecules 205 and 1405 attached to the sample surface 10 and plurality of beads 30 respectively and therefore forming tethers for the beads 30.
At block 1125, the cellular phone 401 (operating as an optical device, e.g., via a video/camera recorder) is configured to video monitor (i.e., video record) the Brownian motion of the plurality of beads 30.
At block 1130, the cellular phone 401 is configured to determine whether the Brownian motion of the plurality of beads 30 in the liquid medium 20 is restricted or not restricted over time.
At block 1135, in response to determining (e.g., via the cellular phone 401) that the Brownian motion of the plurality of beads 30 is restricted, the cellular phone 401 is configured to recognize the presence of the known nucleic acid sequence in the sample, thus indicating that the targeted nucleic acid sequence 210 is the known nucleic acid sequence.
At block 1140, in response to determining that the Brownian motion is not restricted, the cellular phone 401 is configured to recognize that the known nucleic acid sequence is not present in the sample, thus indicating that the targeted nucleic acid sequence 210 is not the known nucleic acid sequence.
Determining whether the Brownian motion of the plurality of beads 30 is restricted or not restricted over time (such as over consecutive video frames of the recorded video) includes: 1) detecting bead positions of the plurality of beads 30 in the liquid medium 20; 2) tracking the bead positions of the plurality of beads 30 over time to obtain bead motion for the plurality of beads 30; and 3) comparing the bead motion tracked for the plurality of beads to free Brownian motion.
Comparing the bead motion tracked for the plurality of beads to free Brownian motion includes determining that the sample contains the known nucleic acid sequence based on the bead motion of the plurality of beads being less than the free Brownian motion.
The bead motion of the plurality of beads being less than the free Brownian motion denotes that the targeted nucleic acid sequence in the sample has tethered the plurality of beads 30 to the sample surface 10. Tethering the plurality of beads 30 to the sample surface restricts the bead motion of the plurality of beads 30. Tethering the plurality of beads 30 to the sample surface 10 restricts the bead motion of the plurality of beads to a circular motion.
The targeted nucleic acid sequence in the sample has a first end and a second end. Tethering the plurality of beads to the sample surface 10 comprises the select segment 205 coated on the sample surface 10 attaching to the first end of the targeted nucleic acid sequence 210 and comprises the first molecule 215 coated on the plurality of beads 30 attaching to the second end of the targeted nucleic acid sequence.
Comparing the bead motion tracked for the plurality of beads 30 to free Brownian motion includes determining that the sample does not contain the known nucleic acid sequence based on the bead motion of the plurality of beads 30 corresponding to the free Brownian motion.
Comparing (by the cellular phone 401) the bead motion tracked for the plurality of beads to free Brownian motion includes: 1) determining a sample diffusion coefficient of the bead motion tracked for the plurality of beads when the sample of the targeted nucleic acid sequence is added to liquid medium; 2) determining a baseline diffusion coefficient for the plurality of beads when no targeted nucleic acid sequence is added to the liquid medium 20; 3) determining that the Brownian motion of the plurality of beads is restricted when the sample diffusion coefficient is less than the baseline diffusion coefficient; 4) determining that the Brownian motion of the plurality of beads is not restricted when the sample diffusion coefficient corresponds to the baseline diffusion coefficient.
In one implementation, the plurality of beads are in the size range of 0.2 to 3.0 microns. The optical device is an electronic communication device having a lens assembly adapter.
Embodiments discussed herein can be utilized in various applications. As suggested herein, there is a growing need for early and fast diagnosis of flu-like symptoms with point-of-care diagnostic kits either at one's home or away in a doctor's office such as at an epidemic center. This is also highlighted by the recent epidemic associated with Ebola virus in Africa. At one time, it was estimated that the currently infected people that need treatment are between 10,000 and 15,000 in the countries Guinea, Sierra Leone, and Liberia. It was predicted that this number would double every month which will result in nearly 50,000 infected people in one month and 100,000 people in two months (“Containing Ebola: What it would take”, Washington Post, Oct. 9, 2014. Embodiments based on the restricted Brownian motion of beads can be applied to develop a cell-phone based diagnostic kit for detecting flu virus, for example. The viral RNA/DNA can be extracted from the blood or saliva of the patient after doing the recommended preparation using commercially available RNA/DNA extraction kits. As discussed in embodiments, the extracted RNA/DNA is to detect the presence of specific RNA or DNA by the tethering the DNA/RNA forms with the specially prepared beads. It is estimated that the diagnosis can probably be done in one to two hours, and the system 480, 580 is completely portable and usable with the cellular phone.
