1
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Liu X, Shi Q, Qi P, Wang Z, Zhang T, Zhang S, Wu J, Guo Z, Chen J, Zhang Q. Recent advances in living cell nucleic acid probes based on nanomaterials for early cancer diagnosis. Asian J Pharm Sci 2024; 19:100910. [PMID: 38948397 PMCID: PMC11214190 DOI: 10.1016/j.ajps.2024.100910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 07/02/2024] Open
Abstract
The early diagnosis of cancer is vital for effective treatment and improved prognosis. Tumor biomarkers, which can be used for the early diagnosis, treatment, and prognostic evaluation of cancer, have emerged as a topic of intense research interest in recent years. Nucleic acid, as a type of tumor biomarker, contains vital genetic information, which is of great significance for the occurrence and development of cancer. Currently, living cell nucleic acid probes, which enable the in situ imaging and dynamic monitoring of nucleic acids, have become a rapidly developing field. This review focuses on living cell nucleic acid probes that can be used for the early diagnosis of tumors. We describe the fundamental design of the probe in terms of three units and focus on the roles of different nanomaterials in probe delivery.
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Affiliation(s)
- Xuyao Liu
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Qi Shi
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Peng Qi
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Ziming Wang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Tongyue Zhang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Sijia Zhang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jiayan Wu
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhaopei Guo
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jie Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Qiang Zhang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
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2
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Jena NR, Shukla PK. Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA. Sci Rep 2023; 13:19246. [PMID: 37935822 PMCID: PMC10630353 DOI: 10.1038/s41598-023-46572-4] [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: 08/21/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
A triple helical DNA can control gene expression, help in homologous recombination, induce mutations to facilitate DNA repair mechanisms, suppress oncogene formations, etc. However, the structure and function of semisynthetic triple helical DNA are not known. To understand this, various triplets formed between eight artificial nucleobases (P, Z, J, V, B, S, X, and K) and four natural DNA bases (G, C, A, and T) are studied herein by employing a reliable density functional theoretic (DFT) method. Initially, the triple helix-forming artificial nucleobases interacted with the duplex DNA containing GC and AT base pairs, and subsequently, triple helix-forming natural bases (G and C) interacted with artificial duplex DNA containing PZ, JV, BS, and XK base pairs. Among the different triplets formed in the first category, the C-JV triplet is found to be the most stable with a binding energy of about - 31 kcal/mol. Similarly, among the second category of triplets, the Z-GC and V-GC triplets are the most stable. Interestingly, Z-GC and V-GC are found to be isoenergetic with a binding energy of about - 30 kcal/mol. The C-JV, and Z-GC or V-GC triplets are about 12-14 kcal/mol more stable than the JV and GC base pairs respectively. Microsolvation of these triplets in 5 explicit water molecules further enhanced their stability by 16-21 kcal/mol. These results along with the consecutive stacking of the C-JV triplet (C-JV/C-JV) data indicate that the synthetic nucleobases can form stable semisynthetic triple helical DNA. However, consideration of a full-length DNA containing one or more semisynthetic bases or base pairs is necessary to understand the formation of semisynthetic DNA in living cells.
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Affiliation(s)
- N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Dumna Airport Road, Khamaria, Jabalpur, 482005, India.
| | - P K Shukla
- Department of Physics, Assam University, Silchar, Assam, 788 011, India
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3
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Rosa-Gastaldo D, Dalla Valle A, Marchetti T, Gabrielli L. Sequence-selective duplex formation and template effect in recognition-encoded oligoanilines. Chem Sci 2023; 14:8878-8888. [PMID: 37621420 PMCID: PMC10445429 DOI: 10.1039/d3sc00880k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
A new family of duplex-forming recognition encoded oligomers, capable of sequence selective duplex formation and template directed synthesis, was developed. Monomers equipped with both amine and aldehyde groups were functionalized with 2-trifluoromethylphenol or phosphine oxide as H-bond recognition units. Duplex formation and assembly properties of homo- and hetero-oligomers were studied by 19F and 1H NMR experiments in chloroform. The designed backbone prevents the undesired 1,2-folding allowing sequence-selective duplex formation, and the stability of the antiparallel duplex is 3-fold higher than the parallel arrangement. Dynamic combinatorial chemistry was exploited for the templated synthesis of complementary oligomers, showing that an aniline dimer can template the formation of the complementary imine. The key role of the H-bond recognition confers to the system the ability to discriminate a mutated donor monomer incapable of H-bonding. Sequence selective duplex formation combined with the template effect makes this system an attractive target for further studies.
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Affiliation(s)
- Daniele Rosa-Gastaldo
- Dipartimento di Scienze Chimiche, Università degli studi di Padova via Marzolo 1 35131 Padova Italy
| | - Andrea Dalla Valle
- Dipartimento di Scienze Chimiche, Università degli studi di Padova via Marzolo 1 35131 Padova Italy
| | - Tommaso Marchetti
- Dipartimento di Scienze Chimiche, Università degli studi di Padova via Marzolo 1 35131 Padova Italy
| | - Luca Gabrielli
- Dipartimento di Scienze Chimiche, Università degli studi di Padova via Marzolo 1 35131 Padova Italy
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4
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Warman H, Slocombe L, Sacchi M. How proton transfer impacts hachimoji DNA. RSC Adv 2023; 13:13384-13396. [PMID: 37143915 PMCID: PMC10152326 DOI: 10.1039/d3ra00983a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023] Open
Abstract
Hachimoji DNA is a synthetic nucleic acid extension of DNA, formed by an additional four bases, Z, P, S, and B, that can encode information and sustain Darwinian evolution. In this paper, we aim to look into the properties of hachimoji DNA and investigate the probability of proton transfer between the bases, resulting in base mismatch under replication. First, we present a proton transfer mechanism for hachimoji DNA, analogous to the one presented by Löwdin years prior. Then, we use density functional theory to calculate proton transfer rates, tunnelling factors and the kinetic isotope effect in hachimoji DNA. We determined that the reaction barriers are sufficiently low that proton transfer is likely to occur even at biological temperatures. Furthermore, the rates of proton transfer of hachimoji DNA are much faster than in Watson-Crick DNA due to the barrier for Z-P and S-B being 30% lower than in G-C and A-T. Suggesting that proton transfer occurs more frequently in hachimoji DNA than canonical DNA, potentially leading to a higher mutation rate.
