1
|
Wang B, Bradley KM, Kim MJ, Laos R, Chen C, Gerloff DL, Manfio L, Yang Z, Benner SA. Enzyme-assisted high throughput sequencing of an expanded genetic alphabet at single base resolution. Nat Commun 2024; 15:4057. [PMID: 38744910 PMCID: PMC11094070 DOI: 10.1038/s41467-024-48408-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
With just four building blocks, low sequence information density, few functional groups, poor control over folding, and difficulties in forming compact folds, natural DNA and RNA have been disappointing platforms from which to evolve receptors, ligands, and catalysts. Accordingly, synthetic biology has created "artificially expanded genetic information systems" (AEGIS) to add nucleotides, functionality, and information density. With the expected improvements seen in AegisBodies and AegisZymes, the task for synthetic biologists shifts to developing for expanded DNA the same analytical tools available to natural DNA. Here we report one of these, an enzyme-assisted sequencing of expanded genetic alphabet (ESEGA) method to sequence six-letter AEGIS DNA. We show how ESEGA analyses this DNA at single base resolution, and applies it to optimized conditions for six-nucleotide PCR, assessing the fidelity of various DNA polymerases, and extending this to AEGIS components with functional groups. This supports the renewed exploitation of expanded DNA alphabets in biotechnology.
Collapse
Affiliation(s)
- Bang Wang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | | | | | - Roberto Laos
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Cen Chen
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | | | - Luran Manfio
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA.
| |
Collapse
|
2
|
Chen XR, Jiang WJ, Guo QH, Liu XY, Cui G, Li L. Theoretical insights into the photophysics of an unnatural base Z: A MS-CASPT2 investigation. Photochem Photobiol 2024; 100:380-392. [PMID: 38041414 DOI: 10.1111/php.13884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/15/2023] [Accepted: 11/01/2023] [Indexed: 12/03/2023]
Abstract
We have employed the highly accurate multistate complete active space second-order perturbation theory (MS-CASPT2) method to investigate the photoinduced excited state relaxation properties of one unnatural base, namely Z. Upon excitation to the S2 state of Z, the internal conversion to the S1 state would be dominant. From the S1 state, two intersystem crossing paths leading to the T2 and T1 states and one internal conversion path to the S0 state are possible. However, considering the large barrier to access the S1 /S0 conical intersection and the strong spin-orbit coupling between S1 and T2 states (>40 cm-1 ), the intersystem crossing to the triplet manifolds is predicted to be more preferred. Arriving at the T2 state, the internal conversion to the T1 state and the intersystem crossing back to the S1 state are both possible considering the S1 /T2 /T1 three-state intersection near the T2 minimum. Upon arrival at the T1 state, the deactivation to S0 can be efficient after overcoming a small barrier to access T1 /S0 crossing point, where the spin-orbit coupling (SOC) is as large as 39.7 cm-1 . Our present work not only provides in-depth insights into the photoinduced process of unnatural base Z, but can also help the future design of novel unnatural bases with better photostability.
Collapse
Affiliation(s)
- Xin-Rui Chen
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Wen-Jun Jiang
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Qian-Hong Guo
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Laicai Li
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| |
Collapse
|
3
|
Wang B, Bradley KM, Kim MJ, Laos R, Chen C, Gerloff DL, Manfio L, Yang Z, Benner SA. Enzyme-Assisted High Throughput Sequencing of an Expanded Genetic Alphabet at Single Base Resolution. RESEARCH SQUARE 2023:rs.3.rs-3678081. [PMID: 38196584 PMCID: PMC10775363 DOI: 10.21203/rs.3.rs-3678081/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Many efforts have sought to apply laboratory in vitro evolution (LIVE) to natural nucleic acid (NA) scaffolds to directly evolve functional molecules. However, synthetic biology can move beyond natural NA scaffolds to create molecular systems whose libraries are far richer reservoirs of functionality than natural NAs. For example, "artificially expanded genetic information systems" (AEGIS) add up to eight nucleotides to the four found in standard NA. Even in its simplest 6-letter versions, AEGIS adds functional groups, information density, and folding motifs that natural NA libraries lack. To complete this vision, however, tools are needed to sequence molecules that are created by AEGIS LIVE. Previous sequencing approaches, including approaches from our laboratories, exhibited limited performance and lost many sequences in diverse library mixtures. Here, we present a new approach that enzymatically transforms the target AEGIS DNA. With higher transliteration efficiency and fidelity, this Enzyme-Assisted Sequencing of Expanded Genetic Alphabet (ESEGA) approach produces substantially better sequences of 6-letter (AGCTZP) DNA than previous transliteration approaches. Therefore, ESEGA facilitates precise analysis of libraries, allowing 'next-generation deep sequencing' to accurately quantify the sequences of 6-letter DNA molecules at single base resolution. We then applied ESEGA to three tasks: (a) defining optimal conditions to perform 6-nucleotide PCR (b) evaluating the fidelity of 6-nucleotide PCR with various DNA polymerases, and (c) extending that evaluation to AEGIS components functionalized with alkynyl and aromatic groups. No other approach at present has this scope, allowing this work to be the next step towards exploiting the potential of expanded DNA alphabets in biotechnology.
