US20030003609A1 - Ultra-fast nucleic acid sequencing device and a method for making and using the same - Google Patents

Abstract

A system and method employing at least one semiconductor device having at least one detecting region which can include, for example, a recess or opening therein, for detecting a charge representative of a component of a polymer, such as a nucleic acid strand, proximate to the detecting region, and a method for manufacturing such a semiconductor device. The system and method can thus be used for sequencing individual nucleotides or bases of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). The semiconductor device includes at least two doped regions, such as two n-type regions implanted in a p-type semiconductor layer or two p-type regions implanted in an n-type semiconductor layer. The detecting region permits a current to pass between the two doped regions in response to the presence of the component of the polymer, such as a base of a DNA or RNA strand. The current has characteristics representative of the component of the polymer, such as characteristics representative of the detected base of the DNA or RNA strand.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS
• This is a continuation of U.S. patent application Ser. No. 09/653,543, filed on Aug. 31, 2000, the entire contents thereof being incorporated herein by reference.[0001]
• Related subject matter is disclosed in a provisional U.S. Patent Application of Jon R. Sauer et al. entitled “Ultra-Fast, Semiconductor-Based Gene Sequencing”, Serial No. 60/199,130, filed Apr. 24, 2000, and of a provisional U.S. Patent Application of Bart Van Zeghbroeck et al. entitled “Charge Sensing and Amplification Device for DNA Sequencing”, Serial No. 60/217,681, filed Jul. 12, 2000, the entire contents of both of said provisional applications being incorporated herein by reference.[0002]
BACKGROUND OF THE INVENTION
• 1. Field of the Invention[0003]
• The present invention relates to a system and method employing a semiconductor device having a detecting region for identifying the individual mers of long-chain polymers, such as carbohydrates and proteins, as well as individual bases of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), and a method for making the semiconductor device. More particularly, the present invention relates to a system and method employing a semiconductor device, similar to a field-effect transistor device, capable of identifying the bases of a DNA/RNA strand to thus enable sequencing of the strand to be performed.[0004]
• 2. Description of the Related Art[0005]
• DNA consists of two very long, helical polynucleotide chains coiled around a common axis. The two strands of the double helix run in opposite directions. The two strands are held together by hydrogen bonds between pairs of bases, consisting of adenine (A), thymine (T), guanine (G), and cytosine (C). Adenine is always paired with thymine, and guanine is always paired with cytosine. Hence, one strand of a double helix is the complement of the other.[0006]
• Genetic information is encoded in the precise sequence of bases along a DNA strand. In normal cells, genetic information is passed from DNA to RNA. Most RNA molecules are single stranded but many contain extensive double helical regions that arise from the folding of the chain into hairpin-like structures.[0007]
• Mapping the DNA sequence is part of a new era of genetic-based medicine embodied by the Human Genome Project. Through the efforts of this project, one day doctors will be able to tailor treatment to individuals based upon their genetic composition, and possibly even correct genetic flaws before birth. However, to accomplish this task it will be necessary to sequence each individual's DNA. Although the human genome sequence variation is approximately 0.1%, this small variation is critical to understanding a person's predisposition to various ailments. In the near future, it is conceivable that medicine will be “DNA personalized”, and a physician will order sequence information just as readily as a cholesterol test is ordered today. Thus, to allow such advances to be in used in everyday life, a faster and more economical method of DNA sequencing is needed.[0008]
• One method of performing DNA sequencing is disclosed in U.S. Pat. No. 5,653,939, the entire content of which is incorporated herein by reference. This method employs a monolithic array of test sites formed on a substrate, such as a semiconductor substrate. Each test site includes probes which are adapted to bond with a predetermined target molecular structure. The bonding of a molecular structure to the probe at a test site changes the electrical, mechanical and optical properties of the test site. Therefore, when a signal is applied to the test sites, the electrical, mechanical, or optical properties of each test site can be measured to determine which probes have bonded with their respective target molecular structure. However, this method is disadvantageous because the array of test sites is complicated to manufacture, and requires the use of multiple probes for detecting different types of target molecular structures.[0009]
• Another method of sequencing is known as gel electrophoresis. In this technology, the DNA is stripped down to a single strand and exposed to a chemical that destroys one of the four nucleotides, for example A, thus producing a strand that has a random distribution of DNA fragments ending in A and labeled at the opposite end. The same procedure is repeated for the other three remaining bases. The DNA fragments are separated by gel electrophoresis according to length. The lengths show the distances from the labeled end to the known bases, and if there are no gaps in coverage, the original DNA strand fragment sequence is determined.[0010]