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Affiliation(s)
- Harry Warman
- School of Physics and Maths, University of Surrey Guildford GU2 7XH UK
| | - Louie Slocombe
- School of Chemistry and Chemical Engineering, University of Surrey Guildford GU2 7XH UK
| | - Marco Sacchi
- School of Chemistry and Chemical Engineering, University of Surrey Guildford GU2 7XH UK
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5
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Tuning Design Parameters of ICAM-1-Targeted 3DNA Nanocarriers to Optimize Pulmonary Targeting Depending on Drug Type. Pharmaceutics 2022; 14:pharmaceutics14071496. [PMID: 35890393 PMCID: PMC9316040 DOI: 10.3390/pharmaceutics14071496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/30/2022] [Accepted: 07/13/2022] [Indexed: 01/27/2023] Open
Abstract
3DNA holds promise as a carrier for drugs that can be intercalated into its core or linked to surface arms. Coupling 3DNA to an antibody targeting intercellular adhesion molecule 1 (ICAM-1) results in high lung-specific biodistributions in vivo. While the role of individual parameters on ICAM-1 targeting has been studied for other nanocarriers, it has never been examined for 3DNA or in a manner capable of revealing the hierarchic interplay among said parameters. In this study, we used 2-layer vs. 4-layer anti-ICAM 3DNA and radiotracing to examine biodistribution in mice. We found that, below saturating conditions and within the ranges tested, the density of targeting antibodies on 3DNA is the most relevant parameter driving lung targeting over liver clearance, compared to the number of antibodies per carrier, total antibody dose, 3DNA dose, 3DNA size, or the administered concentration, which influenced the dose in organs but not the lung specific-over-liver clearance ratio. Data predicts that lung-specific delivery of intercalating (core loaded) drugs can be tuned using this biodistribution pattern, while that of arm-linked (surface loaded) drugs requires a careful parametric balance because increasing anti-ICAM density reduces the number of 3DNA arms available for drug loading.
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Hans S, Kumar N, Gohil N, Khambhati K, Bhattacharjee G, Deb SS, Maurya R, Kumar V, Reshamwala SMS, Singh V. Rebooting life: engineering non-natural nucleic acids, proteins and metabolites in microorganisms. Microb Cell Fact 2022; 21:100. [PMID: 35643549 PMCID: PMC9148472 DOI: 10.1186/s12934-022-01828-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/15/2022] [Indexed: 12/01/2022] Open
Abstract
The surging demand of value-added products has steered the transition of laboratory microbes to microbial cell factories (MCFs) for facilitating production of large quantities of important native and non-native biomolecules. This shift has been possible through rewiring and optimizing different biosynthetic pathways in microbes by exercising frameworks of metabolic engineering and synthetic biology principles. Advances in genome and metabolic engineering have provided a fillip to create novel biomolecules and produce non-natural molecules with multitude of applications. To this end, numerous MCFs have been developed and employed for production of non-natural nucleic acids, proteins and different metabolites to meet various therapeutic, biotechnological and industrial applications. The present review describes recent advances in production of non-natural amino acids, nucleic acids, biofuel candidates and platform chemicals.
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7
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Munyaradzi O, Rundell S, Bong D. Impact of bPNA Backbone Structural Constraints and Composition on Triplex Hybridization with DNA. Chembiochem 2022; 23:e202100707. [PMID: 35167719 PMCID: PMC9136932 DOI: 10.1002/cbic.202100707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/18/2022] [Indexed: 11/07/2022]
Abstract
We report herein a study on the impact of bifacial peptide nucleic acid (bPNA) amino acid composition and backbone modification on DNA binding. A series of bPNA backbone variants with identical net charge were synthesized to display either 4 or 6 melamine (M) bases. These bases form thymine-melamine-thymine (TMT) base-triples, resulting in triplex hybrid stem structures with T-rich DNAs. Analyses of 6 M bPNA-DNA hybrids suggested that hybrid stability was linked to amino acid secondary structure propensities, prompting a more detailed study in shorter 4 M bPNAs. We synthesized 4 M bPNAs predisposed to adopt helical secondary structure via helix-turn nucleation in 7-residue bPNAs using double-click covalent stapling. Generally, hybrid stability improved upon stapling, but amino acid composition had a more significant effect. We also pursued an alternative strategy for bPNA structural preorganization by incorporation of residues with strong backbone amide conformational preferences such as 4R- and 4S-fluoroprolines. Notably, these derivatives exhibited an additional improvement in hybrid stability beyond both unsubstituted proline bPNA analogues and the helically patterned bPNAs. Overall, these findings demonstrate the tunability of bPNA-DNA hybrid stability through bPNA backbone structural propensities and amino acid composition.