Collapse
Affiliation(s)
- Bang Wang
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
- Department of Chemistry, University of Florida, Gainesville, FL, USA, 32611
| | | | - Myong-Jung Kim
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA, 32615
| | - Roberto Laos
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Cen Chen
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Dietlind L. Gerloff
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Luran Manfio
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA, 32615
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA, 32615
| |
Collapse
|
4
|
Dawson G, Spielvogel EH, Diao T. Nickel-Catalyzed Radical Mechanisms: Informing Cross-Coupling for Synthesizing Non-Canonical Biomolecules. Acc Chem Res 2023; 56:3640-3653. [PMID: 38033206 PMCID: PMC10734253 DOI: 10.1021/acs.accounts.3c00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023]
Abstract
Nickel excels at facilitating selective radical chemistry, playing a pivotal role in metalloenzyme catalysis and modern cross-coupling reactions. Radicals, being nonpolar and neutral, exhibit orthogonal reactivity to nucleophilic and basic functional groups commonly present in biomolecules. Harnessing this compatibility, we delve into the application of nickel-catalyzed radical pathways in the synthesis of noncanonical peptides and carbohydrates, critical for chemical biology studies and drug discovery.We previously characterized a sequential reduction mechanism that accounts for chemoselectivity in cross-electrophile coupling reactions. This catalytic cycle begins with nickel(I)-mediated radical generation from alkyl halides, followed by carbon radical capture by nickel(II) complexes, and concludes with reductive elimination. These steps resonate with mechanistic proposals in nickel-catalyzed cross-coupling, photoredox, and electrocatalytic reactions. Herein, we present our insights into each step involving radicals, including initiation, propagation, termination, and the nuances of kinetics, origins of selectivity, and ligand effects.Radical generation from C(sp3) electrophiles via one-electron oxidative addition with low-valent nickel radical intermediates provides the basis for stereoconvergent and cross-electrophile couplings. Our electroanalytical studies elucidate a concerted halogen atom abstraction mechanism, where electron transfer is coupled with halide dissociation. Using this pathway, we have developed a nickel-catalyzed stereoselective radical addition to dehydroalanine, facilitating the synthesis of noncanonical peptides. In this application, chiral ligands modulate the stereochemical outcome through the asymmetric protonation of a nickel-enolate intermediate.The capture of the alkyl radical by nickel(II) expands the scope of cross-coupling, promotes reductive elimination through the formation of high-valent nickel(III) species, and governs chemo- and stereoselectivity. We discovered that nickel(II)-aryl efficiently traps radicals with a barrier ranging from 7 to 9 kcal/mol, followed by fast reductive elimination. In contrast, nickel(II)-alkyl captures radicals to form a nickel(III) species, which was characterized by EPR spectroscopy. However, the subsequent slow reductive elimination resulted in minimal product formation. The observed high diastereoselectivity of radical capture inspired investigations into C-aryl and C-acyl glycosylation reactions. We developed a redox auxiliary that readily couples with natural carbohydrates and produces glycosyl radicals upon photoredox activation. Nickel-catalyzed cross-coupling of the glycosyl radical with bromoarenes and carboxylic acids leads to diverse non-natural glycosides that can facilitate drug discovery.Stoichiometric studies on well-defined d8-nickel complexes have showcased means to promote reductive elimination, including ligand association, oxidation, and oxidative addition.In the final section, we address the influence of auxiliary ligands on the electronic structure and redox activity of organonickel intermediates. Synthesis of a series of low-valent nickel radical complexes and characterization of their electronic structures led us to a postulate that ligand redox activity correlates with coordination geometry. Our data reveal that a change in ligand redox activity can shift the redox potentials of reaction intermediates, potentially altering the mechanism of catalytic reactions. Moreover, coordinating additives and solvents may stabilize nickel radicals during catalysis by adjusting ligand redox activity, which is consistent with known catalytic conditions.
Collapse
Affiliation(s)
- Gregory
A. Dawson
- Department
of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Ethan H. Spielvogel
- Department
of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Tianning Diao
- Department
of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| |
Collapse
|
5
|
Dörrenhaus R, Wagner PK, Kath-Schorr S. Two are not enough: synthetic strategies and applications of unnatural base pairs. Biol Chem 2023; 404:883-896. [PMID: 37354104 DOI: 10.1515/hsz-2023-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 06/26/2023]
Abstract
Nucleic acid chemistry is a rapidly evolving field, and the need for novel nucleotide modifications and artificial nucleotide building blocks for diagnostic and therapeutic use, material science or for studying cellular processes continues unabated. This review focusses on the development and application of unnatural base pairs as part of an expanded genetic alphabet. Not only recent developments in "nature-like" artificial base pairs are presented, but also current synthetic methods to get access to C-glycosidic nucleotides. Wide-ranging viability in synthesis is a prerequisite for the successful use of unnatural base pairs in a broader spectrum and will be discussed.
Collapse
|
6
|
Jena NR, Das P, Shukla PK. Complementary base pair interactions between different rare tautomers of the second-generation artificial genetic alphabets. J Mol Model 2023; 29:125. [PMID: 37014428 DOI: 10.1007/s00894-023-05537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023]
Abstract
The functionality of a semisynthetic DNA in the biological environment will depend on the base pair nature of its complementary base pairs. To understand this, base pair interactions between complementary bases of recently proposed eight second-generation artificial nucleobases are studied herein by considering their rare tautomeric conformations and a dispersion-corrected density functional theoretic method. It is found that the binding energies of two hydrogen-bonded complementary base pairs are more negative than those of the three hydrogen-bonded base pairs. However, as the former base pairs are endothermic, the semisynthetic duplex DNA would involve the latter base pairs.
Collapse
Affiliation(s)
- N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Jabalpur, 482005, India.
| | - P Das
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Jabalpur, 482005, India
| | - P K Shukla
- Department of Physics, Assam University, Silchar, 788011, India
| |
Collapse
|
7
|
Romesberg FE. Discovery, implications and initial use of semi-synthetic organisms with an expanded genetic alphabet/code. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220030. [PMID: 36633274 PMCID: PMC9835597 DOI: 10.1098/rstb.2022.0030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/25/2022] [Indexed: 01/13/2023] Open
Abstract
Much recent interest has focused on developing proteins for human use, such as in medicine. However, natural proteins are made up of only a limited number of canonical amino acids with limited functionalities, and this makes the discovery of variants with some functions difficult. The ability to recombinantly express proteins containing non-canonical amino acids (ncAAs) with properties selected to impart the protein with desired properties is expected to dramatically improve the discovery of proteins with different functions. Perhaps the most straightforward approach to such an expansion of the genetic code is through expansion of the genetic alphabet, so that new codon/anticodon pairs can be created to assign to ncAAs. In this review, I briefly summarize more than 20 years of effort leading ultimately to the discovery of synthetic nucleotides that pair to form an unnatural base pair, which when incorporated into DNA, is stably maintained, transcribed and used to translate proteins in Escherichia coli. In addition to discussing wide ranging conceptual implications, I also describe ongoing efforts at the pharmaceutical company Sanofi to employ the resulting 'semi-synthetic organisms' or SSOs, for the production of next-generation protein therapeutics. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
Collapse
Affiliation(s)
- Floyd E. Romesberg
- Platform Innovation, Synthorx, a Sanofi Company, 11099 N. Torrey Pines Road, Suite 190, La Jolla, CA 92037, USA
| |
Collapse
|
8
|
Neitz H, Bessi I, Kachler V, Michel M, Höbartner C. Tailored Tolane-Perfluorotolane Assembly as Supramolecular Base Pair Replacement in DNA. Angew Chem Int Ed Engl 2023; 62:e202214456. [PMID: 36344446 PMCID: PMC10107946 DOI: 10.1002/anie.202214456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 11/09/2022]
Abstract
Arene-fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane-perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π-stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene-fluoroarene-programmed assembly of DNA.