• This method of DNA sequencing has many drawbacks associated with it. This technique only allows readings of approximately 500 bases, since a DNA strand containing more bases would “ball” up and not be able to be read properly. Also, as strand length increases, the resolution in the length determination decreases rapidly, which also limits analysis of strands to a length of 500 bases. In addition, gel electrophoresis is very slow and not a workable solution for the task of sequencing the genomes of complex organisms. Furthermore, the preparation before and analysis following electrophoresis is inherently expensive and time consuming. Therefore, a need exists for a faster, consistent and more economical means for DNA sequencing.[0011]
• Another approach for sequencing DNA is described in U.S. Pat. Nos. 5,795,782 and 6,015,714, the entire contents of which are incorporated herein by reference. In this technique, two pools of liquid are separated by a biological membrane with an alpha hemolysin pore. As the DNA traverses the membrane, an ionic current through the pore is blocked. Experiments have shown that the length of time during which the ionic current through the pore is blocked is proportional to the length of the DNA fragment. In addition, the amount of blockage and the velocity depend upon which bases are in the narrowest portion of the pore. Thus, there is the potential to determine the base sequence from these phenomena.[0012]
• Among the problems with this technique are that individual nucleotides cannot, as yet, be distinguished. Also, the spatial orientation of the individual nucleotides is difficult to discern. Further, the electrodes measuring the charge flow are a considerable distance from the pore, which adversely affects the accuracy of the measurements. This is largely because of the inherent capacitance of the current-sensing electrodes and the large statistical variation in sensing the small amounts of current. Furthermore, the inherent shot noise and other noise sources distort the signal, incurring additional error. Therefore, a need exists for a more sensitive detection system which discriminates among the bases as they pass through the sequencer.[0013]
SUMMARY OF THE INVENTION
• An object of the present invention is to provide a system and method for accurately and effectively identifying individual bases of DNA or RNA.[0014]
• Another object of the present invention is to provide a system and method employing a semiconductor device for sequencing individual bases of DNA or RNA.[0015]
• A further object of the present invention is to provide a method for manufacturing a semiconductor-based DNA or RNA sequencing device.[0016]
• Another object of the present invention is to provide a system and method for accurately and effectively identifying the individual mers of long-chain polymers, such as carbohydrates or proteins, as well as measuring the lengths of the long-chain polymers.[0017]
• Still another object of the present invention is to provide a system and method employing a semiconductor-based device having a opening therein, for accurately and effectively identifying bases of DNA or RNA by measuring charge at a location where the DNA or RNA molecules traverse the opening in the sequencer, to thus eliminate or at least minimize the effects of shot noise and other noise sources associated with the random movement of the DNA or RNA molecules through the opening.[0018]
• These and other objects of the invention are substantially achieved by providing a system for detecting at least one polymer, comprising at least one semiconductor device having at least one detecting region which is adapted to detect a charge representative of a component of the polymer proximate to the detecting region. The component can include a base in a nucleic acid strand, so that the detecting region is adapted to detect the charge which is representative of the base in the nucleic acid strand. The detecting region is further adapted to generate a signal representative of the detected charge. Also, the detecting region can include a region of the semiconductor device defining a recess in the semiconductor device, or an opening in the semiconductor device having a cross-section sufficient to enable the polymer to enter the opening, so that the detecting region detects the charge of the component in the opening. Furthermore, the semiconductor device preferably further includes at least two doped regions, and the detecting region can pass a current between the two doped regions in response to a presence of the component proximate to the detecting region.[0019]
• The above and other objects of the invention are also substantially achieved by providing a method for detecting at least one polymer, comprising the steps of positioning a portion of the polymer proximate to a detecting region of at least one semiconductor device, and detecting at the detecting region a charge representative of a component of the polymer proximate to the detecting region. The component can include a base in a nucleic acid strand, so that the detecting step detects a charge representative of the base. The method further comprises the step of generating at the detecting region a signal representative of the detected charge. The detecting region can include a region of the semiconductor device defining a recess in the semiconductor device, or an opening in the semiconductor device having a cross-section sufficient to enable the polymer to enter the opening, so that the detecting step detects the charge of the component in the recess or opening. Furthermore, the semiconductor device can further include at least two doped regions, so that the method can further include the step of passing a current between the two doped regions in response to a presence of the component proximate to the detecting region.[0020]
