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Fang L, Velema WA, Lee Y, Xiao L, Mohsen MG, Kietrys AM, Kool ET. Pervasive transcriptome interactions of protein-targeted drugs. Nat Chem 2023; 15:1374-1383. [PMID: 37653232 DOI: 10.1038/s41557-023-01309-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 07/27/2023] [Indexed: 09/02/2023]
Abstract
The off-target toxicity of drugs targeted to proteins imparts substantial health and economic costs. Proteome interaction studies can reveal off-target effects with unintended proteins; however, little attention has been paid to intracellular RNAs as potential off-targets that may contribute to toxicity. To begin to assess this, we developed a reactivity-based RNA profiling methodology and applied it to uncover transcriptome interactions of a set of Food and Drug Administration-approved small-molecule drugs in vivo. We show that these protein-targeted drugs pervasively interact with the human transcriptome and can exert unintended biological effects on RNA functions. In addition, we show that many off-target interactions occur at RNA loci associated with protein binding and structural changes, allowing us to generate hypotheses to infer the biological consequences of RNA off-target binding. The results suggest that rigorous characterization of drugs' transcriptome interactions may help assess target specificity and potentially avoid toxicity and clinical failures.
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Affiliation(s)
- Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Willem A Velema
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Yujeong Lee
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Anna M Kietrys
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA.
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2
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Mohsen MG, Breaker RR. In vitro Selection and in vivo Testing of Riboswitch-inspired Aptamers. Bio Protoc 2023; 13:e4775. [PMID: 37456339 PMCID: PMC10338711 DOI: 10.21769/bioprotoc.4775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/18/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023] Open
Abstract
Engineered aptamers for new compounds are typically produced by using in vitro selection methods. However, aptamers that are developed in vitro might not function as expected when introduced into complex cellular environments. One approach that addresses this concern is the design of initial RNA pools for selection that contain structural scaffolds from naturally occurring riboswitch aptamers. Here, we provide guidance on design and experimental principles for developing riboswitch-inspired aptamers for new ligands. The in vitro selection protocol (based on Capture-SELEX) is generalizable to diverse RNA scaffold types and amenable to multiplexing of ligand candidates. We discuss strategies to avoid propagation of selfish sequences that can easily dominate the selection. We also detail the identification of aptamer candidates using next-generation sequencing and bioinformatics, and subsequent biochemical validation of aptamer candidates. Finally, we describe functional testing of aptamer candidates in bacterial cell culture. Key features Develop riboswitch-inspired aptamers for new ligands using in vitro selection. Ligand candidates can be multiplexed to conserve time and resources. Test aptamer candidates in bacterial cells by grafting the aptamer back onto its expression platform.
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Affiliation(s)
- Michael G. Mohsen
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
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3
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Mohsen MG, Midy MK, Balaji A, Breaker R. Exploiting natural riboswitches for aptamer engineering and validation. Nucleic Acids Res 2023; 51:966-981. [PMID: 36617976 PMCID: PMC9881172 DOI: 10.1093/nar/gkac1218] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/04/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Over the past three decades, researchers have found that some engineered aptamers can be made to work well in test tubes but that these same aptamers might fail to function in cells. To help address this problem, we developed the 'Graftamer' approach, an experimental platform that exploits the architecture of a natural riboswitch to enhance in vitro aptamer selection and accelerate in vivo testing. Starting with combinatorial RNA pools that contain structural features of a guanine riboswitch aptamer interspersed with regions of random sequence, we performed multiplexed in vitro selection with a collection of small molecules. This effort yielded aptamers for quinine, guanine, and caffeine that appear to maintain structural features of the natural guanine riboswitch aptamer. Quinine and caffeine aptamers were each grafted onto a natural guanine riboswitch expression platform and reporter gene expression was monitored to determine that these aptamers function in cells. Additionally, we determined the secondary structure features and survival mechanism of a class of RNA sequences that evade the intended selection strategy, providing insight into improving this approach for future efforts. These results demonstrate that the Graftamer strategy described herein represents a convenient and straightforward approach to develop aptamers and validate their in vivo function.