Collapse
Affiliation(s)
- Hermann Neitz
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Irene Bessi
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Valentin Kachler
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Manuela Michel
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Claudia Höbartner
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
- Center for Nanosystems Chemistry (CNC)University of WürzburgTheodor-Boveri-Weg97074WürzburgGermany
| |
Collapse
|
9
|
Berdis A. Nucleobase-modified nucleosides and nucleotides: Applications in biochemistry, synthetic biology, and drug discovery. Front Chem 2022; 10:1051525. [PMID: 36531317 PMCID: PMC9748101 DOI: 10.3389/fchem.2022.1051525] [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: 09/22/2022] [Accepted: 11/08/2022] [Indexed: 09/29/2023] Open
Abstract
. DNA is often referred to as the "molecule of life" since it contains the genetic blueprint for all forms of life on this planet. The core building blocks composing DNA are deoxynucleotides. While the deoxyribose sugar and phosphate group are ubiquitous, it is the composition and spatial arrangement of the four natural nucleobases, adenine (A), cytosine (C), guanine (G), and thymine (T), that provide diversity in the coding information present in DNA. The ability of DNA to function as the genetic blueprint has historically been attributed to the formation of proper hydrogen bonding interactions made between complementary nucleobases. However, recent chemical and biochemical studies using nucleobase-modified nucleotides that contain "non-hydrogen bonding" functional groups have challenged many of the dogmatic views for the necessity of hydrogen-bonding interactions for DNA stability and function. Based on years of exciting research, this area has expanded tremendously and is thus too expansive to provide a comprehensive review on the topic. As such, this review article provides an opinion highlighting how nucleobase-modified nucleotides are being applied in diverse biomedical fields, focusing on three exciting areas of research. The first section addresses how these analogs are used as mechanistic probes for DNA polymerase activity and fidelity during replication. This section outlines the synthetic logic and medicinal chemistry approaches used to replace hydrogen-bonding functional groups to examine the contributions of shape/size, nucleobase hydrophobicity, and pi-electron interactions. The second section extends these mechanistic studies to provide insight into how nucleobase-modified nucleosides are used in synthetic biology. One example is through expansion of the genetic code in which changing the composition of DNA makes it possible to site-specifically incorporate unnatural amino acids bearing unique functional groups into enzymes and receptors. The final section describes results of pre-clinical studies using nucleobase-modified nucleosides as potential therapeutic agents against diseases such as cancer.
Collapse
Affiliation(s)
- Anthony Berdis
- Department of Chemistry, Cleveland State University, Cleveland, OH, United States
| |
Collapse
|
10
|
Abstract
DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.
Collapse
Affiliation(s)
- Ashis K Basu
- Department of Chemistry, The University of Connecticut Storrs, Storrs, Connecticut 06269, United States
| | - John M Essigmann
- Departments of Chemistry, Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
11
|
Turvey MW, Gabriel KN, Lee W, Taulbee JJ, Kim JK, Chen S, Lau CJ, Kattan RE, Pham JT, Majumdar S, Garcia D, Weiss GA, Collins PG. Single-molecule Taq DNA polymerase dynamics. SCIENCE ADVANCES 2022; 8:eabl3522. [PMID: 35275726 PMCID: PMC8916733 DOI: 10.1126/sciadv.abl3522] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Taq DNA polymerase functions at elevated temperatures with fast conformational dynamics-regimes previously inaccessible to mechanistic, single-molecule studies. Here, single-walled carbon nanotube transistors recorded the motions of Taq molecules processing matched or mismatched template-deoxynucleotide triphosphate pairs from 22° to 85°C. By using four enzyme orientations, the whole-enzyme closures of nucleotide incorporations were distinguished from more rapid, 20-μs closures of Taq's fingers domain testing complementarity and orientation. On average, one transient closure was observed for every nucleotide binding event; even complementary substrate pairs averaged five transient closures between each catalytic incorporation at 72°C. The rate and duration of the transient closures and the catalytic events had almost no temperature dependence, leaving all of Taq's temperature sensitivity to its rate-determining open state.
Collapse
Affiliation(s)
- Mackenzie W. Turvey
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Kristin N. Gabriel
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Wonbae Lee
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Jeffrey J. Taulbee
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Joshua K. Kim
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Silu Chen
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Calvin J. Lau
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Rebecca E. Kattan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Jenifer T. Pham
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Sudipta Majumdar
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | | | - Gregory A. Weiss
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697-3958, USA
| | - Philip G. Collins
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| |
Collapse
|
12
|
Aralov AV, Gubina N, Cabrero C, Tsvetkov VB, Turaev AV, Fedeles BI, Croy RG, Isaakova EA, Melnik D, Dukova S, Ryazantsev DY, Khrulev AA, Varizhuk AM, González C, Zatsepin TS, Essigmann JM. 7,8-Dihydro-8-oxo-1,N6-ethenoadenine: an exclusively Hoogsteen-paired thymine mimic in DNA that induces A→T transversions in Escherichia coli. Nucleic Acids Res 2022; 50:3056-3069. [PMID: 35234900 PMCID: PMC8989528 DOI: 10.1093/nar/gkac148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/09/2022] [Accepted: 02/25/2022] [Indexed: 12/15/2022] Open
Abstract
This work investigated the structural and biological properties of DNA containing 7,8-dihydro-8-oxo-1,N6-ethenoadenine (oxo-ϵA), a non-natural synthetic base that combines structural features of two naturally occurring DNA lesions (7,8-dihydro-8-oxoadenine and 1,N6-ethenoadenine). UV-, CD-, NMR spectroscopies and molecular modeling of DNA duplexes revealed that oxo-ϵA adopts the non-canonical syn conformation (χ = 65º) and fits very well among surrounding residues without inducing major distortions in local helical architecture. The adduct remarkably mimics the natural base thymine. When considered as an adenine-derived DNA lesion, oxo-ϵA was >99% mutagenic in living cells, causing predominantly A→T transversion mutations in Escherichia coli. The adduct in a single-stranded vector was not repaired by base excision repair enzymes (MutM and MutY glycosylases) or the AlkB dioxygenase and did not detectably affect the efficacy of DNA replication in vivo. When the biological and structural data are viewed together, it is likely that the nearly exclusive syn conformation and thymine mimicry of oxo-ϵA defines the selectivity of base pairing in vitro and in vivo, resulting in lesion pairing with A during replication. The base pairing properties of oxo-ϵA, its strong fluorescence and its invisibility to enzymatic repair systems in vivo are features that are sought in novel DNA-based probes and modulators of gene expression.
Collapse
Affiliation(s)
- Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Nina Gubina
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Institute of Theoretical and Experimental Biophysics RAS, Pushchino 142290, Russia
| | - Cristina Cabrero
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid 28006, Spain
| | - Vladimir B Tsvetkov
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia.,World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow 119146, Russia
| | - Anton V Turaev
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia
| | - Bogdan I Fedeles
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert G Croy
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ekaterina A Isaakova
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia
| | - Denis Melnik
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Svetlana Dukova
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Dmitriy Y Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Alexei A Khrulev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid 28006, Spain
| | - Timofei S Zatsepin
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia.,Chemistry Department, Lomonosov Moscow State University, Moscow 119992, Russia
| | - John M Essigmann
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
13
|
Jena NR. Rare Tautomers of Artificially Expanded Genetic Letters and their Effects on the Base pair Stabilities. Chemphyschem 2022; 23:e202100908. [PMID: 35029036 DOI: 10.1002/cphc.202100908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Indexed: 11/11/2022]
Abstract
To expand the existing genetic letters, it is necessary to design robust nucleotides that can function naturally in living cells. Therefore, it is desirable to examine the roles of recently proposed second-generation artificially expanded genetic letters in producing stable duplex DNA. Here, a reliable dispersion-corrected density functional theory method is used to understand the electronic structures and properties of different rare tautomers of proposed expanded genetic letters and their effects on the base pair stabilities in the duplex DNA. It is found that the rare tautomers are not only stable in the aqueous medium but can also base pair with natural bases to produce stable mispairs. Except for J and V, all the artificial genetic letters are found to produce mispairs that are about 1-7 kcal/mol more stable than their complementary counterparts. They are also appreciably more stable than the naturally occurring G:C, A:T, and G:T pairs. The higher base pair stabilities are found to be mainly because of the polarity of monomers and attractive electrostatic interactions.
