WO2008141279A1

WO2008141279A1 - System and method for displaying output of a computation performed by dna logic

Info

Publication number: WO2008141279A1
Application number: PCT/US2008/063414
Authority: WO
Inventors: Joanne Macdonald; Andrew Macdonald; Milan Stojanovic
Original assignee: The Trustees Of Columbia University In The City Of New York
Priority date: 2007-05-11
Filing date: 2008-05-12
Publication date: 2008-11-20

Abstract

Systems and methods for displaying output of a computation performed by DNA logic are provided. Methods include receiving one or more DNA computation inputs, performing at least one computation on the one or more received DNA computation inputs using DNA logic to generate a DNA computation output, and displaying the DNA computation output in a human readable form.

Description

SYSTEM AND METHOD FOR DISPLAYING OUTPUT OF A COMPUTATION PERFORMED BY DNA LOGIC

SPECIFICATION

CROSS REFERENCE TO RELATED APPLICATION

This application claims priority from United States Provisional Patent Application 60/928,705, filed on May 11, 2007, the entire disclosure of which is explicitly incorporated by reference herein.

STATEMENTREGARDINGFEDERALLY SPONSORED RESEARCH

This invention was made with government support under grants HS- 0324845, CCF-0523317, and CHE-0533065 awarded by the National Science Foundation (NSF). The government has certain rights in the invention.

BACKGROUND

Field. The present application relates to techniques for visually displaying the results of computation using DNA logic.

Background Art. Advances in nucleic acid computation over the last decade have shown the potential of these devices for novel computational paradigms in biocompatible contexts. For example, as disclosed by Adelman, nucleic acids have been utilized to solve a directed Hamiltonian Path problem using an array of molecular biological tools such as polymerase chain reaction, ligation, and affinity purification. L.M. Adelman, Molecular computation of solutions to combinatorial problems, 266 Science 1021 (Nov. 11, 1994). To display the results of Hamiltonian Path experiment, the end-user views a gel electrophoresis image and visually compares the resulting band sizes to a set of standards. A similar technique, of interpreting gel electrophoresis images, is used to create programmable finite automaton. Some displays use fluorescence resonance energy transfer (FRET) output detection systems, which take advantage of fluorescence readers and subsequently analyze that data via traditional electronic methods. In using FRET, there exists an upper limit to the number of fluorophore and quencher combinations that can be implemented with deoxyribozyme logic.

SUMMARY Systems and methods for displaying output of a computation performed by DNA logic are disclosed herein.

In some embodiments, methods for displaying output of a computation performed by DNA logic include receiving one or more DNA computation inputs, performing at least one computation on the one or more received DNA computation inputs using DNA logic to generate a DNA computation output, and displaying the DNA computation output in a human readable form. In other embodiments, displaying the DNA computation output in a human readable form includes displaying the DNA computation output in an N-segment display, where N can be seven. In other embodiments, displaying the DNA computation output in human readable form includes displaying the DNA computation output in an X by Y dot matrix, where X can be 5 and Y can be 3. The DNA computation output can include a four-bit value.

In some embodiments of the methods for displaying output of a computation performed by DNA logic, the human readable form includes a plurality of reservoirs, the reservoirs containing at least one DNA logic reagent that is responsive to the DNA computation output. In some embodiments, the DNA logic reagents include a fluorescent substrate and a buffer. In other embodiments, the DNA logic reagents include enzyme-free DNA logic gates.

In some embodiments, a DNA computation input can be a test sample. The test sample can be compared to a predetermined value, for example a flavivirus, and a predetermine glyph can be displayed if the test sample matches the predetermined value.

In some embodiments, systems for displaying output of a computation performed by DNA logic include a receptor for receiving one or more DNA computation inputs, DNA logic for performing at least one computation on the one or more received DNA computation inputs to generate a DNA computation output, and a display unit for displaying the DNA computation output in a human readable form. In some embodiments the display unit includes an N-segment display, where N can be 7. The DNA computation output can be a four-bit value.

The accompanying drawings, which are incorporated and constitute part of this disclosure, illustrate preferred embodiments of the invention and serve to explain the principles of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a diagram of a method implemented in accordance with some embodiments of the disclosed subject matter; FIG. 2 is a diagram illustrating various examples of human readable displays in accordance with some embodiments of the disclosed subject matter;

FIG. 3 is a table illustrating four-bit binary representations of integers in accordance with some embodiments of the disclosed subject matter;

FIG. 4 is a table illustrating a two-bit add operation in accordance with some embodiments of the disclosed subject matter;

FIG. 5 is a table illustrating a two-bit multiplication operation in accordance with some embodiments of the disclosed subject matter;

FIG. 6 is a functional diagram of an example Display Output method from Fig. 1 , using a seven-segment display, in accordance with some embodiments of the disclosed subject matter;

FIG. 7 is a functional diagram of an example Display Output method from Fig. 1, using a 3x5 dot matrix, in accordance with some embodiments of the disclosed subject matter; and

FIG. 8 is a diagram of a method implemented in accordance with some embodiments of the disclosed subject matter.