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Affiliation(s)
- Michael G Mohsen
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA,Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
| | - Matthew K Midy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Aparaajita Balaji
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Ronald R Breaker
- To whom correspondence should be addressed. Tel: +1 203 432 9389; Fax: +1 203 432 6161;
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Lee Y, Onishi Y, McPherson L, Kietrys AM, Hebenbrock M, Jun YW, Das I, Adimoolam S, Ji D, Mohsen MG, Ford JM, Kool ET. Enhancing Repair of Oxidative DNA Damage with Small-Molecule Activators of MTH1. ACS Chem Biol 2022; 17:2074-2087. [PMID: 35830623 DOI: 10.1021/acschembio.2c00038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Impaired DNA repair activity has been shown to greatly increase rates of cancer clinically. It has been hypothesized that upregulating repair activity in susceptible individuals may be a useful strategy for inhibiting tumorigenesis. Here, we report that selected tyrosine kinase (TK) inhibitors including nilotinib, employed clinically in the treatment of chronic myeloid leukemia, are activators of the repair enzyme Human MutT Homolog 1 (MTH1). MTH1 cleanses the oxidatively damaged cellular nucleotide pool by hydrolyzing the oxidized nucleotide 8-oxo-2'-deoxyguanosine (8-oxo-dG)TP, which is a highly mutagenic lesion when incorporated into DNA. Structural optimization of analogues of TK inhibitors resulted in compounds such as SU0448, which induces 1000 ± 100% activation of MTH1 at 10 μM and 410 ± 60% at 5 μM. The compounds are found to increase the activity of the endogenous enzyme, and at least one (SU0448) decreases levels of 8-oxo-dG in cellular DNA. The results suggest the possibility of using MTH1 activators to decrease the frequency of mutagenic nucleotides entering DNA, which may be a promising strategy to suppress tumorigenesis in individuals with elevated cancer risks.
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Affiliation(s)
- Yujeong Lee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yoshiyuki Onishi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Lisa McPherson
- Department of Medicine, Stanford University, Stanford, California 94305, United States
| | - Anna M Kietrys
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Marian Hebenbrock
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yong Woong Jun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ishani Das
- Department of Medicine, Stanford University, Stanford, California 94305, United States
| | - Shanthi Adimoolam
- Department of Medicine, Stanford University, Stanford, California 94305, United States
| | - Debin Ji
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael G Mohsen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - James M Ford
- Department of Medicine, Stanford University, Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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Mohsen MG, Ji D, Kool ET. Polymerase synthesis of four-base DNA from two stable dimeric nucleotides. Nucleic Acids Res 2019; 47:9495-9501. [PMID: 31504784 PMCID: PMC6765132 DOI: 10.1093/nar/gkz741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/12/2019] [Accepted: 08/16/2019] [Indexed: 11/25/2022] Open
Abstract
We document the preparation and properties of dimerized pentaphosphate-bridged deoxynucleotides (dicaptides) that contain reactive components of two different nucleotides simultaneously. Importantly, dicaptides are found to be considerably more stable to hydrolysis than standard dNTPs. Steady-state kinetics studies show that the dimers exhibit reasonably good efficiency with the Klenow fragment of DNA polymerase I, and we identify thermostable enzymes that process them efficiently at high temperature. Experiments show that the dAp5dT dimer successfully acts as a combination of dATP and dTTP in primer extension reactions, and the dGp5dC dimer as a combination of dGTP and dCTP. The two dimers in combination promote successful 4-base primer extension. The final byproduct of the reaction, triphosphate, is shown to be less inhibitory to primer extension than pyrophosphate, the canonical byproduct. Finally, we document PCR amplification of DNA with two dimeric nucleotides, and show that the dimers can promote amplification under extended conditions when PCR with normal dNTPs fails. These dimeric nucleotides represent a novel and simple approach for increasing stability of nucleotides and avoiding inhibition from pyrophosphate.