Various methods, procedures, modules, flow diagrams, tools, applications, circuits, elements, and techniques discussed herein may also incorporate and/or utilize the capabilities of the computer 1200. Moreover, capabilities of the computer 1200 may be utilized to implement features of exemplary embodiments discussed herein. One or more of the capabilities of the computer 1200 may be utilized to implement, incorporate, to connect to, and/or to support any element discussed herein (as understood by one skilled in the art).
Generally, in terms of hardware architecture, the computer 1200 may include one or more processors 1210, computer readable storage memory 1220, and one or more input and/or output (I/O) devices 1270 that are communicatively coupled via a local interface (not shown). The local interface can be, for example but not limited to, one or more buses or other wired or wireless connections, as is known in the art. The local interface may have additional elements, such as controllers, buffers (caches), drivers, repeaters, and receivers, to enable communications. Further, the local interface may include address, control, and/or data connections to enable appropriate communications among the aforementioned components.
The processor 1210 is a hardware device for executing software that can be stored in the memory 1220. The processor 1210 can be virtually any custom made or commercially available processor, a central processing unit (CPU), a data signal processor (DSP), or an auxiliary processor among several processors associated with the computer 1200, and the processor 1210 may be a semiconductor based microprocessor (in the form of a microchip) or a microprocessor. Note that the memory 1220 can have a distributed architecture, where various components are situated remote from one another, but can be accessed by the processor 1210.
The software in the computer readable memory 1220 may include one or more separate programs, each of which comprises an ordered listing of executable instructions for implementing logical functions. The software in the memory 1220 includes a suitable operating system (O/S) 1250, source code 1230, and one or more applications 1260 of the exemplary embodiments. As illustrated, the application 1260 comprises numerous functional components for implementing the features, processes, methods, functions, and operations of the exemplary embodiments. The application 1260 of the computer 1200 may represent numerous applications, agents, software components, modules, interfaces, controllers, etc., as discussed herein but the application 1260 is not meant to be a limitation.
The operating system 1250 may control the execution of other computer programs, and provides scheduling, input-output control, file and data management, memory management, and communication control and related services.
The application 1260 may be a source program, executable program (object code), script, or any other entity comprising a set of instructions to be performed. When a source program, then the program is usually translated via a compiler, assembler, interpreter, or the like, which may or may not be included within the memory 1220, so as to operate properly in connection with the O/S 1250. Furthermore, the application 1260 can be written as (a) an object oriented programming language, which has classes of data and methods, or (b) a procedure programming language, which has routines, subroutines, and/or functions.
The I/O devices 1270 may include input devices (or peripherals) such as, for example but not limited to, a mouse, keyboard, scanner, microphone, camera, etc. Furthermore, the I/O devices 1270 may also include output devices (or peripherals), for example but not limited to, a printer, display, etc. Finally, the I/O devices 1270 may further include devices that communicate both inputs and outputs, for instance but not limited to, a NIC or modulator/demodulator (for accessing remote devices, other files, devices, systems, or a network), a radio frequency (RF) or other transceiver, a telephonic interface, a bridge, a router, etc. The I/O devices 1270 also include components for communicating over various networks, such as the Internet or an intranet. The I/O devices 1270 may be connected to and/or communicate with the processor 1210 utilizing Bluetooth connections and cables (via, e.g., Universal Serial Bus (USB) ports, serial ports, parallel ports, FireWire, HDMI (High-Definition Multimedia Interface), PCIe, InfiniBand®, or proprietary interfaces, etc.).