Throughout the drawings, the same reference numerals and characters, unless otherwise stated, are used to denote like features, elements, components or portions of the illustrated embodiments. Moreover, while the present invention will now be described in detail with reference to the Figs., it is done so in connection with the illustrative embodiments. DETAILED DESCRIPTION

An improved system and method for visually representing the results of computations performed using DNA logic is presented. The methods and systems disclosed utilize silicomimetic techniques to visualize data and computations resulting from the application of DNA logic.

Traditional output events in electronic computing can be applied to DNA computation output decoding. Some simple electronic output displays, which can display digits or alphanumeric characters, are known as segment displays because they are composed of several segments that switch on to give the appearance of a desired glyph. In some electronic formats, the segments can be built using light emitting diodes (LEDs) or liquid crystals. These segment displays are commonly found in seven, fourteen, or sixteen segments versions, although other versions can be used. Fig. 2 illustrates a common example of the seven-segment display 200.

The seven-segment display 200, can be used to produce simplified representations of Arabic numerals and letters of the Latin, Cyrillic, Greek, or other alphabets. Dot- matrix displays, as illustrated in Fig. 2 in the 3x5 dot matrix 210, are also widely used to display text or other graphics. Referring to Fig. 1, a method for displaying output of a computation performed using DNA logic in accordance with an embodiment of the disclosed subject matter will be explained. The method includes receiving DNA computation inputs 101, performing a computation 102 on those received DNA computation inputs, and displaying the DNA computation output 103 from the computation 102. In one embodiment, the DNA computation inputs can be segments of DNA which represent mathematical or arithmetic calculation parameters. The DNA computation inputs can be representative of one or more N-bit values and a command to perform a mathematical operation, where N can be a value, such as two, and the command can be to perform a mathematical operation such as addition, subtraction, multiplication, or division, but not limited to those examples. Moreover, the DNA computation inputs can be representative of one or more N-bit values, whereby the operation to be performed is predetermined and N can be a value, such as two. In other embodiments, the DNA computation inputs can be a biological or molecular sample. In some embodiments, the biological sample can be a biologically-derived nucleic acid, such as a PCR-amplifϊed influenza virus genome, proteins, peptides, analytes and small molecules and aptamers. In some embodiments methods and means of receiving DNA computation inputs include, but are not limited to, collecting isolated DNA, tissues, cell cultures, blood serum, urine samples, environmental samples, or even crushed mosquitoes.

In one embodiment, the computation 102 takes the one or more DNA computation inputs and forwards those one or more DNA computation inputs to the display 103. In other embodiments, the computation 102 takes the DNA computation inputs and performs a computation or operation desired using DNA logic, producing DNA computation output 601. DNA logic can be the application of known DNA logic gates. Some techniques for DNA computation include those described in U.S. Patent Application Publication No. 2004/0070426 to Stojanovic (hereinafter "Stojanovic"), which is incorporated by reference.

The DNA logic gates can be either enzyme-based logic gates (such as deoxyribozyme-based gates), or enzyme-free logic gates. The use of enzyme-free logic gates can decrease the time needed for the visualization of the DNA computation output. The desired computation can be a mathematical operation such as, but not limited to, addition, multiplication, subtraction, or division. The computation 102 can also involve the identification of a specific biological or molecular sample. Moreover, the computation 102 can include the chaining, or cascading, together of multiple mathematical, computational, or identification operations, such as, but not limited to, performing one addition operation, followed by performing a multiplication operation on the output of the addition operation.

The DNA computation output 601 can represent either a single specific value, such as an integer, or can represent a plurality of values. In some embodiments, the DNA computation output can represent an N-bit value, wherein N can be four. Fig. 3 illustrates, in accordance with an embodiment of the disclosed subject matter, a table of possible four-bit values and their integer equivalents. For instance, the four-bit value "0001," as in row 301, represents the integer value "1," while the four-bit value "0111," as in row 307, represents the integer value "7." Binary numbers are known in the art. Moreover, the DNA computation output can represent a pattern, a character value, such as, but not limited to, a letter of the Latin, Cyrillic, Greek, or other alphabet, or other displayable data.

