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Lelyveld VS, Fang Z, Szostak JW. Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity. Science 2023; 382:423-429. [PMID: 37883544 PMCID: PMC10886449 DOI: 10.1126/science.adh5339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
A DNA polymerase with a single mutation and a divalent calcium cofactor catalyzes the synthesis of unnatural N3'→P5' phosphoramidate (NP) bonds to form NP-DNA. However, this template-directed phosphoryl transfer activity remains orders of magnitude slower than native phosphodiester synthesis. Here, we used time-resolved x-ray crystallography to show that NP-DNA synthesis proceeds with a single detectable calcium ion in the active site. Using insights from isotopic and elemental effects, we propose that one-metal-ion electrophilic substrate activation is inferior to the native two-metal-ion mechanism. We found that this deficiency in divalent activation could be ameliorated by trivalent rare earth and post-transition metal cations, substantially enhancing NP-DNA synthesis. Scandium(III), in particular, confers highly specific NP activity with kinetics enhanced by more than 100-fold over calcium(II), yielding NP-DNA strands up to 100 nucleotides in length.
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Affiliation(s)
- Victor S Lelyveld
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ziyuan Fang
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Jack W Szostak
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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2
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Aggarwal T, Hansen WA, Hong J, Ganguly A, York DM, Khare SD, Izgu EC. Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign. ACS Chem Biol 2022; 17:1924-1936. [PMID: 35776893 DOI: 10.1021/acschembio.2c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA polymerases have evolved to feature a highly conserved activity across the tree of life: formation of, without exception, internucleotidyl O-P linkages. Can this linkage selectivity be overcome by design to produce xenonucleic acids? Here, we report that the structure-guided redesign of an archaeal DNA polymerase, 9°N, exhibits a new activity undetectable in the wild-type enzyme: catalyzing the formation of internucleotidyl N-P linkages using 3'-NH2-ddNTPs. Replacing a metal-binding aspartate in the 9°N active site with asparagine was key to the emergence of this unnatural enzyme activity. MD simulations provided insights into how a single substitution enhances the productive positioning of a 3'-amino nucleophile in the active site. Further remodeling of the protein-nucleic acid interface in the finger subdomain yielded a quadruple-mutant variant (9°N-NRQS) displaying DNA-dependent NP-DNA polymerase activity. In addition, the engineered promiscuity of 9°N-NRQS was leveraged for one-pot synthesis of DNA─NP-DNA copolymers. This work sheds light on the molecular basis of substrate fidelity and latent promiscuity in enzymes.
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Affiliation(s)
- Tushar Aggarwal
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - William A Hansen
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Jonathan Hong
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Abir Ganguly
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States.,Laboratory for Biomolecular Simulation Research, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Darrin M York
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States.,Laboratory for Biomolecular Simulation Research, Rutgers University, New Brunswick, New Jersey 08854, United States.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Enver Cagri Izgu
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08901, United States.,Rutgers Center for Lipid Research and New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901, United States
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3
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Wang L, Hast K, Aggarwal T, Baci M, Hong J, Izgu EC. MicroRNA detection in biologically relevant media using a split aptamer platform. Bioorg Med Chem 2022; 69:116909. [PMID: 35779513 DOI: 10.1016/j.bmc.2022.116909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/19/2022] [Accepted: 06/23/2022] [Indexed: 11/02/2022]
Abstract
MicroRNA (miRNA)-based intercellular communication has been implicated in many functional and dysfunctional biological processes. This has raised interest in the potential use of miRNAs as biomarkers for diagnosis and prognosis. Though the list of clinically significant miRNA biomarkers is expanding, it remains challenging to adapt current chemical tools to investigate miRNAs in complex environments native to cells and tissues. We describe here a methodology for rapidly developing aptamer-based fluorescent biosensors that can specifically detect miRNAs in biologically relevant media (10-30% v/v), including medium collected from cultured HeLa cells, human serum, and human plasma. This methodology involves the semi-rational design of the hybridization between DNA oligonucleotides and the miRNA target to build a pool of potential aptamers, and the screening of this pool for high signal-to-background ratio and target specificity. The DNA oligonucleotides are readily available and require no chemical modification, rendering these chemical tools highly adaptable to any novel and niche miRNA target. Following this approach, we developed sensors that detect distinct oncogenic miRNA targets (miR-19b, miR-21, and miR-92a) at concentrations as low as 5 nM without amplification and are selective against single-nucleotide mutants. This work provides a systematic approach toward the development of miRNA biosensors that are easily accessible and can perform in biological environments with minimal sample handling.