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Affiliation(s)
- Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
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8
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Giraud T, Hoschtettler P, Pickaert G, Averlant-Petit MC, Stefan L. Emerging low-molecular weight nucleopeptide-based hydrogels: state of the art, applications, challenges and perspectives. NANOSCALE 2022; 14:4908-4921. [PMID: 35319034 DOI: 10.1039/d1nr06131c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Over the last twenty years, low-molecular weight gelators and, in particular, peptide-based hydrogels, have drawn great attention from scientists thanks to both their inherent advantages in terms of properties and their high modularity (e.g., number and nature of the amino acids). These supramolecular hydrogels originate from specific peptide self-assembly processes that can be driven, modulated and optimized via specific chemical modifications brought to the peptide sequence. Among them, the incorporation of nucleobases, another class of biomolecules well-known for their abilities to self-assemble, has recently appeared as a new promising and burgeoning approach to finely design supramolecular hydrogels. In this minireview, we would like to highlight the interest, high potential, applications and perspectives of these innovative and emerging low-molecular weight nucleopeptide-based hydrogels.
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Affiliation(s)
- Tristan Giraud
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
| | | | | | | | - Loic Stefan
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
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9
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Devari S, Bhunia D, Bong D. Synthesis of bifacial Peptide Nucleic Acids with diketopiperazine backbones. Synlett 2022; 33:965-968. [DOI: 10.1055/a-1802-6873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report herein synthesis of bifacial peptide nucleic acids (bPNAs) with novel diketopiperazine (DKP) backbones that display unnatural melamine (M) bases as well as native bases. To examine the structure-function scope of diketopiperazine bPNAs, we synthesized a set of bPNAs using diaminopropionic acid, diaminobutyric acid, ornithine and lysine derivatives to display the base-tripling motifs, which result in 1, 2, 3, and 4 carbons linking alpha carbon to sidechain amine, respectively. Thermal denaturation of DNA hybrids with these bPNAs revealed that the optimal sidechain linkage was 4 carbons, corresponding to the lysine derivative. Accordingly, monomers displaying two bases per sidechain were prepared via double reductive alkylation of the ε-amine of Fmoc-Lysine with acetaldehyde derivatives of adenine, cytidine, uridine and melamine. With these building blocks in hand, diketopiperazine bPNAs were prepared to display a combination of native and synthetic (melamine) bases. Preliminary melting studies indicate binding signatures of cytidine and melamine-displaying bPNAs to T-rich DNAs, though full characterization of this behavior is ongoing. We anticipate that the straightforward synthetic methodology developed herein will enable further studies on noncanonical nucleic acid hybridization with diketopiperazine backbones.
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Affiliation(s)
- Shekaraiah Devari
- Chemistry & Biochemistry, The Ohio State University, Columbus, United States
| | - Debmalya Bhunia
- Chemistry & Biochemistry, The Ohio State University, Columbus, United States
| | - Dennis Bong
- Chemistry & Biochemistry, The Ohio State University, Columbus, United States
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10
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Rundell S, Munyaradzi O, Bong D. Enhanced Triplex Hybridization of DNA and RNA via Syndiotactic Side Chain Presentation in Minimal bPNAs. Biochemistry 2021; 61:85-91. [PMID: 34955016 DOI: 10.1021/acs.biochem.1c00693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
General design principles for recognition at noncanonical interfaces of DNA and RNA remain elusive. Triplex hybridization of bifacial peptide nucleic acids (bPNAs) with oligo-T/U DNAs and RNAs is a robust recognition platform that can be used to define structure-function relationships in synthetic triplex formation. To this end, a set of minimal (mw < 1 kD) bPNA variants was synthesized to probe the impact of amino acid secondary structural propensity, stereochemistry, and backbone cyclization on hybridization with short, unstructured T-rich DNA and U-rich RNAs. Thermodynamic parameters extracted from optical melting analyses of bPNA variant hybrids indicated that there are two bPNA backbone modifications that significantly improve hybridization: alternating (d, l) configuration in open-chain dipeptides and homochiral dipeptide cyclization to diketopiperazine. Further, binding to DNA is preferred over RNA for all bPNA variants. Thymine-uracil substitutions in DNA substrates revealed that the methyl group of thymine accounts for 71% of ΔΔGDNA-RNA for open-chain bPNAs but only 40% of ΔΔGDNA-RNA for diketopiperazine bPNA, suggesting a greater sensitivity to RNA conformation and more optimized stacking in the cyclic bPNA. Together, these data reveal pressure points for tuning triplex hybridization at the chiral centers of bPNA, backbone conformation, stacking effects at the base triple, and the nucleic acid substrate itself. A structural blueprint for enhancing bPNA targeting of both DNA and RNA substrates includes syndiotactic base presentation (as found in homochiral diketopiperazines and d, l peptides), expansion of base stacking, and further investigation of bPNA backbone preorganization.