Collapse
Affiliation(s)
- N R Jena
- IIITDM Jabalpur, Discipline of Natural Sciences, Dumna Airport Road, Khamaria, India, 482005, Jabalpur, INDIA
| |
Collapse
|
14
|
Geronimo I, Vidossich P, De Vivo M. Local Structural Dynamics at the Metal-Centered Catalytic Site of Polymerases is Critical for Fidelity. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Inacrist Geronimo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Pietro Vidossich
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| |
Collapse
|
15
|
Wei Y, Lam J, Diao T. Synthesis of C-acyl furanosides via the cross-coupling of glycosyl esters with carboxylic acids. Chem Sci 2021; 12:11414-11419. [PMID: 34667550 PMCID: PMC8447929 DOI: 10.1039/d1sc03596g] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022] Open
Abstract
C-Acyl furanosides are versatile synthetic precursors to a variety of natural products, nucleoside analogues, and pharmaceutical molecules. This report addresses the unmet challenge in preparing C-acyl furanosides by developing a cross-coupling reaction between glycosyl esters and carboxylic acids. A key step is the photoredox activation of the glycosyl ester, which promotes the homolysis of the strong anomeric C–O bond through CO2 evolution to afford glycosyl radicals. This method embraces a large scope of furanoses, pyranoses, and carboxylic acids, and is readily applicable to the synthesis of a thymidine analogue and diplobifuranylone B, as well as the late-stage modification of (+)-sclareolide. The convenient preparation of the redox active glycosyl ester from native sugars and the compatibility with common furanoses exemplifies the potential of this method in medicinal chemistry. A cross-coupling of glycosyl esters with carboxylic acids to prepare C-acyl furanosides and pyranosides. The reaction proceeds through photoredox activation of the glycosyl ester to afford glycosyl radicals.![]()
Collapse
Affiliation(s)
- Yongliang Wei
- Department of Chemistry, New York University 100 Washington Square East New York NY 10003 USA
| | - Jenny Lam
- Department of Chemistry, New York University 100 Washington Square East New York NY 10003 USA
| | - Tianning Diao
- Department of Chemistry, New York University 100 Washington Square East New York NY 10003 USA
| |
Collapse
|
16
|
Wei Y, Ben-Zvi B, Diao T. Diastereoselective Synthesis of Aryl C-Glycosides from Glycosyl Esters via C-O Bond Homolysis. Angew Chem Int Ed Engl 2021; 60:9433-9438. [PMID: 33438338 PMCID: PMC8044010 DOI: 10.1002/anie.202014991] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/10/2020] [Indexed: 12/20/2022]
Abstract
C-aryl glycosyl compounds offer better in vivo stability relative to O- and N-glycoside analogues. C-aryl glycosides are extensively investigated as drug candidates and applied to chemical biology studies. Previously, C-aryl glycosides were derived from lactones, glycals, glycosyl stannanes, and halides, via methods displaying various limitations with respect to the scope, functional-group compatibility, and practicality. Challenges remain in the synthesis of C-aryl nucleosides and 2-deoxysugars from easily accessible carbohydrate precursors. Herein, we report a cross-coupling method to prepare C-aryl and heteroaryl glycosides, including nucleosides and 2-deoxysugars, from glycosyl esters and bromoarenes. Activation of the carbohydrate substrates leverages dihydropyridine (DHP) as an activating group followed by decarboxylation to generate a glycosyl radical via C-O bond homolysis. This strategy represents a new means to activate alcohols as a cross-coupling partner. The convenient preparation of glycosyl esters and their stability exemplifies the potential of this method in medicinal chemistry.
Collapse
Affiliation(s)
- Yongliang Wei
- Chemistry Department, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Benjamin Ben-Zvi
- Chemistry Department, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Tianning Diao
- Chemistry Department, New York University, 100 Washington Square East, New York, NY, 10003, USA
| |
Collapse
|
17
|
Wei Y, Ben‐zvi B, Diao T. Diastereoselective Synthesis of Aryl
C
‐Glycosides from Glycosyl Esters via C−O Bond Homolysis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014991] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yongliang Wei
- Chemistry Department New York University 100 Washington Square East New York NY 10003 USA
| | - Benjamin Ben‐zvi
- Chemistry Department New York University 100 Washington Square East New York NY 10003 USA
| | - Tianning Diao
- Chemistry Department New York University 100 Washington Square East New York NY 10003 USA
| |
Collapse
|
18
|
Handa S, Reyna A, Wiryaman T, Ghosh P. Determinants of adenine-mutagenesis in diversity-generating retroelements. Nucleic Acids Res 2021; 49:1033-1045. [PMID: 33367793 PMCID: PMC7826257 DOI: 10.1093/nar/gkaa1240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/01/2023] Open
Abstract
Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.
Collapse
Affiliation(s)
- Sumit Handa
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Andres Reyna
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Timothy Wiryaman
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Partho Ghosh
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| |
Collapse
|
19
|
Burrows CJ. Kool chemistry of DNA and RNA biopolymers. Biopolymers 2021; 112:e23417. [PMID: 33493362 DOI: 10.1002/bip.23417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| |
Collapse
|
20
|
Miao S, Liang Y, Rundell S, Bhunia D, Devari S, Munyaradzi O, Bong D. Unnatural bases for recognition of noncoding nucleic acid interfaces. Biopolymers 2021; 112:e23399. [PMID: 32969496 PMCID: PMC7855516 DOI: 10.1002/bip.23399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022]
Abstract
The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.
Collapse
Affiliation(s)
- Shiqin Miao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Yufeng Liang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah Rundell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Debmalya Bhunia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Shekar Devari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Oliver Munyaradzi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
21
|
McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
Collapse
Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| |
Collapse
|
22
|
Abstract
DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases often precludes their use in practical applications that require modified substrates. Moving beyond natural genetic polymers requires sophisticated enzyme-engineering technologies that can be used to direct the evolution of engineered polymerases that function with tailor-made activities. Such efforts are expected to uniquely drive emerging applications in synthetic biology by enabling the synthesis, replication, and evolution of synthetic genetic polymers with new physicochemical properties.
Collapse
|
23
|
Seio K, Yamaguchi K, Yamazaki A, Kanamori T, Masaki Y. Transcription of DNA duplex containing deoxypseudouridine and deoxypseudoisocytidine, and inhibition of transcription by triplex forming oligonucleotide that recognizes the modified duplex. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:892-904. [PMID: 32126878 DOI: 10.1080/15257770.2020.1714652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We developed new DNA triplexes that contain four base triads T-A·T, A-ψ·CBr, G-PIC·YO, and C-G·Py+, where CBr, YO, Py, ψ, and PIC are 5-bromocytosine, 5-methyl-4-pyrimidone, 2-aminopyridine, the aglycons of deoxypseudouridine, and deoxypseudoisocytidine, respectively. DNA duplex incorporating T-A, A-ψ, G-PIC, and C-G, and triplex forming oligonucleotide incorporating T, CBr, YO, and Py formed the triplex as evaluated by Tm measurements. The triplex formation was successfully applied to the inhibition of transcription of the DNA duplex incorporating T7-promoter sequence modified by the above modified bases.