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Affiliation(s)
- Michael G Mohsen
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Debin Ji
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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McPherson LA, Troccoli CI, Ji D, Bowles AE, Gardiner ML, Mohsen MG, Nagathihalli NS, Nguyen DM, Robbins DJ, Merchant NB, Kool ET, Rai P, Ford JM. Increased MTH1-specific 8-oxodGTPase activity is a hallmark of cancer in colon, lung and pancreatic tissue. DNA Repair (Amst) 2019; 83:102644. [PMID: 31311767 DOI: 10.1016/j.dnarep.2019.102644] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/24/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022]
Abstract
Cellular homeostasis is dependent on a balance between DNA damage and DNA repair mechanisms. Cells are constantly assaulted by both exogenous and endogenous stimuli leading to high levels of reactive oxygen species (ROS) that cause oxidation of the nucleotide dGTP to 8-oxodGTP. If this base is incorporated into DNA and goes unrepaired, it can result in G > T transversions, leading to genomic DNA damage. MutT Homolog 1 (MTH1) is a nucleoside diphosphate X (Nudix) pyrophosphatase that can remove 8-oxodGTP from the nucleotide pool before it is incorporated into DNA by hydrolyzing it into 8-oxodGMP. MTH1 expression has been shown to be elevated in many cancer cells and is thought to be a survival mechanism by which a cancer cell can stave off the effects of high ROS that can result in cell senescence or death. It has recently become a target of interest in cancer because it is thought that inhibiting MTH1 can increase genotoxic damage and cytotoxicity. Determining the role of MTH1 in normal and cancer cells is confounded by an inability to reliably and directly measure its native enzymatic activity. We have used the chimeric ATP-releasing guanine-oxidized (ARGO) probe that combines 8-oxodGTP and ATP to measure MTH1 enzymatic activity in colorectal cancer (CRC), non-small cell lung cancer (NSCLC) and pancreatic ductal adenocarcinoma (PDAC) along with patient-matched normal tissue. MTH1 8-oxodGTPase activity is significantly increased in tumors across all three tissue types, indicating that MTH1 is a marker of cancer. MTH1 activity measured by ARGO assay was compared to mRNA and protein expression measured by RT-qPCR and Western blot in the CRC tissue pairs, revealing a positive correlation between ARGO assay and Western blot, but little correlation with RT-qPCR in these samples. The adoption of the ARGO assay will help in establishing the level of MTH1 activity in model systems and in assessing the effects of MTH1 modulation in the treatment of cancer.
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Affiliation(s)
- Lisa A McPherson
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305-5151, United States
| | - Clara I Troccoli
- Department of Medicine/Division of Medical Oncology, University of Miami Miller School of Medicine, Miami, FL 33136, United States; Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Debin Ji
- Department of Chemistry, Stanford University, Stanford, CA 94305-4401, United States
| | - Annie E Bowles
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305-5151, United States
| | - Makelle L Gardiner
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305-5151, United States
| | - Michael G Mohsen
- Department of Chemistry, Stanford University, Stanford, CA 94305-4401, United States
| | - Nagaraj S Nagathihalli
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, United States; Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Dao M Nguyen
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, United States; Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - David J Robbins
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, United States; Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Nipun B Merchant
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, United States; Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305-4401, United States
| | - Priyamvada Rai
- Department of Medicine/Division of Medical Oncology, University of Miami Miller School of Medicine, Miami, FL 33136, United States; Sylvester Comprehensive Cancer Center, Miami, FL 33136, United States.
| | - James M Ford
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305-5151, United States.
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Mohsen MG, Ji D, Kool ET. Polymerase-amplified release of ATP (POLARA) for detecting single nucleotide variants in RNA and DNA. Chem Sci 2019; 10:3264-3270. [PMID: 30996911 PMCID: PMC6429602 DOI: 10.1039/c8sc03901a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/30/2019] [Indexed: 01/13/2023] Open
Abstract
The identification of single nucleotide polymorphisms (SNP) is increasingly important for diagnosis and treatment of disease. Here we studied the potential use of ATP-releasing nucleotides (ARNs) for identifying SNPs in DNA and RNA targets. Synthesized as derivatives of the four canonical deoxynucleotides, ARNs can be used in the place of deoxynucleoside triphosphates to elongate a primer hybridized to a nucleic acid template, with the leaving group being ATP rather than pyrophosphate. The released ATP is then harnessed in conjunction with luciferase to generate chemiluminescence. Extension on a long target DNA or RNA generates many equivalents of ATP per target strand, providing isothermal amplification of signal. In principle, allele-specific primers could be used in conjunction with ARNs to generate differential luminescence signals with respect to distinct genetic polymorphisms. To test this, varied primer designs, modifications, enzymes and conditions were tested, resulting in an optimized strategy that discriminates between differing nucleic acid templates with single nucleotide resolution. This strategy was then applied to diagnostically relevant alleles resulting in discrimination between known polymorphisms. SNP detection was successfully performed on transcribed mRNA fragments from four different alleles derived from JAK2, BCR-ABL1, BRAF, and HBB. To investigate background interference, wild-type and mutant transcripts of these four alleles were tested and found to be easily distinguishable amid total cellular RNA isolated from human blood. Thus, ARNs have been employed with specialized allele-specific primers to detect diagnostically important SNPs in a novel method that is sensitive, rapid, and isothermal.