Fig. 4 illustrates an embodiment, in accordance with the disclosed subject matter, where the DNA computation inputs represent two two-bit values and those values are added together, producing a DNA computation output 401 that represents a four-bit value. For example, in row 412, where the first input 401 is the two-bit value "01" and the second input 402 is the two-bit value "10," the output 403 is the four-bit value "0011" or the integer value "3." Fig. 5 illustrates an embodiment, in accordance with the disclosed subject matter, where the DNA computation inputs represent two-bit values and those values are multiplied together, producing DNA computation output that represents a four-bit value. For example, in row 517, where the first input 501 is the two-bit value "10" and the second input 502 is the two-bit value "11," the output 503 is the four-bit value "0110" or the integer value "6."

In some embodiments according to the disclosed subject matter, the display DNA computation output 103 takes the DNA computation output and displays 103 the information represented by the DNA computation output on an N-segment display. The N-segment display is not limited in the number of segments it can have, but, as described above, these displays typically are composed of seven, fourteen, or sixteen segment versions. According to some embodiments, a seven-segment display 200, as illustrated in Fig. 2, can be used to display the information represented by the DNA computation output. The seven-segment display 200 has seven portions which can be turned "on" or "off independently. For instance, to display the number "1," the segments labeled 202 and 203 can be turned on, while the remaining segments, 201 , 204, 205, 206, and 207 remain off. Some implementations can require the on/off state of the segments to be swapped.

Fig. 6 represents an embodiment according the disclosed subject matter where DNA computation output 601 is received from the computation 102. The DNA computation output 601 is considered 602 and the segments of a seven-segment display 200, are turned "on" accordingly. For example, if the DNA computation output 601 is equal to the four-bit value "0101," or the integer "5," then that condition 607 will cause segments 201, 206, 207, 203, and 204 to be turned "on" and the remaining segments, 202 and 205, to be turned or left "off." Similarly, if the DNA computation output 601 is equal to the four-bit value "0111," or the integer "7," then that condition 609, will cause segments 201, 202, and 203 to be turned "on" and the remaining segments, 206, 207, 205, and 204 to be turned or left "off."

In other embodiments, the DNA computation output can be displayed in a dot matrix, an illustration of which is shown in the 3x5 dot matrix 210 in Fig. 2. A dot matrix can have a plurality of dots, the state of which can be altered. Fig. 7 illustrates an embodiment, in accordance with the disclosed subject matter, where DNA computation output 601 is received from the computation 102. The DNA computation output is considered 602 and the appropriate dots of the dot matrix display 210 are turned "on." For example, if the DNA computation output 601 is equal to a representation of the character "A," then that condition 703 will cause dots 212, 214, 216, 217, 218, 219, 220, 222, 223, and 225 to be turned "on" and the remaining segments, 211, 213, 215, 221, and 224 are turned or left "off." Similarly, if the DNA computation output 601 is equal to a representation of the character "B," then that condition 705 will cause dots 211, 212, 214, 216, 217, 218, 220, 222, 223, and 224 to be turned "on" and the remaining segments, 213 , 215 , 219, 221 , and 225 to be turned or left "off." The potential characters, numbers, symbols, or patterns that can be displayed by a dot matrix display are not limited to those shown in Fig. 7.

Whether a segment in an N-segment display, or a dot in a dot-matrix display, is "on" or "off is relative to the "on/off state of the other dots and no definition of what specifically constitutes "on" or "off is here asserted. Moreover, while the state of a particular dot is here referred to as "on" or "off," the states of the dots need not be binary. That is, in some embodiments, the dots of a dot matrix, and the segments of an N-segment display, can be displayed with varying degrees of brightness, contrast, clarity, color, or other visible or distinguishable characteristics to display information.

In some embodiments of the disclosed subject matter, the segments of an N-segment display or the dots of a dot matrix display can be formed by wells or reservoirs. These wells or reservoirs can be indentations, buckets, cavities, containers, or other defined spaces in an organized pattern. The wells or reservoirs can contain DNA logic reagents that are responsive to, or exhibit a detectable change when in contact with, the DNA computation outputs 601. In other embodiments, the DNA logic reagents can be responsive to a specific biological or molecular input.

In some embodiments, the DNA logic reagents can be one of a plurality of DNA logic gates. When the DNA logic reagents are one of a plurality of DNA logic gates, the introduction of corresponding biological material, such as one or more oligonucleotides, can result in the fluorescence, or colorimetric response, of specific wells or reservoirs. This fluorescence, or colorimetric response, can be an "on" state of the segment or dot of a display. In some embodiments, a fluorescence plate-reader can be used to visualize the fluorescence state of the individual wells or reservoirs.