• The above and other objects of the invention are further substantially achieved by providing a method for manufacturing a device for detecting a polymer, comprising the steps of providing a semiconductor structure comprising at least one semiconductor layer, and creating a detecting region in the semiconductor structure, such that the detecting region is adapted to detect a charge representative of a component of the polymer proximate to the detecting region. The component can include a base in a nucleic acid strand, and the detecting region can be created to detect a charge representative of the base in the nucleic acid strand. The method can further include the step of creating a recess in the semiconductor structure, or creating an opening in the semiconductor structure having a cross-section sufficient to enable a portion of the polymer to pass therethrough, and being positioned in relation to the detecting region such that the detecting region is adapted to detect the charge representative of the component in the recess or opening. The method can further include the step of forming an insulating layer on a wall of the semiconductor layer having the opening to decrease the cross-section of the opening. Furthermore, the method can include the step of creating at least two doped regions in the semiconductor layer which are positioned with respect to the detecting region such that the detecting region is adapted to pass a current between the doped regions in response to the component of the polymer proximate to the detecting region. The doped regions can be separated by a portion of the semiconductor layer having a different doping, and can be created as a stack of doped regions, each having a first doping and being separated by a layer having a second doping. The doped regions can include either a p-type or an n-type doping.[0021]
BRIEF DESCRIPTION OF THE DRAWINGS
• These and other objects, advantages and novel features of the invention will be more readily appreciated from the following detailed description when read in conjunction with the accompanying drawings, in which:[0022]
• FIG. 1 illustrates a system for performing DNA or RNA sequencing comprising a DNA or RNA sequencer constructed in accordance with an embodiment of the present invention;[0023]
• FIG. 2 illustrates a top view of the DNA or RNA sequencer shown in FIG. 1;[0024]
• FIG. 3 is a graph showing an example of the waveform representing the current detected by a current detector in the system shown in FIG. 1 as the adenine (A), thymine (T), guanine (G), and cytosine (C) bases of a DNA or RNA sequence pass through the DNA or RNA sequencer;[0025]
• FIG. 4 illustrates a cross-sectional view of a silicon-on-insulator (SOI) substrate from which a DNA or RNA sequencer as shown in FIG. 1 is fabricated in accordance with an embodiment of the present invention;[0026]
• FIG. 5 illustrates a cross-sectional view of the SOI substrate shown in FIG. 5 having shallow and deep n-type regions formed in the silicon layer, and a portion of the substrate etched away;[0027]
• FIG. 6 illustrates a cross-sectional view of the SOI substrate shown in FIG. 5 in which a portion of the insulator has been etched away and another shallow n-type region has been formed in the silicon layer;[0028]
• FIG. 7 illustrates a cross-sectional view of the SOI substrate having an opening etched therethrough;[0029]
• FIG. 8 illustrates a top view of the SOI substrate as shown in FIG. 7;[0030]
• FIG. 9 illustrates a cross-sectional view of the SOI substrate shown in FIG. 7 having an oxidation layer formed on the silicon layer and on the walls forming the opening therein;[0031]
• FIG. 10 illustrates a top view of the SOI substrate as shown in FIG. 9;[0032]
• FIG. 11 illustrates a detailed cross-sectional view of the SOI substrate shown in FIG. 7 having an oxidation layer formed on the silicon layer and on the walls forming the opening therein;[0033]
• FIG. 12 illustrates a top view of the SOI substrate shown in FIG. 11;[0034]
• FIG. 13 illustrates a detailed cross-sectional view of an exemplary configuration of the opening in SOI substrate shown in FIG. 7;[0035]
• FIG. 14 illustrates a top view of the opening shown in FIG. 13;[0036]
• FIG. 15 illustrates a cross-sectional view of the SOI substrate as shown in FIG. 9 having holes etched in the oxidation layer and metal contacts formed over the holes to contact the shallow and deep n-type regions, respectively;[0037]
• FIG. 16 illustrates a cross-sectional view of the DNA or RNA sequencer shown in FIG. 1 having been fabricated in accordance with the manufacturing steps shown in FIGS.[0038]4-15;
• FIG. 17 illustrates a top view of a DNA or RNA sequencer having multiple detectors formed by multiple n-type regions according to another embodiment of the present invention;[0039]
• FIG. 18 illustrates a cross-sectional view of a DNA or RNA sequencer according to another embodiment of the present invention;[0040]
• FIG. 19 illustrates a cross-sectional view of a DNA or RNA sequencer according to a further embodiment of the present invention;[0041]
• FIG. 20 illustrates a cross-sectional view of a DNA or RNA sequencer according to a further embodiment of the present invention; and[0042]
• FIG. 21 illustrates a top view of the DNA or RNA sequencer shown in FIG. 20.[0043]
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
• FIGS. 1 and 2 illustrate a[0044]system100 for detecting the presence of a polymer, such as DNA or RNA, a protein or carbohydrate, or a long chain polymer such as petroleum, and, more preferably, for identifying the individual mers of the polymer or long chain polymer, as well as the length of the polymer or long chain polymer. Thesystem100 is preferably adaptable for performing sequencing of nucleic acids, such as DNA or RNA sequencing, according to an embodiment of the present invention. Accordingly, for purposes of this description, thesystem100 will be discussed in relation to nucleic acid sequencing.