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Affiliation(s)
- Michael G Mohsen
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Debin Ji
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Eric T Kool
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
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Abstract
Nucleic acid amplification is a hugely important technology for biology and medicine. While the polymerase chain reaction (PCR) has been highly useful and effective, its reliance on heating and cooling cycles places some constraints on its utility. For example, the heating step of PCR can destroy biological molecules under investigation and heat/cool cycles are not applicable in living systems. Thus, isothermal approaches to DNA and RNA amplification are under widespread study. Perhaps the simplest of these are the rolling circle approaches, including rolling circle amplification (RCA) and rolling circle transcription (RCT). In this strategy, a very small circular oligonucleotide (e.g., 25-100 nucleotides in length) acts as a template for a DNA or an RNA polymerase, producing long repeating product strands that serve as amplified copies of the circle sequence. Here we describe the early developments and studies involving circular oligonucleotides that ultimately led to the burgeoning rolling circle technologies currently under development. This Account starts with our studies on the design of circular oligonucleotides as novel DNA- and RNA-binding motifs. We describe how we developed chemical and biochemical strategies for synthesis of well-defined circular oligonucleotides having defined sequence and open (unpaired) structure, and we outline the unusual ways in which circular DNAs can interact with other nucleic acids. We proceed next to the discovery of DNA and RNA polymerase activity on these very small cyclic DNAs. DNA polymerase "rolling circle" activities were discovered concurrently in our laboratory and that of Andrew Fire. We describe the surprising efficiency of this process even on shockingly small circular DNAs, producing repeating DNAs thousands of nucleotides in length. RNA polymerase activity on circular oligonucleotides was first documented in our group in 1995; especially surprising in this case was the finding that the process occurs efficiently even without promoter sequences in the circle. We describe how one can encode cleavable sites into the product DNAs and RNAs from RCA/RCT, which can then be resolved into large quantities of almost pure oligonucleotides. Our Account then proceeds with a summary describing a broad variety of tools and methods built in many laboratories around the rolling circle concept. Among the important developments are the discovery of highly efficient DNA polymerases for RCA; the invention of exponential ("hyperbranched") RCA amplification made possible by use of a second primer; the development of the "padlock" process for detection of nucleic acids and proteins coupled with RCA; the use of circular oligonucleotides as vectors in cells to encode biologically active RNAs via RCT; and the use of small DNA circles to encode and extend human telomeres. Finally, we finish with some ideas about where the field may go in the future.
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Affiliation(s)
- Michael G Mohsen
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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9
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Affiliation(s)
- Debin Ji
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | | | | | - Eric T. Kool
- Department of Chemistry Stanford University Stanford CA 94305 USA
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Ji D, Mohsen MG, Harcourt EM, Kool ET. ATP-Releasing Nucleotides: Linking DNA Synthesis to Luciferase Signaling. Angew Chem Int Ed Engl 2016; 55:2087-91. [PMID: 26836342 DOI: 10.1002/anie.201509131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/20/2015] [Indexed: 12/13/2022]
Abstract
A new strategy is reported for the production of luminescence signals from DNA synthesis through the use of chimeric nucleoside tetraphosphate dimers in which ATP, rather than pyrophosphate, is the leaving group. ATP-releasing nucleotides (ARNs) were synthesized as derivatives of the four canonical nucleotides. All four derivatives are good substrates for DNA polymerase, with Km values averaging 13-fold higher than those of natural dNTPs, and kcat values within 1.5-fold of those of native nucleotides. Importantly, ARNs were found to yield very little background signal with luciferase. DNA synthesis experiments show that the ATP byproduct can be harnessed to elicit a chemiluminescence signal in the presence of luciferase. When using a polymerase together with the chimeric nucleotides, target DNAs/RNAs trigger the release of stoichiometrically large quantities of ATP, thereby allowing sensitive isothermal luminescence detection of nucleic acids as diverse as phage DNAs and short miRNAs.
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Affiliation(s)
- Debin Ji
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Michael G Mohsen
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Emily M Harcourt
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
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