Collapse
Affiliation(s)
- Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kei Yamaguchi
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ayano Yamazaki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
24
|
Johnson A, Karimi A, Luedtke NW. Enzymatic Incorporation of a Coumarin–Guanine Base Pair. Angew Chem Int Ed Engl 2019; 58:16839-16843. [DOI: 10.1002/anie.201910059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Aaron Johnson
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Ashkan Karimi
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nathan W. Luedtke
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| |
Collapse
|
25
|
Johnson A, Karimi A, Luedtke NW. Enzymatic Incorporation of a Coumarin–Guanine Base Pair. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Aaron Johnson
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Ashkan Karimi
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nathan W. Luedtke
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| |
Collapse
|
26
|
Affiliation(s)
- Floyd E. Romesberg
- Department of ChemistryThe Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| |
Collapse
|
27
|
Dien VT, Holcomb M, Feldman AW, Fischer EC, Dwyer TJ, Romesberg FE. Progress Toward a Semi-Synthetic Organism with an Unrestricted Expanded Genetic Alphabet. J Am Chem Soc 2018; 140:16115-16123. [PMID: 30418780 DOI: 10.1021/jacs.8b08416] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have developed a family of unnatural base pairs (UBPs), exemplified by the pair formed between dNaM and dTPT3, for which pairing is mediated not by complementary hydrogen bonding but by hydrophobic and packing forces. These UBPs enabled the creation of the first semisynthetic organisms (SSOs) that store increased genetic information and use it to produce proteins containing noncanonical amino acids. However, retention of the UBPs was poor in some sequence contexts. Here, to optimize the SSO, we synthesize two novel benzothiophene-based dNaM analogs, dPTMO and dMTMO, and characterize the corresponding UBPs, dPTMO-dTPT3 and dMTMO-dTPT3. We demonstrate that these UBPs perform similarly to, or slightly worse than, dNaM-dTPT3 in vitro. However, in the in vivo environment of an SSO, retention of dMTMO-dTPT3, and especially dPTMO-dTPT3, is significantly higher than that of dNaM-dTPT3. This more optimal in vivo retention results from better replication, as opposed to more efficient import of the requisite unnatural nucleoside triphosphates. Modeling studies suggest that the more optimal replication results from specific internucleobase interactions mediated by the thiophene sulfur atoms. Finally, we show that dMTMO and dPTMO efficiently template the transcription of RNA containing TPT3 and that their improved retention in DNA results in more efficient production of proteins with noncanonical amino acids. This is the first instance of using performance within the SSO as part of the UBP evaluation and optimization process. From a general perspective, the results demonstrate the importance of evaluating synthetic biology "parts" in their in vivo context and further demonstrate the ability of hydrophobic and packing interactions to replace the complementary hydrogen bonding that underlies the replication of natural base pairs. From a more practical perspective, the identification of dMTMO-dTPT3 and especially dPTMO-dTPT3 represents significant progress toward the development of SSOs with an unrestricted ability to store and retrieve increased information.
Collapse
Affiliation(s)
- Vivian T Dien
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 United States
| | - Matthew Holcomb
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 United States
| | - Aaron W Feldman
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 United States
| | - Emil C Fischer
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 United States
| | - Tammy J Dwyer
- Department of Chemistry and Biochemistry , University of San Diego , San Diego , California 92110 , United States
| | - Floyd E Romesberg
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 United States
| |
Collapse
|
28
|
Dien VT, Morris SE, Karadeema RJ, Romesberg FE. Expansion of the genetic code via expansion of the genetic alphabet. Curr Opin Chem Biol 2018; 46:196-202. [PMID: 30205312 DOI: 10.1016/j.cbpa.2018.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/14/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022]
Abstract
Current methods to expand the genetic code enable site-specific incorporation of non-canonical amino acids (ncAAs) into proteins in eukaryotic and prokaryotic cells. However, current methods are limited by the number of codons possible, their orthogonality, and possibly their effects on protein synthesis and folding. An alternative approach relies on unnatural base pairs to create a virtually unlimited number of genuinely new codons that are efficiently translated and highly orthogonal because they direct ncAA incorporation using forces other than the complementary hydrogen bonds employed by their natural counterparts. This review outlines progress and achievements made towards developing a functional unnatural base pair and its use to generate semi-synthetic organisms with an expanded genetic alphabet that serves as the basis of an expanded genetic code.
Collapse
Affiliation(s)
- Vivian T Dien
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sydney E Morris
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rebekah J Karadeema
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
29
|
Tomori T, Nagaoka K, Takeshita L, Shiozawa T, Miyatake Y, Masaki Y, Sekine M, Seio K. Deoxynucleoside Triphosphate Containing Pyridazin-3-one Aglycon as a Thymidine Triphosphate Substitute for Primer Extension and Chain Elongation by Klenow Fragments. J Org Chem 2018; 83:8353-8363. [PMID: 29952565 DOI: 10.1021/acs.joc.8b00918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Deoxynucleoside 5'-triphosphate was synthesized with 3-oxo-2 H-pyridazin-6-yl (PzO)-a uracil analogue lacking a 2-keto group-as the nucleobase. Theoretical analyses and hybridization experiments indicated that PzO recognizes adenine (A) for formation of a Watson-Crick base pair. Primer extension reactions using nucleoside 5'-triphosphate and the Klenow fragment revealed that the synthetic nucleoside 5'-triphosphate was incorporated into the 3' end of the primer through recognition of A in the template strand. Moreover, the 3'-nucleotide residue harboring PzO as the base was resistant to the 3'-exonuclease activity of Klenow fragment exo+. The primer bearing the PzO base at the 3' end could function in subsequent chain elongation. These properties of PzO were attributed to the presence of an endocyclic nitrogen atom at the position ortho to the glycosidic bond, which was presumed to form an H-bond with the amino acid residue of DNA polymerase for effective recognition of the 3' end of the primer for primer extension. These results provide a basis for designing new nucleobases by combining a nitrogen atom at the position ortho to the glycosidic bond and base-pairing sites for Watson-Crick hydrogen bonding.