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Affiliation(s)
- Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
| | - Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
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11
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Thompson AS, Barrett SE, Weiden AG, Venkatesh A, Seto MKC, Gottlieb SZP, Leconte AM. Accurate and Efficient One-Pot Reverse Transcription and Amplification of 2'-Fluoro-Modified Nucleic Acids by Commercial DNA Polymerases. Biochemistry 2020; 59:2833-2841. [PMID: 32659079 DOI: 10.1021/acs.biochem.0c00494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA is a foundational tool in biotechnology and synthetic biology but is limited by sensitivity to DNA-modifying enzymes. Recently, researchers have identified DNA polymerases that can enzymatically synthesize long oligonucleotides of modified DNA (M-DNA) that are resistant to DNA-modifying enzymes. Most applications require M-DNA to be reverse transcribed, typically using a RNA reverse transcriptase, back into natural DNA for sequence analysis or further manipulation. Here, we tested commercially available DNA-dependent DNA polymerases for their ability to reverse transcribe and amplify M-DNA in a one-pot reaction. Three of the six polymerases chosen (Phusion, Q5, and Deep Vent) could reverse transcribe and amplify synthetic 2'F M-DNA in a single reaction with <5 × 10-3 error per base pair. We further used Q5 DNA polymerase to reverse transcribe and amplify M-DNA synthesized by two candidate M-DNA polymerases (SFP1 and SFM4-6), allowing for quantification of the frequency, types, and locations of errors made during M-DNA synthesis. From these studies, we identify SFP1 as one of the most accurate M-DNA polymerases identified to date. Collectively, these studies establish a simple, robust method for the conversion of 2'F M-DNA to DNA in <1 h using commercially available materials, significantly improving the ease of use of M-DNA.
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Affiliation(s)
- Arianna S Thompson
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Susanna E Barrett
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Aurora G Weiden
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Ananya Venkatesh
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Madison K C Seto
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Simone Z P Gottlieb
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Aaron M Leconte
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
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12
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Gabrielli L, Hunter CA. Supramolecular catalysis by recognition-encoded oligomers: discovery of a synthetic imine polymerase. Chem Sci 2020; 11:7408-7414. [PMID: 34123021 PMCID: PMC8159439 DOI: 10.1039/d0sc02234a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
All key chemical transformations in biology are catalysed by linear oligomers. Catalytic properties could be programmed into synthetic oligomers in the same way as they are programmed into proteins, and an example of the discovery of emergent catalytic properties in a synthetic oligomer is reported. Dynamic combinatorial chemistry experiments designed to study the templating of a recognition-encoded oligomer by the complementary sequence have uncovered an unexpected imine polymerase activity. Libraries of equilibrating imines were formed by coupling diamine linkers with monomer building blocks composed of dialdehydes functionalised with either a trifluoromethyl phenol (D) or phosphine oxide (A) H-bond recognition unit. However, addition of the AAA trimer to a mixture of the phenol dialdehyde and the diamine linker did not template the formation of the DDD oligo-imine. Instead, AAA was found to be a catalyst, leading to rapid formation of long oligomers of D. AAA catalysed a number of different imine formation reactions, but a complementary phenol recognition group on the aldehyde reaction partner is an essential requirement. Competitive inhibition by an unreactive phenol confirmed the role of H-bonding in substrate recognition. AAA accelerates the rate of imine formation in toluene by a factor of 20. The kinetic parameters for this enzyme-like catalysis are estimated as 1 × 10-3 s-1 for k cat and the dissociation constant for substrate binding is 300 μM. The corresponding DDD trimer was found to catalyse oligomerisation the phosphine oxide dialdehyde with the diamine linker, suggesting an important role for the backbone in catalysis. This unexpected imine polymerase activity in a duplex-forming synthetic oligomer suggests that there are many interesting processes to be discovered in the chemistry of synthetic recognition-encoded oligomers that will parallel those found in natural biopolymers.
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Affiliation(s)
- Luca Gabrielli
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK .,Department of Chemistry, University of Padova via F. Marzolo 1 Padova 35131 Italy
| | - Christopher A Hunter
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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13
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Sharpe DJ, Röder K, Wales DJ. Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers. J Phys Chem B 2020; 124:4062-4068. [PMID: 32336100 PMCID: PMC7304908 DOI: 10.1021/acs.jpcb.0c01420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Artificial
analogues of the natural nucleic acids have attracted
interest as a diverse class of information storage molecules capable
of self-replication. In this study, we use the computational potential
energy landscape framework to investigate the structural and dynamical
properties of xylo- and deoxyxylo-nucleic acids (XyNA and dXyNA),
which are derived from their respective RNA and DNA analogues by inversion
of a single chiral center in the sugar moiety of the nucleotides.
For an octameric XyNA sequence and the analogue dXyNA, we observe
facile conformational transitions between a left-handed helix, which
is the free energy global minimum, and a ladder-type structure with
approximately zero helicity. The competing ensembles are better separated
in the dXyNA, making it a more suitable candidate for a molecular
switch, whereas the XyNA exhibits additional flexibility. Both energy
landscapes exhibit greater frustration than we observe in RNA or DNA,
in agreement with the higher degree of optimization expected from
the principle of minimal frustration in evolved biomolecules.
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Affiliation(s)
- Daniel J Sharpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Konstantin Röder
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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14
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Gabrielli L, Núñez-Villanueva D, Hunter CA. Two-component assembly of recognition-encoded oligomers that form stable H-bonded duplexes. Chem Sci 2019; 11:561-566. [PMID: 32206273 PMCID: PMC7069511 DOI: 10.1039/c9sc04250d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/19/2019] [Indexed: 12/17/2022] Open
Abstract
Imine chemistry was used to assemble oligomers displaying phenol and phosphine oxide side chains that selectively base-pair to give duplexes, which are stable in chloroform solution.