The computer 1200 includes one or more antennas 1275 for transmitting and receiving over-the-air-signals (e.g., radio signals such as microwave signals, GPS signals, etc.) via a transceiver 1280.
When the computer 1200 is in operation, the processor 1210 is configured to execute software stored within the memory 1220, to communicate data to and from the memory 1220, and to generally control operations of the computer 1200 pursuant to the software. The application 1260 and the O/S 1250 are read, in whole or in part, by the processor 1210, perhaps buffered within the processor 1210, and then executed.
When the application 1260 is implemented in software it should be noted that the application 1260 can be stored on virtually any computer readable storage medium for use by or in connection with any computer related system or method.
The application 1260 can be embodied in any computer-readable medium for use by or in connection with an instruction execution system, apparatus, server, or device, such as a computer-based system, processor-containing system, or other system that can fetch the instructions from the instruction execution system, apparatus, or device and execute the instructions.
In exemplary embodiments, where the application 1260 is implemented in hardware, the application 1260 can be implemented with any one or a combination of the following technologies, which are each well known in the art: a discrete logic circuit(s) having logic gates for implementing logic functions upon data signals, an application specific integrated circuit (ASIC) having appropriate combinational logic gates, a programmable gate array(s) (PGA), a field programmable gate array (FPGA), etc.
It is understood that the computer 1200 includes non-limiting examples of software and hardware components that may be included in various devices, servers, and systems discussed herein, and it is understood that additional software and hardware components may be included in the various devices and systems discussed in exemplary embodiments.
As will be appreciated by one skilled in the art, one or more aspects of the present invention may be embodied as a system, method or computer program product. Accordingly, one or more aspects of the present invention may take the form of an entirely hardware embodiment, an entirely software embodiment (including firmware, resident software, micro-code, etc.) or an embodiment combining software and hardware aspects that may all generally be referred to herein as a “circuit,” “module” or “system”. Furthermore, one or more aspects of the present invention may take the form of a computer program product embodied in one or more computer readable medium(s) having computer readable program code embodied thereon.
Any combination of one or more computer readable medium(s) may be utilized. The computer readable medium may be a computer readable storage medium. A computer readable storage medium may be, for example, but not limited to, an electronic, magnetic, optical, electromagnetic, infrared or semiconductor system, apparatus, or device, or any suitable combination of the foregoing. More specific examples (a non-exhaustive list) of the computer readable storage medium include the following: an electrical connection having one or more wires, a portable computer diskette, a hard disk, a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or Flash memory), an optical fiber, a portable compact disc read-only memory (CD-ROM), an optical storage device, a magnetic storage device, or any suitable combination of the foregoing. In the context of this document, a computer readable storage medium may be any tangible medium that can contain or store a program for use by or in connection with an instruction execution system, apparatus, or device.
The descriptions of the various embodiments of the present invention have been presented for purposes of illustration, but are not intended to be exhaustive or limited to the embodiments disclosed. Many modifications and variations will be apparent to those of ordinary skill in the art without departing from the scope and spirit of the described embodiments. The terminology used herein was chosen to best explain the principles of the embodiments, the practical application or technical improvement over technologies found in the marketplace, or to enable others of ordinary skill in the art to understand the embodiments disclosed herein.
The present invention may be a system, a method, and/or a computer program product. The computer program product may include a computer readable storage medium (or media) having computer readable program instructions thereon for causing a processor to carry out aspects of the present invention.
The computer readable storage medium can be a tangible device that can retain and store instructions for use by an instruction execution device. The computer readable storage medium may be, for example, but is not limited to, an electronic storage device, a magnetic storage device, an optical storage device, an electromagnetic storage device, a semiconductor storage device, or any suitable combination of the foregoing. A non-exhaustive list of more specific examples of the computer readable storage medium includes the following: a portable computer diskette, a hard disk, a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or Flash memory), a static random access memory (SRAM), a portable compact disc read-only memory (CD-ROM), a digital versatile disk (DVD), a memory stick, a floppy disk, a mechanically encoded device such as punch-cards or raised structures in a groove having instructions recorded thereon, and any suitable combination of the foregoing. A computer readable storage medium, as used herein, is not to be construed as being transitory signals per se, such as radio waves or other freely propagating electromagnetic waves, electromagnetic waves propagating through a waveguide or other transmission media (e.g., light pulses passing through a fiber-optic cable), or electrical signals transmitted through a wire.