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Affiliation(s)
- Liming Wang
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Kern Hast
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Tushar Aggarwal
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Melih Baci
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Jonathan Hong
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Enver Cagri Izgu
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ 08901, USA
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4
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Procházková E, Filo J, Cigáň M, Baszczyňski O. Sterically-Controlled Self-Immolation in Phosphoramidate Linkers Triggered by Light. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Eliška Procházková
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences, Flemingovo nám. 542/2; 116 10 Prague Czech Republic
| | - Juraj Filo
- Institute of Chemistry, Faculty of Natural Sciences; Comenius University, Ilkovičova 6; Bratislava 842 15 Slovakia
| | - Marek Cigáň
- Institute of Chemistry, Faculty of Natural Sciences; Comenius University, Ilkovičova 6; Bratislava 842 15 Slovakia
| | - Ondřej Baszczyňski
- Department of Organic Chemistry, Faculty of Science; Charles University, Hlavova 2030/8; 128 43 Prague Czech Republic
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5
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Lelyveld VS, O'Flaherty DK, Zhou L, Izgu EC, Szostak JW. DNA polymerase activity on synthetic N3'→P5' phosphoramidate DNA templates. Nucleic Acids Res 2019; 47:8941-8949. [PMID: 31428779 PMCID: PMC6755091 DOI: 10.1093/nar/gkz707] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/29/2019] [Accepted: 08/01/2019] [Indexed: 11/12/2022] Open
Abstract
Genetic polymers that could plausibly govern life in the universe might inhabit a broad swath of chemical space. A subset of these genetic systems can exchange information with RNA and DNA and could therefore form the basis for model protocells in the laboratory. N3'→P5' phosphoramidate (NP) DNA is defined by a conservative linkage substitution and has shown promise as a protocellular genetic material, but much remains unknown about its functionality and fidelity due to limited enzymatic tools. Conveniently, we find widespread NP-DNA-dependent DNA polymerase activity among reverse transcriptases, an observation consistent with structural studies of the RNA-like conformation of NP-DNA duplexes. Here, we analyze the consequences of this unnatural template linkage on the kinetics and fidelity of DNA polymerization activity catalyzed by wild-type and variant reverse transcriptases. Template-associated deficits in kinetics and fidelity suggest that even highly conservative template modifications give rise to error-prone DNA polymerase activity. Enzymatic copying of NP-DNA sequences is nevertheless an important step toward the future study and engineering of this synthetic genetic polymer.