A new family of recognition-encoded oligomers that form stable duplexes in chloroform have been prepared. Monomer building blocks composed of dialdehydes functionalised with either a trifluoromethylphenol or phosphine oxide H-bond recognition unit were prepared. The dialdehydes were coupled with diamines by imine formation and then reduction to give homo-oligomers between one and three recognition units in length. Duplex formation was characterised by 19F and 1H NMR titration experiments in toluene and in chloroform. For duplexes formed between length complementary H-bond donor and acceptor homo-oligomers, an order of magnitude increase in stability was observed for every base-pair added to the duplex in chloroform. The effective molarity for the intramolecular H-bonds responsible for zipping up the duplex is 30 mM, which results in the fully assembled duplex in all cases. The uniform increase in duplex stability with oligomer length suggests that the backbone structure and geometry is likely to be compatible with the formation of extended duplexes in longer oligomers.
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Affiliation(s)
- Luca Gabrielli
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Diego Núñez-Villanueva
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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15
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Simon MD, Machyna M. Principles and Practices of Hybridization Capture Experiments to Study Long Noncoding RNAs That Act on Chromatin. Cold Spring Harb Perspect Biol 2019; 11:11/11/a032276. [PMID: 31676573 DOI: 10.1101/cshperspect.a032276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The diverse roles of cellular RNAs can be studied by purifying RNAs of interest together with the biomolecules they bind. Biotinylated antisense oligonucleotides that hybridize specifically to the RNA of interest provide a general approach to develop affinity reagents for these experiments. Such oligonucleotides can be used to enrich endogenous RNAs from cross-linked chromatin extracts to study the genomic binding sites of RNAs. These hybridization capture protocols are evolving modular experiments that are compatible with a range of cross-linkers and conditions. This review discusses the principles of these hybridization capture experiments as well as considerations and controls necessary to interpret the resulting data without being misled by artifactual signals.
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Affiliation(s)
- Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Martin Machyna
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
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16
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Cleaves HJ, Butch C, Burger PB, Goodwin J, Meringer M. One Among Millions: The Chemical Space of Nucleic Acid-Like Molecules. J Chem Inf Model 2019; 59:4266-4277. [PMID: 31498614 DOI: 10.1021/acs.jcim.9b00632] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Biology encodes hereditary information in DNA and RNA, which are finely tuned to their biological functions and modes of biological production. The central role of nucleic acids in biological information flow makes them key targets of pharmaceutical research. Indeed, other nucleic acid-like polymers can play similar roles to natural nucleic acids both in vivo and in vitro; yet despite remarkable advances over the last few decades, much remains unknown regarding which structures are compatible with molecular information storage. Chemical space describes the structures and properties of molecules that could exist within a given molecular formula or other classification system. Using structure generation methods, we explore nucleic acid analogues within the formula ranges BC3-7H5-15O2-4 and BC3-6H5-15N1-2O0-4, where B is a recognition element (e.g., a nucleobase). Other restrictions included two obligatory points of attachment for inclusion into a linear polymer and substructures predicting chemical stability. These sets contain 86,007 (CHO) and 75,309 (CHNO) compositionally isomeric structures, representing 706,568 CHO and 454,422 CHNO stereoisomers, that diversely and densely occupy this space. These libraries point toward there being large spaces of unexplored chemistry relevant to pharmacology and biochemistry and efforts to understand the origins of life.
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Affiliation(s)
- Henderson James Cleaves
- Earth-Life Science Institute , Tokyo Institute of Technology , 2-12-IE-1 Ookayama , Meguro-ku , Tokyo 152-8551 , Japan.,Institute for Advanced Study , Princeton , New Jersey 08540 , United States.,Blue Marble Space Institute for Science , 1515 Gallatin St. NW , Washington , DC 20011 , United States
| | - Christopher Butch
- Earth-Life Science Institute , Tokyo Institute of Technology , 2-12-IE-1 Ookayama , Meguro-ku , Tokyo 152-8551 , Japan.,Blue Marble Space Institute for Science , 1515 Gallatin St. NW , Washington , DC 20011 , United States.,Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Pieter Buys Burger
- Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Jay Goodwin
- Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Markus Meringer
- German Aerospace Center (DLR) , Earth Observation Center (EOC) , Münchner Straße 20 , 82234 Oberpfaffenhofen-Wessling , Germany
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17
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Chawla M, Minenkov Y, Vu KB, Oliva R, Cavallo L. Structural and Energetic Impact of Non-natural 7-Deaza-8-azaguanine, 7-Deaza-8-azaisoguanine, and Their 7-Substituted Derivatives on Hydrogen-Bond Pairing with Cytosine and Isocytosine. Chembiochem 2019; 20:2262-2270. [PMID: 30983115 DOI: 10.1002/cbic.201900245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Indexed: 12/12/2022]
Abstract
The impact of 7-deaza-8-azaguanine (DAG) and 7-deaza-8-azaisoguanine (DAiG) modifications on the geometry and stability of the G:C Watson-Crick (cWW) base pair and the G:iC and iG:C reverse Watson-Crick (tWW) base pairs has been characterized theoretically. In addition, the effect on the same base pairs of seven C7-substituted DAG and DAiG derivatives, some of which have been previously experimentally characterized, has been investigated. Calculations indicate that all of these modifications have a negligible impact on the geometry of the above base pairs, and that modification of the heterocycle skeleton has a small impact on the base-pair interaction energies. Instead, base-pair interaction energies are dependent on the nature of the C7 substituent. For the 7-substituted DAG-C cWW systems, a linear correlation between the base-pair interaction energy and the Hammett constant of the 7-substituent is found, with higher interaction energies corresponding to more electron-withdrawing substituents. Therefore, the explored modifications are expected to be accommodated in both parallel and antiparallel nucleic acid duplexes without perturbing their geometry, while the strength of a base pair (and duplex) featuring a DAG modification can, in principle, be tuned by incorporating different substituents at the C7 position.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
| | - Yury Minenkov
- Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, Moscow Region, 141700, Russia
| | - Khanh B Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ho Chi Minh City, Vietnam
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
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18
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Lackey HH, Peterson EM, Chen Z, Harris JM, Heemstra JM. Thermostability Trends of TNA:DNA Duplexes Reveal Strong Purine Dependence. ACS Synth Biol 2019; 8:1144-1152. [PMID: 30964657 DOI: 10.1021/acssynbio.9b00028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of high fidelity polymerases and streamlined synthesis of threose nucleic acid (TNA) triphosphates and phosphoramidites has made TNA accessible as a motif for generating nuclease-resistant high-affinity aptamers, antisense oligos, and synthetic genetic biopolymers. Little is known, however, about the thermostability trends of TNA:DNA duplexes. Here we investigate the thermostability of 14 TNA:DNA duplexes with the goal of elucidating the fundamental factors governing TNA:DNA duplex stability. We find that purine content in TNA significantly influences the stability and conformation of TNA:DNA duplexes. Low TNA purine content destabilizes duplexes, with Tm values often 5 °C lower than analogous DNA:DNA and RNA:DNA duplexes. By contrast, TNA:DNA duplexes having high TNA purine content display greater stability than DNA:DNA or RNA:DNA duplexes having the same sequences. High TNA purine content leads TNA:DNA duplexes to adopt conformations similar to RNA:RNA (A-form) configuration, whereas duplexes with low TNA purine content have conformations more similar to DNA:DNA (B-form) configuration. These insights provide a basis for understanding and predicting TNA:DNA duplex stability, which is anticipated to guide the practical use of TNA in biotechnology applications.