• The[0045]system100 includes a nucleicacid sequencing device102 which, as described in more detail below, is a semiconductor device. Specifically, the nucleicacid sequencing device102 resembles a field-effect transistor, such as a MOSFET, in that it includes two doped regions, adrain region104 and asource region106. However, unlike a MOSFET, the nucleic acid sequencing device does not include a gate region for reasons discussed below.
• The nucleic[0046]acid sequencing device102 is disposed in acontainer108 that includes a liquid110 such as water, gel, or any other suitable solution. It is important to note that thesolution110 can be an insulating medium, such as oil, or any other suitable insulating medium. In addition, thecontainer108 does not need to include a medium such as a liquid. Rather, thecontainer108 can be sealed and evacuated to create a vacuum in which nucleicacid sequencing device102 is disposed. Also, although FIG. 1 shows only a single nucleicacid sequencing device102 in thecontainer108 for exemplary purposes, the container can include multiple nucleicacid sequencing devices102 for performing multiple DNA sequencing measurements in parallel.
• The liquid[0047]110 or other medium or vacuum incontainer108 includes the nucleic acid strands or portions ofnucleic acid strands111 to be sequenced by nucleicacid sequencing device102. As further shown,voltage source112, such as a direct current voltage source, is coupled in series with acurrent meter114 byleads116 across drain andsource regions104 and106, respectively. In this example, the positive lead ofvoltage source112 is coupled to thedrain region104 while the negative lead ofvoltage source112 is coupled via thecurrent meter114 to sourceregion106.
• The voltage potential applied across drain and[0048]source regions104 and106 of nucleicacid sequencing device102 creates a gradient across drain andsource regions104 and106, which draws the nucleic acid strands into opening118 of the nucleicacid sequencing device102. That is, thenucleic acid strands111 move through theopening118 because of the local gradient. Alternatively or in addition, the liquid can include an ionic solution. In this event, the local gradient causes the ions in the solution to flow through theopening118, which assists thenucleic acid strands111, such as DNA or RNA, to move through theopening118 as well.
• [0049]Additional electrodes113 and115 positioned in the medium110 and connected toadditional voltage sources117 and121 would further facilitate the movement of the nucleic acid strands towards theopening118. In other words, theexternal electrodes113 and115 are used to apply an electric field within the medium110. This field causes all of the charged particles, including thenucleic acid strand111, to flow either toward thehole118 or away from thehole118. Thuselectrodes113 and115 are used as a means to steer thenucleic acid strands111 into or out of thehole118. In order to connectvoltage sources112 and117 to thenucleic acid sequencer102,metal contacts123 are coupled to the n-type dopedregion128 and130, described in more detail below. Theelectrodes113 and115 could also provide a high frequency voltage which is superimposed on the DC voltage by an alternatingvoltage source125. This high frequency voltage, which can have a frequency in the radio frequency range, such as the megahertz range (e.g., 10 MHz), causes thenucleic acid strand111 and ions to oscillate. This oscillation makes passage of thenucleic acid strand111 through thehole118 smoother, in a manner similar to shaking a salt shaker to enable the salt grains to pass through the openings in the shaker. Alternatively, adevice127, such as an acoustic wave generator, can be disposed in the liquid110 or at any other suitable location, and is controlled to send sonic vibrations through thedevice102 to provide a similar mechanical shaking function.
• As can be appreciated by one skilled in the art, the nucleic acid strands each include different combinations of bases A, C, G and T, which each contain a particular magnitude and polarity of ionic charge. The charge gradient between drain and[0050]source regions104 and106, or otherwise across theopening118, will thus cause the charged nucleic acid strands to traverse theopening118. Alternatively, another voltage source (not shown) can be used to create a difference in voltage potential between theopening118 and the liquid. Also, a pressure differential can be applied across theopening118 to control the flow of the DNA independent from the voltage applied between the source and drain104 and106.
• In addition, the[0051]DNA sequencer102 can attract the nucleic acid strands to theopening118 by applying a positive voltage to the medium110 relative to thevoltage source112. Furthermore, the nucleic acid strands in the medium110 can be pushed in and out of theopening118 and be analyzed multiple times by reversing the polarity across drain andsource regions104 and106, respectively.
• As described in more detail below, the[0052]opening118 is configured to have a diameter within the nanometer range, for example, within the range of about 1 nm to about 10 nm. Therefore, only one DNA strand can pass through opening118 at any given time. As a DNA strand passes throughopening118, the sequence of bases induce image charges which form achannel119 between the drain andsource regions104 and106 that extends vertically along the walls of thedevice defining opening118. As a voltage is applied between thesource136 and drain128 by means of thevoltage source112, these image charges in the channel flow from source to drain, resulting in a current flow which can be detected by thecurrent meter114. Alternatively, the bases induce a charge variation inchannel119, leading to a current variation as detected bycurrent meter114. Any variation of the ion flow through the opening due to the presence of the DNA strand would also cause a variation to the image charge in thechannel119 and results in a current variation as detected bycurrent meter114.
