1
|
Yoo H, Lee JY, Park KS, Oh SS. Lead-start isothermal polymerase amplification controlled by DNAzymatic switches. NANOSCALE 2022; 14:7828-7836. [PMID: 35583083 DOI: 10.1039/d1nr07894a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As DNA polymerases are even active at ambient temperature, there is inevitable non-specific amplification; to avoid the undesired amplification of analytes, a heat activation-based polymerase chain reaction (PCR), called hot-start PCR, is widely used to be highly precise and quantitative in detection. Unlike thermocycling amplification, isothermal amplification, compatible for point-of-care (PoC) tests, cannot be benefited by the heat-activation technique, making the method qualitative rather than quantitative. In this work, we newly developed a lead ion (Pb2+) activation technique, called lead-start isothermal amplification, allowing on-demand activation or deactivation of DNA polymerases at room temperature. We systematically correlated the DNA polymerase inhibition by the TQ30 aptamer with Pb2+-responsive strand cleavage by the GR5 DNAzyme, and relying on the type of interconnectors, Pb2+ successfully served as an initiator or a terminator of isothermal DNA amplification. Our lead-start isothermal amplification was exceptionally Pb2+-specific, dramatically increasing the enzymatic activity of DNA polymerase (>25 times) only by Pb2+ introduction. Despite one-by-one sample preparation, a number of reactions can begin and end at the same time, sharing the identical amplification conditions, and thereby allowing their quantitative analysis and comparison. Using a portable UV lamp and a smartphone camera, we also succeeded in quantifying the amounts of clinically important and human papillomavirus type 16 genes in human serum and SARS-CoV-2's nucleocapsid genes in human serum and saliva, and the limit of detection was as low as 0.1 nM, highly applicable for actual PoC tests in the field with no purification process.
Collapse
Affiliation(s)
- Hyebin Yoo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea.
| | - Ju Young Lee
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, 44429, South Korea
| | - Ki Soo Park
- Department of Biological Engineering, Konkuk University, Seoul, 05029, South Korea.
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea.
| |
Collapse
|
2
|
Patino Diaz A, Bracaglia S, Ranallo S, Patino T, Porchetta A, Ricci F. Programmable Cell-Free Transcriptional Switches for Antibody Detection. J Am Chem Soc 2022; 144:5820-5826. [PMID: 35316049 PMCID: PMC8990998 DOI: 10.1021/jacs.1c11706] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
We report here the
development of a cell-free in vitro transcription
system for the detection of specific target antibodies.
The approach is based on the use of programmable antigen-conjugated
DNA-based conformational switches that, upon binding to a target antibody,
can trigger the cell-free transcription of a light-up fluorescence-activating
RNA aptamer. The system couples the unique programmability and responsiveness
of DNA-based systems with the specificity and sensitivity offered
by in vitro genetic circuitries and commercially
available transcription kits. We demonstrate that cell-free transcriptional
switches can efficiently measure antibody levels directly in blood
serum. Thanks to the programmable nature of the sensing platform,
the method can be adapted to different antibodies: we demonstrate
here the sensitive, rapid, and cost-effective detection of three different
antibodies and the possible use of this approach for the simultaneous
detection of two antibodies in the same solution.
Collapse
Affiliation(s)
- Aitor Patino Diaz
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Sara Bracaglia
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Simona Ranallo
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Tania Patino
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| |
Collapse
|
3
|
Climent-Catala A, Ouldridge TE, Stan GBV, Bae W. Building an RNA-Based Toggle Switch Using Inhibitory RNA Aptamers. ACS Synth Biol 2022; 11:562-569. [PMID: 35133150 PMCID: PMC9007568 DOI: 10.1021/acssynbio.1c00580] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Synthetic
RNA systems offer unique advantages such as faster response,
increased specificity, and programmability compared to conventional
protein-based networks. Here, we demonstrate an in vitro RNA-based toggle switch using RNA aptamers capable of inhibiting
the transcriptional activity of T7 or SP6 RNA polymerases. The activities
of both polymerases are monitored simultaneously by using Broccoli
and malachite green light-up aptamer systems. In our toggle switch,
a T7 promoter drives the expression of SP6 inhibitory aptamers, and
an SP6 promoter expresses T7 inhibitory aptamers. We show that the
two distinct states originating from the mutual inhibition of aptamers
can be toggled by adding DNA sequences to sequester the RNA inhibitory
aptamers. Finally, we assessed our RNA-based toggle switch in degrading
conditions by introducing controlled degradation of RNAs using a mix
of RNases. Our results demonstrate that the RNA-based toggle switch
could be used as a control element for nucleic acid networks in synthetic
biology applications.