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Affiliation(s)
- Hershel H. Lackey
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric M. Peterson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Zhe Chen
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Joel M. Harris
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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19
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Huy Le B, Nguyen VT, Seo YJ. Site-specific incorporation of multiple units of functional nucleotides into DNA using a step-wise approach with polymerase and its application to monitoring DNA structural changes. Chem Commun (Camb) 2019; 55:2158-2161. [PMID: 30675606 DOI: 10.1039/c8cc09444f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have developed a new method, a step-wise approach with polymerase, for site-specific incorporation of multiple units of functional nucleotides into DNA to form hairpin secondary structures. The fluorescence of the resulting DNA incorporating the functional nucleotides varied upon transitioning from single-strand to hairpin and duplex structures.
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Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences, Chonbuk National University, South Korea
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20
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Vichier-Guerre S, Dugué L, Pochet S. 2'-Deoxyribonucleoside 5'-triphosphates bearing 4-phenyl and 4-pyrimidinyl imidazoles as DNA polymerase substrates. Org Biomol Chem 2019; 17:290-301. [PMID: 30543241 DOI: 10.1039/c8ob02464b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed a versatile access to a series of 4-substituted imidazole 2'-deoxynucleoside triphosphate bearing functionalized phenyl or pyrimidinyl rings. 4-Iodo-1H-imidazole was enzymatically converted into the corresponding 2'-deoxynucleoside, which was then chemically derived into its 5'-triphosphate, followed by 4-arylation via Suzuki-Miyaura coupling using (hetero)arylboronic acids. Both KF (exo-) and Deep Vent (exo-) DNA polymerases incorporated these modified nucleotides in primer-extension assays, adenine being the preferred pairing partner in the template. The 4-(3-aminophenyl)imidazole derivative (3APh) was the most efficiently inserted opposite A by KF (exo-) with only a 37-fold lower efficiency (Vmax/KM) than that of the correct dTTP. No further extension occurred after the incorporation of a single aryl-imidazole nucleotide. Interestingly, the aryl-imidazole dNTPs were found to undergo successive incorporation by calf thymus terminal deoxynucleotidyl transferase with different tailing efficiencies among this series and with a marked preference for 2APyr polymerization.
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Affiliation(s)
- Sophie Vichier-Guerre
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS, UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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21
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Szczypiński FT, Hunter CA. Building blocks for recognition-encoded oligoesters that form H-bonded duplexes. Chem Sci 2019; 10:2444-2451. [PMID: 30881672 PMCID: PMC6385898 DOI: 10.1039/c8sc04896g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/03/2019] [Indexed: 12/20/2022] Open
Abstract
A long-short base-pairing scheme hinders intramolecular folding and allows the use of flexible backbones in duplex-forming oligomers.
Competition from intramolecular folding is a major challenge in the design of synthetic oligomers that form intermolecular duplexes in a sequence-selective manner. One strategy is to use very rigid backbones that prevent folding, but this design can prejudice duplex formation if the geometry is not exactly right. The alternative approach found in nucleic acids is to use bases (or recognition units) that have different dimensions. A long-short base-pairing scheme makes folding geometrically difficult and is compatible with the flexible backbones that are required to guarantee duplex formation. A monomer building block equipped with a long hydrogen bond donor (phenol, D) recognition unit and a monomer building block equipped with a short hydrogen bond acceptor (phosphine oxide, A) recognition unit were prepared with differentially protected alcohol and carboxylic acid groups. These compounds were used to synthesise the homo and hetero-sequence 2-mers AA, DD and AD. 19F and 31P NMR experiments were used to characterize the assembly properties of these compounds in toluene solution. AA and DD form a stable doubly-hydrogen-bonded duplex with an effective molarity of 20 mM for formation of the second intramolecular hydrogen bond. AD forms a duplex of similar stability. There is no evidence of intramolecular folding in the monomeric state of this compound, which shows that the long-short base-pairing scheme is effective. The ester coupling chemistry used here is an attractive method for the synthesis of long oligomers, and the properties of the 2-mers indicate that this molecular architecture should give longer mixed sequence oligomers that show high fidelity sequence-selective duplex formation.