Computer readable program instructions described herein can be downloaded to respective computing/processing devices from a computer readable storage medium or to an external computer or external storage device via a network, for example, the Internet, a local area network, a wide area network and/or a wireless network. The network may comprise copper transmission cables, optical transmission fibers, wireless transmission, routers, firewalls, switches, gateway computers and/or edge servers. A network adapter card or network interface in each computing/processing device receives computer readable program instructions from the network and forwards the computer readable program instructions for storage in a computer readable storage medium within the respective computing/processing device.
Computer readable program instructions for carrying out operations of the present invention may be assembler instructions, instruction-set-architecture (ISA) instructions, machine instructions, machine dependent instructions, microcode, firmware instructions, state-setting data, or either source code or object code written in any combination of one or more programming languages, including an object oriented programming language such as Smalltalk, C++ or the like, and conventional procedural programming languages, such as the “C” programming language or similar programming languages. The computer readable program instructions may execute entirely on the user's computer, partly on the user's computer, as a stand-alone software package, and partly on a remote computer or entirely on the remote computer or server. In the latter scenario, the remote computer may be connected to the user's computer through any type of network, including a local area network (LAN) or a wide area network (WAN), or the connection may be made to an external computer (for example, through the Internet using an Internet Service Provider). In some embodiments, electronic circuitry including, for example, programmable logic circuitry, field-programmable gate arrays (FPGA), or programmable logic arrays (PLA) may execute the computer readable program instructions by utilizing state information of the computer readable program instructions to personalize the electronic circuitry, in order to perform aspects of the present invention.
Aspects of the present invention are described herein with reference to flowchart illustrations and/or block diagrams of methods, apparatus (systems), and computer program products according to embodiments of the invention. It will be understood that each block of the flowchart illustrations and/or block diagrams, and combinations of blocks in the flowchart illustrations and/or block diagrams, can be implemented by computer readable program instructions.
These computer readable program instructions may be provided to a processor of a general purpose computer, special purpose computer, or other programmable data processing apparatus to produce a machine, such that the instructions, which execute via the processor of the computer or other programmable data processing apparatus, create means for implementing the functions/acts specified in the flowchart and/or block diagram block or blocks. These computer readable program instructions may also be stored in a computer readable storage medium that can direct a computer, a programmable data processing apparatus, and/or other devices to function in a particular manner, such that the computer readable storage medium having instructions stored therein comprises an article of manufacture including instructions which implement aspects of the function/act specified in the flowchart and/or block diagram block or blocks.
The computer readable program instructions may also be loaded onto a computer, other programmable data processing apparatus, or other device to cause a series of operational steps to be performed on the computer, other programmable apparatus or other device to produce a computer implemented process, such that the instructions which execute on the computer, other programmable apparatus, or other device implement the functions/acts specified in the flowchart and/or block diagram block or blocks.
The flowchart and block diagrams in the Figures illustrate the architecture, functionality, and operation of possible implementations of systems, methods, and computer program products according to various embodiments of the present invention. In this regard, each block in the flowchart or block diagrams may represent a module, segment, or portion of instructions, which comprises one or more executable instructions for implementing the specified logical function(s). In some alternative implementations, the functions noted in the block may occur out of the order noted in the figures. For example, two blocks shown in succession may, in fact, be executed substantially concurrently, or the blocks may sometimes be executed in the reverse order, depending upon the functionality involved. It will also be noted that each block of the block diagrams and/or flowchart illustration, and combinations of blocks in the block diagrams and/or flowchart illustration, can be implemented by special purpose hardware-based systems that perform the specified functions or acts or carry out combinations of special purpose hardware and computer instructions.
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| 20160349182 A1 | Dec 2016 | US |