In another embodiment, the wells or reservoirs can have clear bottoms. In this embodiment, and others, a UV-light box can be used to display the different states of the DNA logic reagents in the wells or reservoirs. In an embodiment using Tetramethyl rhodamine (TAMRA) fluorescence can be seen as a pink color. In another embodiment using Fluorescein, fluorescence can be seen as a green color.

In another embodiment the segments of the N-segment display, or dots of the dot matrix display, can be formed by application of the DNA logic reagents to a textile in a defined pattern. One possible application of this embodiment is the textual or visual display of complex information about a medical or environmental test in an easily useable format.

In some embodiments, the disclosed system can be cascaded with an upstream event where an oligonucleotide is created or destroyed, such as genomic DNA detection via polymerase chain reaction. Such cascading can be used for, but is not limited to, applications in urine analysis, such a pregnancy test, pathogen detection, or genetic disease detection. In other embodiments, by using aptamer technologies, proteins, peptides, small molecules, and analytes can be cascaded or chained into the input 101. One application of the aptamer technologies with regard to the disclosed subject matter is the detection of environmental conditions. In some embodiments according to the disclosed subject matter, inputting 101 can input a genetic component, the computation 102 can identify a specific virus such as West Nile, Yellow Fever, Dengue, or another biological target and the displaying 103 can display a recognizable figure to signify the identity of the virus or biological target. For example, the reservoirs can be arranged in such a pattern that a "1" is displayed upon detection of West Nile virus, a "2" is displayed upon the detection of Yellow Fever, a "3" is displayed upon detection of Dengue, etc. In other embodiments, the DNA logic can be implemented through the use of spiegelmeric analogs of ribozymes and attendant ribonucleic catalysts. By applying the technology of spiegelmers, the disclosed subject matter can be capable of detection in situations where deoxyribozyme substrates might normally be degraded by the presence of RNAses. This is particularly relevant in lieu of environmental sampling described above.

In other embodiments, gold nanoparticles can be used in the output 103 as a way to visualize the output of the computation 102 without the need for intervening equipment such as a UV-light box. In this enzyme-free approach, gold nanoparticles can be attached to nucleic acids such that a DNA output would cause aggregation of the nanoparticles, leading to the formation of a color, visible without the aid of intervening equipment. In one preferred embodiment, preparation 800 can begin with pre- purification of oligonucleotide gates and inputs from Integrated DNA technologies (IDT, Coralville, IA) using polyacrylamide gel electrophoresis (PAGE) purification or standard desalting respectively 801. Oligonucleotides can be resuspended with sterile DEPC-treated water 802 to 10-1000 μM (gates) and 1-10 mM (inputs). Fluorescent- labeled substrates from TriLink BioTechnologies (San Diego, CA) can be pre-labeled with fluorophore/quencher combinations of Tetramethylrhodamine (T AMRA)/B lack- Hole 2 (BH2) or Fluorescein (F)/Black Hole 1 (BHl) 803, double-HPLC purified, and resuspended with sterile DEPC-treated water 804 to 250-1000 μM. Then, 10-500 nM gates and 50-2500 nM complementary oligonucleotides can be mixed with 1-10 uM substrates in Ix buffer 805 (50 mM HEPES, pH 7.0; 1 M NaCl; 1 mM ZnC12).

Mixtures (12.5-100 μL) can be placed into individual wells of a black 96-1536-well microtiter plate with clear well bottoms, and inputs (.25-5 μL) can be added to a final concentration of .1-5 μM 806. Fluorescence activity can be monitored every 3-60 minutes for 1-24 hours using an Envision 2101 multilabel reader (PerkinElmer Instruments, Shelton, CT) using 5% excitation light, 50% gain, and filters: λex = 485 ± 14 nm, λem - 535 ± 25 nm for fluorescein fluorescence; and λex = 535 ± 25 nm, λem = 595 ± 60 nm for TAMRA fluorescence 807. Fluorescence can also be observed visually by placing the plates over a UV-emitting light box, at various time intervals, and subsequent digital photography. In some embodiments, the computation 102 and displaying 103 can be performed at the same, or near the same time. In further embodiments, the computation 102 and displaying 103 can be performed in the same medium, such as, but not limited to, within a reservoir or well. In some embodiments, predictive oligonucleotide interaction models and design libraries can be used to design logic gate structures without the need of complete laboratory implementation. For example, a circuit design program for DNA calculators can consider the criteria for which calculations are required, determine the minimal number of gates with unique solutions for a particular segment, and combine gates iteratively until a solution is reached. Such an iterative technique can predict a simpler set of logic gates than that designed using other known techniques. Further, predictive oligonucleotide interaction models and design libraries can anticipate higher-level logic functions not yet developed in molecular logic gate forms. Such anticipated higher-level logic functions can be used to design new paths for molecular logic gate design, either through the development of alternative logic calculations not currently available, an increase in the number of input recognition regions controlling an individual gate, or through the implementation of cascading logic.