• Each different type of bases A, C, G, and T induces a current having a particular magnitude and waveform representative of the particular charge associated with its respective type of bases. In other words, an A type base will induce a current in a channel between the drain and source regions of the nucleic[0053]acid sequencing device102 having a magnitude and waveform indicative of the A type base. Similarly, the C, T and G bases will each induce a current having a particular magnitude and waveform.
• An example of a waveform of the detected current is shown in FIG. 3, which symbolically illustrates the shape, magnitude, and time resolution of the expected signals generated by the presence of the A, C, G and T bases. The magnitude of current is typically in the microampere (μA) range, which is a multiplication factor of 10[0054]⁶greater than the ion current flowing through theopening118, which is in the picoampere range. A calculation of the electrostatic potential of the individual bases shows the complementary distribution of charges that lead to the hydrogen bonding. For example, the T-A and C-G pairs have similar distributions when paired viewed from the outside, but, when unpaired, as would be the case when analyzing single-stranded DNA, the surfaces where the hydrogen bonding occurs are distinctive. The larger A and G bases are roughly complementary (positive and negative reversed) on the hydrogen bonding surface with similar behavior for the smaller T and C bases.
• Accordingly, as the DNA strand passes through[0055]opening118, the sequence of bases in the strand can be detected and thus ascertained by interpreting the waveform and magnitude of the induced current detected bycurrent meter114. Thesystem100 therefore enables DNA sequencing to be performed in a very accurate and efficient manner.
• The preferred method of fabricating a nucleic[0056]acid sequencing device102 will now be described with reference to FIGS.4-16. As shown in FIG. 4, the fabrication process begins with awafer120, such as a silicon-on-insulator (SOI) substrate comprising asilicon substrate122, a silicon dioxide (SiO₂)layer124, and a thin layer of p-type silicon126. In this example, thesilicon substrate122 has a thickness within the range of about 300 μm to about 600 μm, thesilicon dioxide layer124 has a thickness within the range of about 200 to 6400 nm, and the p-type silicon layer126 has a thickness of about 1 μm or less.
• As shown in FIG. 5, a doped n-[0057]type region128 is created in the p-type silicon layer126 by ion implantation, and annealing or diffusion of an n-type dopant, such as arsenic, phosphorous or the like. As illustrated, the n-type region128 is a shallow region which does not pass entirely through p-type silicon126. A deep n-type region130 is also created in the p-type silicon126 as illustrated in FIG. 5. The deep n-type region130 passes all the way through the p-type silicon126 tosilicon dioxide124 and is created by known methods, such as diffusion, or ion implantation and annealing of an n-type material which can be identical or similar to the n-type material used to create n-type region128. As further illustrated in FIG. 5, thesilicon substrate122 is etched along its (111) plane by known etching methods, such as etching in potassium hydroxide (KOH) or the like. As illustrated, the etching process etches away a central portion ofsilicon substrate122 down to thesilicon dioxide124 to create anopening132 in thesilicon substrate122.
• As shown in FIG. 6, the portion of the[0058]silicon dioxide124 exposed inopening132 is etched away by conventional etching methods, such as etching in hydrofluoric acid, reactive etching or the like. Another shallow n-type region124 is created in the area of the p-type silicon126 exposed at opening132 by known methods, such implantation or diffusion of an n-type material identical or similar to those used to create n-type regions128 and130.
• Opening[0059]118 (see FIGS. 1 and 2) is then formed through the n-type region128, p-type silicon126 and bottom n-type region134 as shown, for example, in FIGS. 7 and 8 by reactive ion etching using Freon (CF₄), optical lithography, electron-beam lithography or any other fine-line lithography, which results in an opening having a diameter of about 10 nm. As shown in FIG. 9, the diameter of the opening can be further decreased by oxidizing the silicon, thus forming asilicon dioxide layer136 over the p-type silicon layer126 and thewalls forming opening118. As shown in detail in FIGS. 11 and 12, the resulting oxide has a volume larger than the silicon consumed during the oxidation process, which further narrows the diameter ofopening118. It is desirable if the diameter of opening118 can be as small as 1 nm.
• Although for illustration purposes FIGS. 1, 2 and[0060]3-9show opening118 as being a cylindrically-shaped opening, it is preferable for opening118 to have a funnel shape as shown, for example, in FIGS. 13 and 14. This funnel-shapedopening118 is created by performing V-groove etching of the (100) p-type silicon layer126 using potassium hydroxide (KOH), which results in V-shaped grooves formed along the (111) planes138 of the p-type silicon126. The V-shaped or funnel-shaped opening, as shown explicitly in FIG. 14, facilitates movement of a DNA strand throughopening118, and minimizes the possibility that the DNA strand will become balled up upon itself and thus have difficulty passing throughopening118. Oxidation and V-groove etching can be combined to yield even smaller openings. Additionally, anodic oxidation can be used instead of thermal oxidation, as described above. Anodic oxidation has the additional advantage of allowing for monitoring of the hole size during oxidation so that the process can be stopped when the optimum hole size is achieved.