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Affiliation(s)
- Victor S Lelyveld
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Enver Cagri Izgu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
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6
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Guo Y, Zhao X, Liu Q. Dispersion-corrected DFT study on the structural transformations and absorption properties of crystalline 3′-Amino-3′-deoxyadenosine. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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Gryaznov SM. Oligonucleotide n3'-->p5' phosphoramidates and thio-phoshoramidates as potential therapeutic agents. Chem Biodivers 2010; 7:477-93. [PMID: 20232321 DOI: 10.1002/cbdv.200900187] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Nucleic acids analogues, i.e., oligonucleotide N3'-->P5' phosphoramidates and N3'-->P5' thio-phosphoramidates, containing 3'-amino-3'-deoxy nucleosides with various 2'-substituents were synthesized and extensively studied. These compounds resist nuclease hydrolysis and form stable duplexes with complementary native phosphodiester DNA and, particularly, RNA strands. An increase in duplexes' melting temperature, DeltaT(m), relative to their phosphodiester counterparts, reaches 2.2-4.0 degrees per modified nucleoside. 2'-OH- (RNA-like), 2'-O-Me-, and 2'-ribo-F-nucleoside substitutions result in the highest degree of duplex stabilization. Moreover, under close to physiological salt and pH conditions, the 2'-deoxy- and 2'-fluoro-phosphoramidate compounds form extremely stable triple-stranded complexes with either single- or double-stranded phosphodiester DNA oligonucleotides. Melting temperature, T(m), of these triplexes exceeds T(m) values for the isosequential phosphodiester counterparts by up to 35 degrees . 2'-Deoxy-N3'-->P5' phosphoramidates adopt RNA-like C3'-endo or N-type nucleoside sugar-ring conformations and hence can be used as stable RNA mimetics. Duplexes formed by 2'-deoxy phosphoramidates with complementary RNA strands are not substrates for RNase H-mediated cleavage in vitro. Oligonucleotide phosphoramidates and especially thio-phosphoramidates conjugated with lipid groups are cell-permeable and demonstrate high biological target specific activity in vitro. In vivo, these compounds show good bioavailability and efficient biodistribution to all major organs, while exerting acceptable toxicity at therapeutically relevant doses. Short oligonucleotide N3'-->P5' thio-phosphoramidate conjugated to 5'-palmitoyl group, designated as GRN163L (Imetelstat), was recently introduced as a potent human telomerase inhibitor. GRN163L is not an antisense agent; it is a direct competitive inhibitor of human telomerase, which directly binds to the active site of the enzyme and thus inhibits its activity. This compound is currently in multiple Phase-I and Phase-I/II clinical trials as potential broad-spectrum anticancer agent.
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Affiliation(s)
- Sergei M Gryaznov
- Geron Corporation, 230 Constitution Drive, Menlo Park, CA 94025, USA.
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8
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Stivers JT, Nagarajan R. Probing enzyme phosphoester interactions by combining mutagenesis and chemical modification of phosphate ester oxygens. Chem Rev 2007; 106:3443-67. [PMID: 16895336 PMCID: PMC2729714 DOI: 10.1021/cr050317n] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.
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9
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Banait NS, Gryaznov SM. DNA and RNA analogues – oligonucleotide phosphoramidates with bridging nitrogen. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.12.4.543] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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10
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Bartley LE, Zhuang X, Das R, Chu S, Herschlag D. Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. J Mol Biol 2003; 328:1011-26. [PMID: 12729738 DOI: 10.1016/s0022-2836(03)00272-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Docking of the P1 duplex into the pre-folded core of the Tetrahymena group I ribozyme exemplifies the formation of tertiary interactions in the context of a complex, structured RNA. We have applied Phi-analysis to P1 docking, which compares the effects of modifications on the rate constant for docking (k(dock)) with the effects on the docking equilibrium (K(dock)). To accomplish this we used a single molecule fluorescence resonance energy transfer assay that allows direct determination of the rate constants for formation of thermodynamically favorable, as well as unfavorable, states. Modification of the eight groups of the P1 duplex that make tertiary interactions with the core and changes in solution conditions decrease K(dock) up to 500-fold, whereas k(dock) changes by </=2-fold. The absence of effects on k(dock), both from atomic modifications and global perturbations, strongly suggests that the transition state for docking is early and does not closely resemble the docked state. These results, the slow rate of docking of 3s(-1), and the observation that a modification that is expected to increase the degrees of freedom between the P1 duplex and the ribozyme core accelerates docking, suggest a model in which a kinetic trap(s) slows docking substantially. Nonetheless, urea does not increase k(dock), suggesting that there is little change in the exposed surface area between the trapped, undocked state and the transition state. The findings highlight that urea and temperature dependencies can be inadequate to diagnose the presence of kinetic traps in a folding process. The results described here, combined with previous work, provide an in-depth view of an RNA tertiary structure formation event and suggest that large, highly structured RNAs may have local regions that are misordered.
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Affiliation(s)
- Laura E Bartley
- Department of Biochemistry, B400 Beckman Center, Stanford University, Stanford, CA 94305-5307, USA
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