Predictive oligonucleotide interaction models and design libraries can be implemented in software stored on computer readable storage media, such as a hard disk, flash disk, magnetic tape, optical disk, network drive, or other computer readable medium. The software can be performed by a processor capable of reading the stored software and carrying out the instructions therein.

The foregoing merely illustrates the principles of the disclosed subject matter. Various modifications and alterations to the described embodiments will be apparent to those skilled in the art in view of the teachings herein. It will thus be appreciated that those skilled in the art will be able to devise numerous techniques which, although not explicitly described herein, embody the principles of the disclosed subject matter and are thus within the spirit and scope of the invention.

Claims

1. A method for displaying output of a computation performed by DNA logic, comprising:

receiving one or more DNA computation inputs;

performing at least one computation on said one or more received DNA computation inputs using said DNA logic to generate a DNA computation output; and

displaying said DNA computation output in a human readable form.

2. The method of claim 1 , wherein said displaying said DNA computation output in a human readable form comprises displaying said DNA computation output in an

N-segment display.

3. The method of claim 2, wherein N is seven.

4. The method of claim 1, wherein said displaying said DNA computation output in a human readable form comprises displaying said DNA computation output in an X by Y dot matrix.

5. The method of claim 4, wherein X is 5 and Y is 3.

6. The method of claim 1, wherein said DNA computation output comprises a four-bit value.

7. The method of claim 1, wherein said human readable form comprises a plurality of reservoirs, said reservoirs containing at least one DNA logic reagent that is responsive to said DNA computation output.

8. The method of claim 7, wherein said at least one DNA logic reagent comprises a fluorescent substrate and a buffer.

9. The method of claim 7, wherein said at least one DNA logic reagent comprises a non-enzymatic DNA logic gate.

10. The method of claim 1 , wherein said DNA computation input is a test sample.

11. The method of claim 10, wherein performing at least one computation comprises determining whether said test sample matches at least one predetermined value.

12. The method of claim 11 wherein said at least one predetermined value is a flavivirus.

13. The method of claim 11, wherein displaying said DNA computation output in a human readable form comprises displaying a predetermined glyph if said test sample matches said at least one predetermined value.

14. A system for displaying output of a computation performed by DNA logic, comprising:

means for receiving one or more DNA computation inputs;

means, coupled to said receiving means, for performing at least one computation on said one or more received DNA computation inputs using said DNA logic to generate a DNA computation output; and

a display unit, coupled to said computation means and receiving said DNA computation output therefrom, for displaying said DNA computation output in a human readable form.

15. The system of claim 14, wherein said display unit comprises an N-segment display.

16. The system of claim 15, wherein N is seven.

17. The system of claim 14, wherein said display unit comprises an X by Y dot matrix.

18. The system of claim 17, wherein X is 5 and Y is 3.

19. The system of claim 14, wherein said DNA computation output comprises a four-bit value.

20. The system of claim 14, wherein said human readable form comprises a plurality of reservoirs, said reservoirs containing at least one DNA logic reagent that is responsive to said DNA computation output.

21. The system of claim 20, wherein said at least one DNA logic reagent comprises a fluorescent substrate and a buffer.

22. The system of claim 20, wherein said at least one DNA logic reagent comprises a non-enzymatic DNA logic gate.

23. The system of claim 14, wherein said DNA computation input is a test sample.

24. The method of claim 23, wherein performing at least one computation comprises determining whether said test sample matches at least one predetermined value.

25. The method of claim 24 wherein said at least one predetermined value is a flavi virus.

26. The method of claim 24, wherein displaying said DNA computation output in a human readable form comprises displaying a predetermined glyph if said test sample matches said at least one predetermined value.

27. A system for displaying output of a computation performed by DNA logic, comprising:

a receiver for receiving one or more DNA computation inputs;

DNA logic, coupled to said receiver, for performing at least one computation on said one or more received DNA computation inputs to generate a DNA computation output; and

a display unit, coupled to and receiving said DNA computation output from said DNA logic, for displaying said DNA computation output in a human readable form.

28. The system of claim 27, wherein said DNA logic and said display unit are integrated.