Collapse
Affiliation(s)
- Alicia Climent-Catala
- Imperial College Centre for Synthetic Biology, London, SW7 2AZ, U.K
- Department of Chemistry, Imperial College London, London, SW7 2AZ, U.K
| | - Thomas E. Ouldridge
- Imperial College Centre for Synthetic Biology, London, SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, U.K
| | - Guy-Bart V. Stan
- Imperial College Centre for Synthetic Biology, London, SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, U.K
| | - Wooli Bae
- Imperial College Centre for Synthetic Biology, London, SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, U.K
| |
Collapse
|
4
|
Kim J, Quijano JF, Kim J, Yeung E, Murray RM. Synthetic logic circuits using RNA aptamer against T7 RNA polymerase. Biotechnol J 2021; 17:e2000449. [PMID: 33813787 DOI: 10.1002/biot.202000449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/05/2021] [Accepted: 03/30/2021] [Indexed: 12/23/2022]
Abstract
Recent advances in nucleic acids engineering introduced several RNA-based regulatory components for synthetic gene circuits, expanding the toolsets to engineer organisms. In this work, we designed genetic circuits implementing an RNA aptamer previously described to have the capability of binding to the T7 RNA polymerase and inhibiting its activity in vitro. We first demonstrated the utility of the RNA aptamer in combination with programmable synthetic transcription networks in vitro. As a step to quickly assess the feasibility of aptamer functions in vivo, we tested the aptamer and its sequence variants in the cell-free expression system, verifying the aptamer functionality in the cell-free testbed. The expression of aptamer in E. coli demonstrated control over GFP expression driven by T7 RNA polymerase, indicating its ability to serve as building blocks for logic circuits and transcriptional cascades. This work elucidates the potential of T7 RNA polymerase aptamer as regulators for synthetic biological circuits and metabolic engineering.
Collapse
Affiliation(s)
- Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Juan F Quijano
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Jeongwon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Enoch Yeung
- Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, California, USA.,Department of Mechanical Engineering, University of California, Santa Barbara, California, USA
| | - Richard M Murray
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.,Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, California, USA
| |
Collapse
|
5
|
Cuba Samaniego C, Franco E. Ultrasensitive molecular controllers for quasi-integral feedback. Cell Syst 2021; 12:272-288.e3. [PMID: 33539724 DOI: 10.1016/j.cels.2021.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 09/22/2020] [Accepted: 01/11/2021] [Indexed: 12/24/2022]
Abstract
Feedback control has enabled the success of automated technologies by mitigating the effects of variability, unknown disturbances, and noise. While it is known that biological feedback loops reduce the impact of noise and help shape kinetic responses, many questions remain about how to design molecular integral controllers. Here, we propose a modular strategy to build molecular quasi-integral feedback controllers, which involves following two design principles. The first principle is to utilize an ultrasensitive response, which determines the gain of the controller and influences the steady-state error. The second is to use a tunable threshold of the ultrasensitive response, which determines the equilibrium point of the system. We describe a reaction network, named brink controller, that satisfies these conditions by combining molecular sequestration and an activation/deactivation cycle. With computational models, we examine potential biological implementations of brink controllers, and we illustrate different example applications.
Collapse
Affiliation(s)
- Christian Cuba Samaniego
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Elisa Franco
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA; Bioengineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; Mechanical Engineering, University of California at Riverside, Riverside, CA 92521, USA.
| |
Collapse
|
6
|
Morita Y, Leslie M, Kameyama H, Volk DE, Tanaka T. Aptamer Therapeutics in Cancer: Current and Future. Cancers (Basel) 2018; 10:cancers10030080. [PMID: 29562664 PMCID: PMC5876655 DOI: 10.3390/cancers10030080] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/14/2022] Open
Abstract
Aptamer-related technologies represent a revolutionary advancement in the capacity to rapidly develop new classes of targeting ligands. Structurally distinct RNA and DNA oligonucleotides, aptamers mimic small, protein-binding molecules and exhibit high binding affinity and selectivity. Although their molecular weight is relatively small—approximately one-tenth that of monoclonal antibodies—their complex tertiary folded structures create sufficient recognition surface area for tight interaction with target molecules. Additionally, unlike antibodies, aptamers can be readily chemically synthesized and modified. In addition, aptamers’ long storage period and low immunogenicity are favorable properties for clinical utility. Due to their flexibility of chemical modification, aptamers are conjugated to other chemical entities including chemotherapeutic agents, siRNA, nanoparticles, and solid phase surfaces for therapeutic and diagnostic applications. However, as relatively small sized oligonucleotides, aptamers present several challenges for successful clinical translation. Their short plasma half-lives due to nuclease degradation and rapid renal excretion necessitate further structural modification of aptamers for clinical application. Since the US Food and Drug Administration (FDA) approval of the first aptamer drug, Macugen® (pegaptanib), which treats wet-age-related macular degeneration, several aptamer therapeutics for oncology have followed and shown promise in pre-clinical models as well as clinical trials. This review discusses the advantages and challenges of aptamers and introduces therapeutic aptamers under investigation and in clinical trials for cancer treatments.