• Turning now to FIG. 15, holes[0061]140 are etched into thesilicon dioxide136 to expose n-type region128 and n-type region130.Metal contacts142 are then deposited ontosilicon dioxide layer136 and intoholes140 to contact the respective n-type regions128 and130. Aninsulator144 is then deposited overmetal contacts142 as shown in FIG. 16, thus resulting indevice102 as shown in FIG. 1.
• As further shown in FIG. 1, a portion of[0062]insulator144 can be removed so that leads116 can be connected to the n-type regions128 and130, which thus form thedrain regions104 andsource106, respectively. Anadditional insulator146 is deposited overinsulator144 to seal the openings through which leads116 extend to contact n-type regions128 and130. The completeddevice102 can then be operated to perform the DNA sequencing as discussed above.
• Additional embodiments of the[0063]device102 can also be fabricated. For example, FIG. 17 illustrates a top view of a nucleic acid sequencing device according to another embodiment of the present invention. In this embodiment, the steps described above with regard to FIGS. 3 through 16 are performed to form the n-type regions which ultimately form the drain and source regions. However, in this embodiment, the n-type region128 shown, for example, in FIG. 5, is formed as four separate n-type regions,150 in a p-type silicon layer similar to p-type silicon layer126 described above. Asilicon dioxide layer152 covers the p-type silicon layer into which n-type regions150 have been created.Holes156 are etched intosilicon dioxide layer152 so thatmetal contacts158 that are deposited onsilicon dioxide layer152 can contact n-type regions150. By detecting current flowing between the four drain regions formed by n-type regions150 and the source region (not shown), the spatial orientation of the bases on the DNA strand passing throughopening152 can be detected.
• FIG. 18 is a cross section of a nucleic acid sequencing device[0064]160 according to another embodiment of the present invention. Similar to nucleicacid sequencing device102,160 includes asilicon substrate162, asilicon dioxide layer164, an n-type region166 implanted in p-type silicon168, and a second n-type region170 implanted in p-type silicon168. Nucleic acid sequencing device160 further has anopening172 passing therethrough. The opening can be cylindrical, or can be a V-shaped or funnel-shaped opening as described above. Asilicon dioxide layer174 covers p-type silicon layer168, n-type region170 and n-type region166 as shown, and decreases the diameter of opening172 in the manner described above. An opening is etched intosilicon dioxide layer172 to allow a lead176 to be attached to n-type region170. Anotherlead176 is also attached to an exposed portion of n-type region166, so that avoltage source178 can apply a potential across thedrain region180 formed by n-type region170 andsource region182 formed n-type region166. The nucleic acid sequencing device160 can thus be used to detect the bases of aDNA strand182 in a manner described above.
• FIG. 19 illustrates a[0065]DNA sequencing system186 according to another embodiment of the present invention.System186 includes a multi-layer nucleic acid sequencing device188 which, in this example, comprises three MOSFET-type devices stacked on top of each other. That is, device188 includes asilicon substrate190 similar tosilicon substrate122 described above. Asilicon dioxide layer192 is present onsilicon substrate190. The device188 further includes an n-type doped silicon region194, a p-typesilicon dioxide region196, an n-type dopedsilicon region198, a p-typesilicon dioxide region200, an n-type dopedregion silicon region202, a p-typesilicon dioxide region204 and an n-type dopedsilicon region206. Regions194 through206 are stacked on top of each other as shown explicitly in FIG. 19. However, as can be appreciated by one skilled in the art, the polarity of the layers can be reversed for this embodiment, and for any of the other embodiments discussed herein. That is, the device188 can comprise a p-type doped silicon region194, an n-typesilicon dioxide region196, a p-type dopedsilicon region198, and so on.
• Additionally, a thin[0066]silicon dioxide layer208 is formed over the layers as illustrated, and is also formed on thewalls forming opening210 to decrease the diameter of opening210 in a manner described above with regard toopening118. Also, opening210 can be cylindrically shaped, a V-shaped groove or a funnel-shaped groove as described above. Holes are formed insilicon dioxide layer208 so that leads212 can be attached toregions194,198,202 and206 to couplevoltage source214,216 and218 andcurrent meters220,222 and224 to device188 as will now be described.Voltage sources214,216 and218 andcurrent meters220,222 and224 are similar tovoltage source112 andcurrent meter114, respectively, as described above.