Collapse
Affiliation(s)
- Takahito Tomori
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Kento Nagaoka
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Leo Takeshita
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Takashi Shiozawa
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Yuya Miyatake
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Yoshiaki Masaki
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Mitsuo Sekine
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Kohji Seio
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| |
Collapse
|
30
|
Wang Y, Ng N, Liu E, Lam CH, Perrin DM. Systematic study of constraints imposed by modified nucleoside triphosphates with protein-like side chains for use in in vitro selection. Org Biomol Chem 2018; 15:610-618. [PMID: 27942671 DOI: 10.1039/c6ob02335e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Successful selection of modified DNAzymes depends on the potential for modified nucleoside triphosphates (dNTPs) to replace their unmodified counterparts in enzyme catalyzed primer extension reactions and, once incorporated, to serve as template bases for information transfer prior to PCR amplification. To date, the most densely modified DNAzymes have been selected from three modified dNTPs: 8-histaminyl-deoxyadenosine (dAimTP), 5-guanidinoallyl-deoxyuridine (dUgaTP), and 5-aminoallyl-deoxycytidine (dCaaTP) to provide several RNA-cleaving DNAzymes with greatly enhanced rate constants compared to unmodified counterparts. Here we report biophysical and enzymatic properties of these three modified nucleosides in the context of specific oligonucleotide sequences to understand how these three modified nucleobases function in combinatorial selection. The base-pairing abilities of oligonucleotides bearing one or three modified nucleosides were investigated by thermal denaturation studies and as templates for enzymatic polymerization with both modified and unmodified dNTPs. While we address certain shortcomings in the use of modified dNTPs, we also provide key evidence of faithful incorporation and enzymatic read-out, which strongly supports their continued use in in vitro selection.
Collapse
Affiliation(s)
- Yajun Wang
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Nicole Ng
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Erkai Liu
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Curtis H Lam
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - David M Perrin
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| |
Collapse
|
31
|
Abstract
![]()
The information available to any organism is encoded in a four
nucleotide, two base pair genetic code. Since its earliest days, the
field of synthetic biology has endeavored to impart organisms with
novel attributes and functions, and perhaps the most fundamental approach
to this goal is the creation of a fifth and sixth nucleotide that
pair to form a third, unnatural base pair (UBP) and thus allow for
the storage and retrieval of increased information. Achieving this
goal, by definition, requires synthetic chemistry to create unnatural
nucleotides and a medicinal chemistry-like approach to guide their
optimization. With this perspective, almost 20 years ago we began
designing unnatural nucleotides with the ultimate goal of developing
UBPs that function in vivo, and thus serve as the
foundation of semi-synthetic organisms (SSOs) capable of storing and
retrieving increased information. From the beginning, our efforts
focused on the development of nucleotides that bear predominantly
hydrophobic nucleobases and thus that pair not based on the complementary
hydrogen bonds that are so prominent among the natural base pairs
but rather via hydrophobic and packing interactions. It was envisioned
that such a pairing mechanism would provide a basal level of selectivity
against pairing with natural nucleotides, which we expected would
be the greatest challenge; however, this choice mandated starting
with analogs that have little or no homology to their natural counterparts
and that, perhaps not surprisingly, performed poorly. Progress toward
their optimization was driven by the construction of structure–activity
relationships, initially from in vitro steady-state
kinetic analysis, then later from pre-steady-state and PCR-based assays,
and ultimately from performance in vivo, with the
results augmented three times with screens that explored combinations
of the unnatural nucleotides that were too numerous to fully characterize
individually. The structure–activity relationship data identified
multiple features required by the UBP, and perhaps most prominent
among them was a substituent ortho to the glycosidic linkage that
is capable of both hydrophobic packing and hydrogen bonding, and nucleobases
that stably stack with flanking natural nucleobases in lieu of the potentially more stabilizing stacking interactions afforded
by cross strand intercalation. Most importantly, after the examination
of hundreds of unnatural nucleotides and thousands of candidate UBPs,
the efforts ultimately resulted in the identification of a family
of UBPs that are well recognized by DNA polymerases when incorporated
into DNA and that have been used to create SSOs that store and retrieve
increased information. In addition to achieving a longstanding goal
of synthetic biology, the results have important implications for
our understanding of both the molecules and forces that can underlie
biological processes, so long considered the purview of molecules
benefiting from eons of evolution, and highlight the promise of applying
the approaches and methodologies of synthetic and medical chemistry
in the pursuit of synthetic biology.
Collapse
Affiliation(s)
- Aaron W. Feldman
- Department of Chemistry, The Scripps Research Institute, La
Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La
Jolla, California 92037, United States
| |
Collapse
|
32
|
Jian Y, Maximowitsch E, Liu D, Adhikari S, Li L, Domratcheva T. Indications of 5' to 3' Interbase Electron Transfer as the First Step of Pyrimidine Dimer Formation Probed by a Dinucleotide Analog. Chemistry 2017; 23:7526-7537. [PMID: 28370554 DOI: 10.1002/chem.201700045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 12/12/2022]
Abstract
Pyrimidine dimers are the most common DNA lesions generated under UV radiation. To reveal the molecular mechanisms behind their formation, it is of significance to reveal the roles of each pyrimidine residue. We thus replaced the 5'-pyrimidine residue with a photochemically inert xylene moiety (X). The electron-rich X can be readily oxidized but not reduced, defining the direction of interbase electron transfer (ET). Irradiation of the XpT dinucleotide under 254 nm UV light generates two major photoproducts: a pyrimidine (6-4) pyrimidone analog (6-4PP) and an analog of the so-called spore photoproduct (SP). Both products are formed by reaction at C4=O of the photo-excited 3'-thymidine (T), which indicates that excitation of a single "driver" residue is sufficient to trigger pyrimidine dimerization. Our quantum-chemical calculations demonstrated that photo-excited 3'-T accepts an electron from 5'-X. The resulting charge-separated radical pair lowers its energy upon formation of interbase covalent bonds, eventually yielding 6-4PP and SP.
Collapse
Affiliation(s)
- Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,School of Chemistry & Chemical Engineering, Shaanxi Normal University (SNNU), No. 620, West Chang'an Avenue, Xi'an, Shaanxi, 710119, P. R. China
| | - Egle Maximowitsch
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Degang Liu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Surya Adhikari
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| |
Collapse
|
33
|
Dorigundla AR, Gurrapu R, Batchu VR. Stereoselective synthesis of peracetylated (−)-gloeosporiol via acid catalysed intramolecular etherification. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2016.12.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
34
|
Shivalingam A, Tyburn AES, El-Sagheer AH, Brown T. Molecular Requirements of High-Fidelity Replication-Competent DNA Backbones for Orthogonal Chemical Ligation. J Am Chem Soc 2017; 139:1575-1583. [PMID: 28097865 DOI: 10.1021/jacs.6b11530] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The molecular properties of the phosphodiester backbone that made it the evolutionary choice for the enzymatic replication of genetic information are not well understood. To address this, and to develop new chemical ligation strategies for assembly of biocompatible modified DNA, we have synthesized oligonucleotides containing several structurally and electronically varied artificial linkages. This has yielded a new highly promising ligation method based on amide backbone formation that is chemically orthogonal to CuAAC "click" ligation. A study of kinetics and fidelity of replication through these artificial linkages by primer extension, PCR, and deep sequencing reveals that a subtle interplay between backbone flexibility, steric factors, and ability to hydrogen bond to the polymerase modulates rapid and accurate information decoding. Even minor phosphorothioate modifications can impair the copying process, yet some radical triazole and amide DNA backbones perform surprisingly well, indicating that the phosphate group is not essential. These findings have implications in the field of synthetic biology.