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Affiliation(s)
- Filip T Szczypiński
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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22
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Bauwens B, Rozenski J, Herdewijn P, Robben J. A Single Amino Acid Substitution in Therminator DNA Polymerase Increases Incorporation Efficiency of Deoxyxylonucleotides. Chembiochem 2018; 19:2410-2420. [PMID: 30204290 DOI: 10.1002/cbic.201800411] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 11/11/2022]
Abstract
Deoxyxylonucleic acid (dxNA) is a synthetic polymer that might have potential for heredity and evolution. Because of dxNA's unusual backbone geometry, sequence information stored in it is presumed to be inaccessible to natural nucleic acids or proteins. Despite a large structural similarity with natural nucleotides, incorporation of 2'-deoxyxylonucleotides (dxNTs) through the action of polymerases is limited. We present the identification of a mutant of the DNA polymerase Therminator with increased tolerance to deoxyxylose-induced backbone distortions. Whereas the original polymerase stops after incorporation of two consecutive dxNTs, the mutant is able to catalyse the extension of incorporated dxNTs with 2'-deoxyribonucleotides (dNTs) and the incorporation of up to four dxNTs alternates with dNTs, thereby translocating a highly distorted double helix throughout the entire polymerase. A single His-to-Arg substitution very close to the catalytic site residues is held to be responsible for interaction with the primer phosphate groups and for stabilizing nucleotide sugar-induced distortions during incorporation and translocation.
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Affiliation(s)
- Boris Bauwens
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium
| | - Jef Rozenski
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1030, 3000, Leuven, Belgium
| | - Piet Herdewijn
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1030, 3000, Leuven, Belgium
| | - Johan Robben
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium
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23
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Swain J, Iadevaia G, Hunter CA. H-Bonded Duplexes based on a Phenylacetylene Backbone. J Am Chem Soc 2018; 140:11526-11536. [PMID: 30179469 PMCID: PMC6148443 DOI: 10.1021/jacs.8b08087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Indexed: 11/30/2022]
Abstract
Complementary phenylacetylene oligomers equipped with phenol and phosphine oxide recognition sites form stable multiply H-bonded duplexes in toluene solution. Oligomers were prepared by Sonogashira coupling of diiodobenzene and bis-acetylene building blocks in the presence of monoacetylene chain terminators. The product mixtures were separated by reverse phase preparative high-pressure liquid chromatography to give a series of pure oligomers up to seven recognition units in length. Duplex formation between length complementary homo-oligomers was demonstrated by 31P NMR denaturation experiments using dimethyl sulfoxide as a competing H-bond acceptor. The denaturation experiments were used to determine the association constants for duplex formation, which increase by nearly 2 orders of magnitude for every phenol-phosphine oxide base-pair added. These experiments show that the phenylacetylene backbone supports formation of extended duplexes with multiple cooperative intermolecular H-bonding interactions, and together with previous studies on the mixed sequence phenylacetylene 2-mer, suggest that this supramolecular architecture is a promising candidate for the development of synthetic information molecules that parallel the properties of nucleic acids.
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Affiliation(s)
- Jonathan
A. Swain
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Giulia Iadevaia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Christopher A. Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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24
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Tomaszewska-Antczak A, Jastrzębska K, Maciaszek A, Mikołajczyk B, Guga P. P-Stereodefined phosphorothioate analogs of glycol nucleic acids-synthesis and structural properties. RSC Adv 2018; 8:24942-24952. [PMID: 35542141 PMCID: PMC9082371 DOI: 10.1039/c8ra05568h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/02/2018] [Indexed: 11/21/2022] Open
Abstract
Enantiomerically pure, protected acyclic nucleosides of the GNA type (glycol nucleic acids) (GN′), obtained from (R)-(+)- and (S)-(−)-glycidols and the four canonical DNA nucleobases (Ade, Cyt, Gua and Thy), were transformed into 3′-O-DMT-protected 2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane derivatives (OTP-GN′) containing a second stereogenic center at the phosphorus atom. These monomers were chromatographically separated into P-diastereoisomers, which were further used for the synthesis of P-stereodefined “dinucleoside” phosphorothioates GNPST (GN = GA, GC, GG, GT). The absolute configuration at the phosphorus atom for all eight GNPST was established enzymatically and verified chemically, and correlated with chromatographic mobility of the OTP-GN′ monomers on silica gel. The GNPS units (derived from (R)-(+)-glycidol) were introduced into self-complementary PS-(DNA/GNA) octamers of preselected, uniform absolute configuration at P-atoms. Thermal dissociation experiments showed that the thermodynamic stability of the duplexes depends on the stereochemistry of the phosphorus centers and relative arrangement of the GN units in the oligonucleotide strands. These results correlate with the changes of conformation assessed from circular dichroism spectra. The stability of P-stereodefined PS-(DNA/GNA) duplexes depends on the stereochemistry of the phosphorus centers and arrangement of –GNPS– units in the strands.![]()
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Affiliation(s)
- Agnieszka Tomaszewska-Antczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Katarzyna Jastrzębska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Anna Maciaszek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Barbara Mikołajczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
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25
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Iadevaia G, Núñez-Villanueva D, Stross AE, Hunter CA. Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers. Org Biomol Chem 2018; 16:4183-4190. [PMID: 29790563 PMCID: PMC5989393 DOI: 10.1039/c8ob00819a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 04/30/2018] [Indexed: 01/06/2023]
Abstract
Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.