• Specifically, leads[0067]212couple voltage source214 andcurrent meter220 in series to n-type dopedsilicon region202 and n-type dopedsilicon region206. Therefore,voltage source214 applies a voltage acrossregions202 and206 which are separated by p-typesilicon dioxide region204.Leads212 alsocouple voltage source216 andcurrent meter222 to n-type dopedsilicon region198 and n-type dopedsilicon region202 as shown. Furthermore, leads212couple voltage source218 andcurrent meter224 to n-type doped silicon region194 and n-type dopedsilicon region202 as shown. Accordingly, as can be appreciated from FIG. 19, n-type dopedsilicon region198 and n-type doped silicon region194 act as the drain and source regions, respectively, of one MOSFET, n-type dopedsilicon region202 and n-type dopedsilicon region198 act as drain and source regions, respectively, of a second MOSFET, and n-type dopedsilicon region206 and n-type dopedsilicon region202 act as drain and source regions, respectively, of a third MOSFET. These three MOSFET type devices can measure the current induced by the bases of a DNA strand passing throughopening210, and thus take multiple measurements of these bases to improve accuracy.
• It is also noted that a nucleic acid sequencing device above can be configured to sense the bases of a nucleic acid strand without it being necessary for the DNA strand to pass through an opening in the devices, as shown in FIGS. 20 and 21. That is, using the techniques described above, a nucleic[0068]acid sequencing device226, similar to nucleicacid sequencing device102 shown in FIG. 1, can be fabricated having its drain and source regions proximate to a surface. It is noted that like components shown in FIGS. 1, 20 and21 are identified with like reference numbers. However, in place of anopening118, one ormore grooves228 can optionally be formed in the surface extending from the drain region to the source region. Alternatively, no grooves are formed in the surface, but rather, the detection area for detectingnucleic acid strands111 is present between the drain and source regions. Techniques similar to those discussed above, such as the application of voltage potentials, by means ofvoltage sources117 and121, and creation of a pressure differential in thecontainer108 can be used to move thenucleic acid strands111 in a horizontal direction along the surface of the device over thegrooves228. The bases in the nucleic acid strands create animage charge channel230 between the drain and source regions which allows current to flow between the drain and source regions. The current induced in the nucleic acid sequencing device by the bases can be measured in a manner similar to that described above.
• Again, it is noted that the[0069]device226 differs from the other embodiments represented in FIGS. 1, 17 and19 in that thechannel230 containing the image charge is horizontal rather than vertical. The structure no longer contains ahole118 as in thedevice102 shown in FIGS. 1, 17 and19, but rather this embodiment contains a charge sensitive region just abovechannel230. Similar to FIG. 1, theexternal electrodes113 and115 are used to apply an electric field which steers thenucleic acid strands111 towards or away from the charge sensitive region. That is, the motion of thenucleic acid strands111 is controlled by applying a voltage to theexternal electrodes113 and115 relative to the voltage applied to the dopedregions130. Additional electrodes (not shown) can be added to move thenucleic acid strands111 perpendicular to the plane shown in FIG. 20.
• The charge sensitive region of the device is located just above the[0070]channel230 and between the twodoped regions130. Identification of individual bases requires that the distance between the two doped regions is on the order of a single base and that the motion of thenucleic acid strand111 is such that each base is successively placed above the charge sensitive region. This horizontal configuration enables more parallel as well as sequential analysis of thenucleic acid strands111 and does not require the fabrication of a small opening. Additional surface processing, such as the formation ofgrooves228 as discussed above that channel thenucleic acid strands111 can be used to further enhance this approach.
• The horizontal embodiment shown in FIGS. 19 and 20 is also of interest to detect the presence of a large number of[0071]nucleic acid strands111. For instance, using an electrophoresis gel as the medium, one starts by placingnucleic acid strands111 of different length between theelectrodes113 and115. A negative voltage is applied to theelectrodes113 and115, relative to the dopedregions130. Thenucleic acid strands111 will then move towards the charge sensitive region. The smaller strands will move faster and the larger strands will move slower. The smaller strands will therefore arrive first at the charge sensitive region, followed by the larger ones. The charge accumulated in the charge sensitive region and therefore also the image charge in thechannel230 therefore increases “staircase-like” with time. This results in a staircase-like increase or decrease of the current measured bycurrent meter114.
• While this operation does not yield the identification of the individual bases of a single DNA/RNA strands, it does provide a measurement of the length of strands equivalent to the one obtained by an electrophoresis measurement. The advantage over standard electrophoresis is that a real-time measurement of the position of the DNA/RNA strands is obtained. In addition, the dimensions can be reduced dramatically since micron-sized devices can readily be made, while standard electrophoresis uses mm if not cm-sized drift regions. This size reduction leads to faster measurements requiring less DNA/RNA strands, while also reducing the cost of a single charge sensing device.[0072]
• Although only several exemplary embodiments of the present invention have been described in detail above, those skilled in the art will readily appreciate that many modifications are possible in the exemplary embodiments without materially departing from the novel teachings and advantages of this invention. Accordingly, all such modifications are intended to be included within the scope of this invention as defined in the following claims.[0073]