Collapse
Affiliation(s)
- Arun Shivalingam
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Agnes E S Tyburn
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University , Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K
| |
Collapse
|
35
|
|
36
|
Pairas GN, Tsoungas PG. H-Bond: Τhe Chemistry-Biology H-Bridge. ChemistrySelect 2016; 1:4520-4532. [PMID: 32328512 PMCID: PMC7169486 DOI: 10.1002/slct.201600770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.
Collapse
Affiliation(s)
- George N. Pairas
- Department of PharmacyLaboratory of Medicinal ChemistryUniversity of PatrasGR-265 04PatrasGreece
| | - Petros G. Tsoungas
- Laboratory of BiochemistryHellenic Pasteur Institute127 Vas. Sofias Ave.GR-115 21AthensGreece
| |
Collapse
|
37
|
Mehta AP, Li H, Reed SA, Supekova L, Javahishvili T, Schultz PG. Replacement of Thymidine by a Modified Base in the Escherichia coli Genome. J Am Chem Soc 2016; 138:7272-5. [PMID: 27213685 DOI: 10.1021/jacs.6b03904] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Prokaryotic and eukaryotic genomic DNA is comprised of the four building blocks A, G, C, and T. We have begun to explore the consequences of replacing a large fraction or all of a nucleoside in genomic DNA with a modified nucleoside. As a first step we have investigated the possibility of replacement of T by 2'-deoxy-5-(hydroxymethyl)uridine (5hmU) in the genomic DNA of Escherichia coli. Metabolic engineering with phage genes followed by random mutagenesis enabled us to achieve approximately 75% replacement of T by 5hmU in the E. coli genome and in plasmids.
Collapse
Affiliation(s)
- Angad P Mehta
- The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Han Li
- The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sean A Reed
- The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lubica Supekova
- The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tsotne Javahishvili
- The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
38
|
Berdis AJ, McCutcheon D. The use of non-natural nucleotides to probe template-independent DNA synthesis. Chembiochem 2016; 8:1399-408. [PMID: 17607682 DOI: 10.1002/cbic.200700096] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The vast majority of DNA polymerases use the complementary templating strand of DNA to guide each nucleotide incorporation. There are instances, however, in which polymerases can efficiently incorporate nucleotides in the absence of templating information. This process, known as translesion DNA synthesis, can alter the proper genetic code of an organism. To further elucidate the mechanism of template-independent DNA synthesis, we monitored the incorporation of various nucleotides at the "blunt-end" of duplex DNA by the high-fidelity bacteriophage T4 DNA polymerase. Although natural nucleotides are not incorporated at the blunt-end, a limited subset of non-natural indolyl analogues containing extensive pi-electron surface areas are efficiently utilized by the T4 DNA polymerase. These analogues possess high binding affinities that are remarkably similar to those measured during incorporation opposite an abasic site. In contrast, the k(pol) values are significantly lower during blunt-end extension when compared to incorporation opposite an abasic site. These kinetic differences suggest that the single-stranded region of the DNA template plays an important role during polymerization through stacking interactions with downstream bases, interactions with key amino acid residues, or both. In addition, we demonstrate that terminal deoxynucleotide transferase, a template-independent enzyme, can efficiently incorporate many of these non-natural nucleotides. However, that this unique polymerase cannot extend large, bulky non-natural nucleotides suggests that elongation is limited by steric constraints imposed by structural features present within the polymerase. Regardless, the kinetic data obtained from using either DNA polymerase indicate that template-independent synthesis can occur without the contributions of hydrogen-bonding interactions and suggest that pi-electron interactions play an important role in polymerization efficiency when templating information is not present.
Collapse
Affiliation(s)
- Anthony J Berdis
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | | |
Collapse
|
39
|
Chawla M, Credendino R, Chermak E, Oliva R, Cavallo L. Theoretical Characterization of the H-Bonding and Stacking Potential of Two Nonstandard Nucleobases Expanding the Genetic Alphabet. J Phys Chem B 2016; 120:2216-24. [DOI: 10.1021/acs.jpcb.6b00125] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mohit Chawla
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raffaele Credendino
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Edrisse Chermak
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department
of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Luigi Cavallo
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
40
|
Synthesis of Pyridone-based Nucleoside Analogues as Substrates or Inhibitors of DNA Polymerases. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:163-77. [PMID: 26854871 DOI: 10.1080/15257770.2015.1122197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The synthesis and characterization of novel acyclic and cyclic pyridone-based nucleosides and nucleotides is described. In total, seven nucleosides and four nucleotides were synthesized. None of the tested nucleosides showed inhibitory properties against Klenow exo- polymerase and M.MuLV and HIV-1 reverse transcriptases. The nucleotides containing 4-chloro- and 4-bromo-2-pyridone as a nucleobase were accepted by the Klenow fragment, but at the expense of fidelity and extension efficiency.
Collapse
|
41
|
Bag SS, Talukdar S, Das SK, Pradhan MK, Mukherjee S. Donor/acceptor chromophores-decorated triazolyl unnatural nucleosides: synthesis, photophysical properties and study of interaction with BSA. Org Biomol Chem 2016; 14:5088-108. [DOI: 10.1039/c6ob00500d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the syntheses and photophysical properties of some triazolyl donor/acceptor unnatural nucleosides and studies on the interaction of one of the fluorescent nucleosides with BSA.
Collapse
Affiliation(s)
- Subhendu Sekhar Bag
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Sangita Talukdar
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Suman Kalyan Das
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Manoj Kumar Pradhan
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Soumen Mukherjee
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| |
Collapse
|
42
|
Choi JS, Dasari A, Hu P, Benkovic SJ, Berdis AJ. The use of modified and non-natural nucleotides provide unique insights into pro-mutagenic replication catalyzed by polymerase eta. Nucleic Acids Res 2015; 44:1022-35. [PMID: 26717984 PMCID: PMC4756837 DOI: 10.1093/nar/gkv1509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/10/2015] [Indexed: 12/25/2022] Open
Abstract
This report evaluates the pro-mutagenic behavior of 8-oxo-guanine (8-oxo-G) by quantifying the ability of high-fidelity and specialized DNA polymerases to incorporate natural and modified nucleotides opposite this lesion. Although high-fidelity DNA polymerases such as pol δ and the bacteriophage T4 DNA polymerase replicating 8-oxo-G in an error-prone manner, they display remarkably low efficiencies for TLS compared to normal DNA synthesis. In contrast, pol η shows a combination of high efficiency and low fidelity when replicating 8-oxo-G. These combined properties are consistent with a pro-mutagenic role for pol η when replicating this DNA lesion. Studies using modified nucleotide analogs show that pol η relies heavily on hydrogen-bonding interactions during translesion DNA synthesis. However, nucleobase modifications such as alkylation to the N2 position of guanine significantly increase error-prone synthesis catalyzed by pol η when replicating 8-oxo-G. Molecular modeling studies demonstrate the existence of a hydrophobic pocket in pol η that participates in the increased utilization of certain hydrophobic nucleotides. A model is proposed for enhanced pro-mutagenic replication catalyzed by pol η that couples efficient incorporation of damaged nucleotides opposite oxidized DNA lesions created by reactive oxygen species. The biological implications of this model toward increasing mutagenic events in lung cancer are discussed.