Collapse
Affiliation(s)
- Yoshihiro Morita
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - Macall Leslie
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - Hiroyasu Kameyama
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - David E Volk
- McGovern Medical School, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 1825 Hermann Pressler, Houston, TX 77030, USA.
| | - Takemi Tanaka
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
- Department of Pathology, College of Medicine, University of Oklahoma Health Sciences Center, 940 SL Young Blvd, Oklahoma City, OK 73104, USA.
| |
Collapse
|
7
|
Abstract
Life is sustained by a variety of cyclic processes such as cell division, muscle contraction, and neuron firing. The periodic signals powering these processes often direct a variety of other downstream systems, which operate at different time scales and must have the capacity to divide or multiply the period of the master clock. Period modulation is also an important challenge in synthetic molecular systems, where slow and fast components may have to be coordinated simultaneously by a single oscillator whose frequency is often difficult to tune. Circuits that can multiply the period of a clock signal (frequency dividers), such as binary counters and flip-flops, are commonly encountered in electronic systems, but design principles to obtain similar devices in biological systems are still unclear. We take inspiration from the architecture of electronic flip-flops, and we propose to build biomolecular period-doubling networks by combining a bistable switch with negative feedback modules that preprocess the circuit inputs. We identify a network motif and we show it can be "realized" using different biomolecular components; two of the realizations we propose rely on transcriptional gene networks and one on nucleic acid strand displacement systems. We examine the capacity of each realization to perform period-doubling by studying how bistability of the motif is affected by the presence of the input; for this purpose, we employ mathematical tools from algebraic geometry that provide us with valuable insights on the input/output behavior as a function of the realization parameters. We show that transcriptional network realizations operate correctly also in a stochastic regime when processing oscillations from the repressilator, a canonical synthetic in vivo oscillator. Finally, we compare the performance of different realizations in a range of realistic parameters via numerical sensitivity analysis of the period-doubling region, computed with respect to the input period and amplitude. Our mathematical and computational analysis suggests that the motif we propose is generally robust with respect to specific implementation details: functionally equivalent circuits can be built as long as the species-interaction topology is respected. This indicates that experimental construction of the circuit is possible with a variety of components within the rapidly expanding libraries available in synthetic biology.
Collapse
Affiliation(s)
- Christian Cuba Samaniego
- Mechanical Engineering, University of California at Riverside , Riverside, California 92521, United States
| | - Elisa Franco
- Mechanical Engineering, University of California at Riverside , Riverside, California 92521, United States
| |
Collapse
|
8
|
Lloyd J, Tran CH, Wadhwani K, Cuba Samaniego C, Subramanian HKK, Franco E. Dynamic Control of Aptamer-Ligand Activity Using Strand Displacement Reactions. ACS Synth Biol 2018; 7:30-37. [PMID: 29028334 DOI: 10.1021/acssynbio.7b00277] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleic acid aptamers are an expandable toolkit of sensors and regulators. To employ aptamer regulators within nonequilibrium molecular networks, the aptamer-ligand interactions should be tunable over time, so that functions within a given system can be activated or suppressed on demand. This is accomplished through complementary sequences to aptamers, which achieve programmable aptamer-ligand dissociation by displacing the aptamer from the ligand. We demonstrate the effectiveness of our simple approach on light-up aptamers as well as on aptamers inhibiting viral RNA polymerases, dynamically controlling the functionality of the aptamer-ligand complex. Mathematical models allow us to obtain estimates for the aptamer displacement kinetics. Our results suggest that aptamers, paired with their complement, could be used to build dynamic nucleic acid networks with direct control over a variety of aptamer-controllable enzymes and their downstream pathways.