Claims (32)

What is claimed is:

1. A system for detecting at least one polymer, comprising:

at least one semiconductor device having at least one detecting region, adapted to detect a charge representative of a component of said polymer proximate to said detecting region.

2. A system as claimed inclaim 1, wherein:

said component includes a base in a nucleic acid strand; and

said detecting region is adapted to detect said charge representative of said base in said nucleic acid strand.

3. A system as claimed inclaim 1, wherein:

said detecting region is further adapted to generate a signal representative of said detected charge.

4. A system as claimed inclaim 1, wherein:

said detecting region includes a region of said semiconductor device defining an opening in said semiconductor device having a cross-section sufficient to enable said polymer to enter said opening, such that said detecting region is adapted to detect said charge of said component in said opening.

5. A system as claimed inclaim 4, further comprising:

an excitation device, adapted to generate movement in said semiconductor device to facilitate movement of said polymer through said opening.

6. A system as claimed inclaim 1, wherein:

said detecting region includes a region of said semiconductor device defining a recess in said semiconductor device, such that said detecting region is adapted to detect said charge of said component in said recess.

7. A system as claimed inclaim 1, wherein:

said semiconductor device includes a plurality of said detecting regions; and

each said detecting region is adapted to detect a charge representative of a component of said at least one polymer proximate thereto.

8. A system as claimed inclaim 1, wherein:

said semiconductor device further includes at least two doped regions; and

said detecting region is adapted to pass a current between said two doped regions in response to a presence of said component proximate to said detecting region.

9. A system as claimed inclaim 1, wherein:

said semiconductor device includes a plurality of doped regions, and a respective detecting region associated with each respective pair of said doped regions, such that each said respective detecting region is adapted, in response to a presence of a component proximate thereto, to pass a respective current between its said respective pair of doped regions.

10. A system as claimed inclaim 1, further comprising:

a plurality of said semiconductor devices.

11. A system as claimed inclaim 1, further comprising:

a detector, adapted to detect a signal generated by said detecting region in response to said component proximate thereto.

12. A method for detecting at least one polymer, comprising the steps of:

positioning a portion of said polymer proximate to a detecting region of at least one semiconductor device; and

at said detecting region, detecting a charge representative of a component of said polymer proximate to said detecting region.

13. A method as claimed inclaim 12, wherein:

said component includes a base in a nucleic acid strand; and

said detecting step detects said charge representative of said base in said nucleic acid strand.

14. A method as claimed inclaim 12, further comprising the step of:

generating at said detecting region a signal representative of said detected charge.

15. A method as claimed inclaim 12, wherein:

said detecting region includes a region of said semiconductor device defining an opening in said semiconductor device having a cross-section sufficient to enable said polymer to enter said opening; and

said detecting step detects said charge of said component in said opening.

16. A method as claimed inclaim 15, further comprising the step of:

generating movement in said semiconductor device to facilitate movement of said polymer through said opening.

17. A method as claimed inclaim 12, wherein:

said detecting region includes a region of said semiconductor device defining a recess in said semiconductor device; and

said detecting step detects said charge of said component in said recess.

18. A method as claimed inclaim 12, wherein:

said semiconductor device includes a plurality of said detecting regions; and

said detecting step includes the step of detecting, at each said detecting region, a charge representative of a component of said at least one polymer proximate thereto.

19. A method as claimed inclaim 12, wherein:

said semiconductor device further includes at least two doped regions; and

said method further includes the step of passing a current between said two doped regions in response to a presence of said component proximate to said detecting region.

20. A method as claimed inclaim 12, wherein:

said semiconductor device includes a plurality of doped regions, and a respective detecting region associated with each respective pair of said doped regions; and

said method further includes the step of passing, at each said respective detecting region in response to a presence of a component proximate thereto, a respective current between its said respective pair of doped regions.

21. A method as claimed inclaim 12, wherein:

said positioning step positions a respective portion of each of a plurality of said polymers proximate to a respective detecting region of a respective semiconductor device; and

said detecting step detects, at each said respective detecting region, a charge representative of a component of said respective polymer proximate to said respective detecting region.

22. A method as claimed inclaim 12, further comprising the step of:

detecting a signal generated by said detecting region in response to said component proximate thereto.

23. A method for manufacturing a device for detecting a polymer, comprising the steps of:

providing a semiconductor structure comprising at least one semiconductor layer; and

creating a detecting region in said semiconductor structure, said detecting region being adapted to detect a charge representative of a component of said polymer proximate to said detecting region.

24. A method as claimed inclaim 23, wherein:

said component includes a base in a nucleic acid strand; and

said creating step creates said detecting region which is adapted to detect said charge representative of said base in said nucleic acid strand.

25. A method as claimed inclaim 23, further comprising the step of:

creating an opening in said semiconductor structure, said opening having a cross-section sufficient to enable a portion of said polymer to pass therethrough, and being positioned in relation to said detecting region such that said detecting region is adapted to detect said charge representative of said component in said opening.

26. A method as claimed inclaim 25, wherein said opening creating step includes the step of:

forming an insulating layer on a wall of said semiconductor layer forming said opening to decrease said cross-section of said opening.

27. A method as claimed inclaim 23, further comprising the step of:

creating a recess in said semiconductor structure, positioned in relation to said detecting region such that said detecting region is adapted to detect said charge representative of said component in said recess.

28. A method as claimed inclaim 23, further comprising the steps of:

creating at least two doped regions in said semiconductor layer, said doped regions being positioned with respect to said detecting region such that said detecting region is adapted to pass a current between said doped regions in response to said component of said polymer proximate thereto.

29. A method as claimed inclaim 28, wherein:

said doped region creating step creates said doped regions having a first doping such that said doped regions are separated by a portion of said semiconductor layer having a second doping.

30. A method as claimed inclaim 28, wherein:

said doped region creating step creates said doped regions as a stack of doped regions, each having a first doping and being separated by a layer having a second doping.

31. A method as claimed inclaim 28, wherein:

each of said doped regions includes a p-type doping.

32. A method as claimed inclaim 28, wherein:

each of said doped regions includes an n-type doping.

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