Collapse
Affiliation(s)
- Jung-Suk Choi
- Department of Chemistry, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA
| | - Anvesh Dasari
- Department of Chemistry, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA
| | - Peter Hu
- Department of Chemistry, The Pennsylvania State University, 413 Wartik Building, University Park, PA 16802, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, 413 Wartik Building, University Park, PA 16802, USA
| | - Anthony J Berdis
- Department of Chemistry, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA Center for Gene Regulation in Health and Disease, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA Case Comprehensive Cancer Center, 10900 Euclid Avenue, Cleveland OH 44106, USA
| |
Collapse
|
43
|
Abstract
Two new C-nucleoside analogues, BCX4430, an imino-C-nucleoside, and GS-6620, a phosphoramidate derivative of 1'-cyano-2'-C-methyl-4-aza-7,9-dideazaadenosine C-nucleoside, have been recently described as effective against filovirus infections (Marburg) and hepatitis C virus (HCV), respectively. The first C-nucleoside analogues were described about half a century ago. The C-nucleoside pseudouridine is a natural component of RNA, and various other C-nucleoside analogues have been reported previously for their antiviral and/or anticancer potential, the most prominent being pyrazofurin, tiazofurin, and selenazofurin. In the meantime, showdomycin, formycin, and various triazole, pyrazine, pyridine, dihydroxyphenyl, thienopyrimidine, pyrazolotriazine, and porphyrin C-nucleoside analogues have been described. It would be worth revisiting these C-nucleosides and derivatives thereof, including their phosphoramidates, for their therapeutic potential in the treatment of virus infections and, where appropriate, cancer as well.
Collapse
Affiliation(s)
- Erik De Clercq
- Rega Institute for Medical Research, KU Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| |
Collapse
|
44
|
Abstract
All biological information, since the last common ancestor of all life on Earth, has been encoded by a genetic alphabet consisting of only four nucleotides that form two base pairs. Long-standing efforts to develop two synthetic nucleotides that form a third, unnatural base pair (UBP) have recently yielded three promising candidates, one based on alternative hydrogen bonding, and two based on hydrophobic and packing forces. All three of these UBPs are replicated and transcribed with remarkable efficiency and fidelity, and the latter two thus demonstrate that hydrogen bonding is not unique in its ability to underlie the storage and retrieval of genetic information. This Review highlights these recent developments as well as the applications enabled by the UBPs, including the expansion of the evolution process to include new functionality and the creation of semi-synthetic life that stores increased information.
Collapse
Affiliation(s)
- Denis A Malyshev
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA).
| |
Collapse
|
45
|
|
46
|
Liu Z, Wang D, Cao M, Han Y, Xu H, Wang Y. Enhanced Molecular Recognition between Nucleobases and Guanine-5'-monophosphate-disodium (GMP) by Surfactant Aggregates in Aqueous Solution. ACS APPLIED MATERIALS & INTERFACES 2015; 7:15078-15087. [PMID: 26106937 DOI: 10.1021/acsami.5b04441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Only specific base pairs on DNA can bind with each other through hydrogen bonds, which is called the Watson-Crick (W/C) pairing rule. However, without the constraint of DNA chains, the nucleobases in bulk aqueous solution usually do not follow the W/C pairing rule anymore because of the strong competitive effect of water and the multi-interaction edges of nucleobases. The present work applied surfactant aggregates noncovalently functionalized by nucleotide to enhance the recognition between nucleobases without DNA chains in aqueous solution, and it revealed the effects of their self-assembling ability and morphologies on the recognition. The cationic ammonium monomeric, dimeric, and trimeric surfactants DTAB, 12-3-12, and 12-3-12-3-12 were chosen. The surfactants with guanine-5'-monophosphate-disodium (GMP) form micelles, vesicles, and fingerprint-like and plate-like aggregates bearing the hydrogen-bonding sites of GMP, respectively. The binding parameters of these aggregates with adenine (A), uracil (U), guanine (G), and cytosine(C) indicate that the surfactants can promote W/C recognitions in aqueous solution when they form vesicles (GMP/DTAB) or plate-like aggregates (GMP/12-3-12) with proper molecular packing compactness, which not only provide hydrophobic environments but also shield non-W/C recognition edges. However, the GMP/12-3-12 micelles with loose molecular packing, the GMP/12-3-12 fingerprint-like aggregates where the hydrogen bond sites of GMP are occupied by itself, and the GMP/12-3-12-3-12 vesicles with too strong self-assembling ability cannot promote W/C recognition. This work provides insight into how to design self-assemblies with the performance of enhanced molecule recognition.
Collapse
Affiliation(s)
- Zhang Liu
- †Key Laboratory of Colloid and Interface Science, Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Dong Wang
- ‡Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Meiwen Cao
- ‡Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Yuchun Han
- †Key Laboratory of Colloid and Interface Science, Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hai Xu
- ‡Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Yilin Wang
- †Key Laboratory of Colloid and Interface Science, Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| |
Collapse
|
47
|
Schindler D, Waldminghaus T. Synthetic chromosomes. FEMS Microbiol Rev 2015; 39:871-91. [DOI: 10.1093/femsre/fuv030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
|
48
|
|
49
|
Ségurel L, Wyman MJ, Przeworski M. Determinants of Mutation Rate Variation in the Human Germline. Annu Rev Genomics Hum Genet 2014; 15:47-70. [DOI: 10.1146/annurev-genom-031714-125740] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Laure Ségurel
- Laboratoire Éco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle–Centre National de la Recherche Scientifique–Université Paris 7 Diderot, Paris 75231, France;
| | - Minyoung J. Wyman
- Department of Biological Sciences, Columbia University, New York, NY 10027;
| | - Molly Przeworski
- Department of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637;
| |
Collapse
|
50
|
Pezo V, Schepers G, Lambertucci C, Marlière P, Herdewijn P. Probing ambiguous base-pairs by genetic transformation with XNA templates. Chembiochem 2014; 15:2255-8. [PMID: 25158283 DOI: 10.1002/cbic.201402226] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Indexed: 11/11/2022]
Abstract
The templating potential of anhydrohexitol oligonucleotides bearing ambiguous bases was studied in vivo, by using a selection screen for mosaic heteroduplex plasmids in Escherichia coli. 1,5-Anhydro-2,3-dideoxy-2-(5-nitroindazol-1-yl)-D-arabino-hexitol showed the greatest ambiguity among the three nucleosides tested. At most two successive ambiguous bases could be tolerated on hexitol templates read in bacterial cells. Hexitol nucleosides bearing simplified heterocycles thus stand as promising monomers for generating random DNA sequences in vivo from defined synthetic oligonucleotides.
Collapse
Affiliation(s)
- Valérie Pezo
- CEA, DSV, IG, Genoscope, 2 rue Gaston Crémieux 91057 Evry Cedex (France); ISSB, Génopole genavenir6, Equipe Xénome, 5 rue Henri Desbruères 91030 Evry Cedex (France)
| | | | | | | | | |
Collapse
|