Collapse
Affiliation(s)
- Jonathan Lloyd
- Bioengineering, University of California at Riverside, Riverside, California 92521, United States
| | - Claire H. Tran
- Bioengineering, University of California at Riverside, Riverside, California 92521, United States
| | - Krishen Wadhwani
- Bioengineering, University of California at Riverside, Riverside, California 92521, United States
| | - Christian Cuba Samaniego
- Mechanical
Engineering, University of California at Riverside, Riverside, California 92521, United States
| | - Hari K. K. Subramanian
- Mechanical
Engineering, University of California at Riverside, Riverside, California 92521, United States
| | - Elisa Franco
- Mechanical
Engineering, University of California at Riverside, Riverside, California 92521, United States
| |
Collapse
|
9
|
Cuba Samaniego C, Giordano G, Blanchini F, Franco E. Stability analysis of an artificial biomolecular oscillator with non-cooperative regulatory interactions. JOURNAL OF BIOLOGICAL DYNAMICS 2017; 11:102-120. [PMID: 27830588 DOI: 10.1080/17513758.2016.1245790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Oscillators are essential to fuel autonomous behaviours in molecular systems. Artificial oscillators built with programmable biological molecules such as DNA and RNA are generally easy to build and tune, and can serve as timers for biological computation and regulation. We describe a new artificial nucleic acid biochemical reaction network, and we demonstrate its capacity to exhibit oscillatory solutions. This network can be built in vitro using nucleic acids and three bacteriophage enzymes, and has the potential to be implemented in cells. Numerical simulations suggest that oscillations occur in a realistic range of reaction rates and concentrations.
Collapse
Affiliation(s)
| | - Giulia Giordano
- b Department of Automatic Control and LCCC Linnaeus Center , Lund University , Lund , Sweden
| | - Franco Blanchini
- c Mathematics and Computer Science , University of Udine , Udine , Italy
| | - Elisa Franco
- a Mechanical Engineering , University of California at Riverside , Riverside , CA , USA
| |
Collapse
|
10
|
Cuba Samaniego C, Franco E. An ultrasensitive biomolecular network for robust feedback control. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.ifacol.2017.08.2466] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
11
|
Franco E, Giordano G, Forsberg PO, Murray RM. Negative autoregulation matches production and demand in synthetic transcriptional networks. ACS Synth Biol 2014; 3:589-99. [PMID: 24697805 DOI: 10.1021/sb400157z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a negative feedback architecture that regulates activity of artificial genes, or "genelets", to meet their output downstream demand, achieving robustness with respect to uncertain open-loop output production rates. In particular, we consider the case where the outputs of two genelets interact to form a single assembled product. We show with analysis and experiments that negative autoregulation matches the production and demand of the outputs: the magnitude of the regulatory signal is proportional to the "error" between the circuit output concentration and its actual demand. This two-device system is experimentally implemented using in vitro transcriptional networks, where reactions are systematically designed by optimizing nucleic acid sequences with publicly available software packages. We build a predictive ordinary differential equation (ODE) model that captures the dynamics of the system and can be used to numerically assess the scalability of this architecture to larger sets of interconnected genes. Finally, with numerical simulations we contrast our negative autoregulation scheme with a cross-activation architecture, which is less scalable and results in slower response times.
Collapse
Affiliation(s)
- Elisa Franco
- Mechanical Engineering, University of California at Riverside, Riverside, California 92521, United States
| | - Giulia Giordano
- Mathematics and Computer Science, University of Udine, 33100 Udine, Italy
| | | | - Richard M. Murray
- Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
12
|
Ohuchi S, Mori Y, Nakamura Y. Evolution of an inhibitory RNA aptamer against T7 RNA polymerase. FEBS Open Bio 2012; 2:203-7. [PMID: 23650601 PMCID: PMC3642155 DOI: 10.1016/j.fob.2012.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/06/2012] [Accepted: 07/10/2012] [Indexed: 12/27/2022] Open
Abstract
Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. In this study, we isolated an RNA aptamer that specifically inhibits transcription of T7 RNA polymerase (RNAP). The 38-nucleotide aptamer, which was a shortened variant of an initial SELEX isolate, showed moderate inhibitory activity. By stepwise doped-SELEX, we isolated evolved variants with strong inhibitory activity. A 29-nucleotide variant of a doped-SELEX isolate showed 50% inhibitory concentration at 11 nM under typical in vitro transcription conditions. Pull-down experiments revealed that the aptamer inhibited the association of T7 RNAP with T7 promoter DNA.
Collapse
Affiliation(s)
- Shoji Ohuchi
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | | | | |
Collapse
|