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Affiliation(s)
- Giulia Iadevaia
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
| | - Diego Núñez-Villanueva
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
| | - Alexander E. Stross
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
| | - Christopher A. Hunter
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
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26
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Ogami K, Okada Y, Chiba K. A Pot-economical Liquid-phase Peptide Nucleic Acid Synthesis Enabled by a Soluble Tag-assisted Method. CHEM LETT 2018. [DOI: 10.1246/cl.170971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Keisuke Ogami
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Yohei Okada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazuhiro Chiba
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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27
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Zhang S, Geryak R, Geldmeier J, Kim S, Tsukruk VV. Synthesis, Assembly, and Applications of Hybrid Nanostructures for Biosensing. Chem Rev 2017; 117:12942-13038. [DOI: 10.1021/acs.chemrev.7b00088] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shuaidi Zhang
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Ren Geryak
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Jeffrey Geldmeier
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Sunghan Kim
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Vladimir V. Tsukruk
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
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28
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Stross A, Iadevaia G, Núñez-Villanueva D, Hunter CA. Sequence-Selective Formation of Synthetic H-Bonded Duplexes. J Am Chem Soc 2017; 139:12655-12663. [PMID: 28857551 PMCID: PMC5627343 DOI: 10.1021/jacs.7b06619] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 11/30/2022]
Abstract
Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M-1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor-acceptor sequences are avoided.
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Affiliation(s)
- Alexander
E. Stross
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Giulia Iadevaia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Diego Núñez-Villanueva
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christopher A. Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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29
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Ghosh S, Chakrabarti R. Spontaneous Unzipping of Xylonucleic Acid Assisted by a Single-Walled Carbon Nanotube: A Computational Study. J Phys Chem B 2016; 120:3642-52. [DOI: 10.1021/acs.jpcb.6b02035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Soumadwip Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 40076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 40076, India
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30
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Iadevaia G, Stross AE, Neumann A, Hunter CA. Mix and match backbones for the formation of H-bonded duplexes. Chem Sci 2016; 7:1760-1767. [PMID: 28936325 PMCID: PMC5592378 DOI: 10.1039/c5sc04467g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/18/2015] [Indexed: 11/21/2022] Open
Abstract
The formation of well-defined supramolecular assemblies involves competition between intermolecular and intramolecular interactions, which is quantified by effective molarity. Formation of a duplex between two oligomers equipped with recognition sites displayed along a non-interacting backbone requires that once one intermolecular interaction has been formed, all subsequent interactions take place in an intramolecular sense. The efficiency of this process is governed by the geometric complementarity and conformational flexibility of the backbone linking the recognition sites. Here we report a series of phosphine oxide H-bond acceptor AA 2-mers and phenol H-bond donor DD 2-mers, where the two recognition sites are connected by isomeric backbone modules that vary in geometry and flexibility. All AA and DD combinations form stable AA·DD duplexes, where two cooperative H-bonds lead to an increase in stability of an order of magnitude compared with the corresponding A·D complexes that can only form one H-bond. For all six possible backbone combinations, the effective molarity for duplex formation is approximately constant (7-20 mM). Thus strict complementarity and high degrees of preorganisation are not required for efficient supramolecular assembly. Provided there is some flexibility, quite different backbone modules can be used interchangeably to construct stable H-bonded duplexes.
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Affiliation(s)
- Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Alexander E Stross
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Anja Neumann
- Department of Chemistry , University of Sheffield , Sheffield S3 7HF , UK
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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Engelen W, Janssen BMG, Merkx M. DNA-based control of protein activity. Chem Commun (Camb) 2016; 52:3598-610. [PMID: 26812623 PMCID: PMC4767025 DOI: 10.1039/c5cc09853j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA has emerged as a highly versatile construction material for nanometer-sized structures and sophisticated molecular machines and circuits. The successful application of nucleic acid based systems greatly relies on their ability to autonomously sense and act on their environment. In this feature article, the development of DNA-based strategies to dynamically control protein activity via oligonucleotide triggers is discussed. Depending on the desired application, protein activity can be controlled by directly conjugating them to an oligonucleotide handle, or expressing them as a fusion protein with DNA binding motifs. To control proteins without modifying them chemically or genetically, multivalent ligands and aptamers that reversibly inhibit their function provide valuable tools to regulate proteins in a noncovalent manner. The goal of this feature article is to give an overview of strategies developed to control protein activity via oligonucleotide-based triggers, as well as hurdles yet to be taken to obtain fully autonomous systems that interrogate, process and act on their environments by means of DNA-based protein control.
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Affiliation(s)
- W Engelen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
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Anosova I, Kowal EA, Dunn MR, Chaput JC, Van Horn WD, Egli M. The structural diversity of artificial genetic polymers. Nucleic Acids Res 2015; 44:1007-21. [PMID: 26673703 PMCID: PMC4756832 DOI: 10.1093/nar/gkv1472] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/30/2015] [Indexed: 11/13/2022] Open
Abstract
Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson-Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space.
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Affiliation(s)
- Irina Anosova
- The Biodesign Institute, Virginia G. Piper Center for Personalized Diagnostics, School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Ewa A Kowal
- Department of Biochemistry, Center for Structural Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, School of Medicine, Nashville, TN 37232-0146, USA
| | - Matthew R Dunn
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, CA 92697, USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, CA 92697, USA
| | - Wade D Van Horn
- The Biodesign Institute, Virginia G. Piper Center for Personalized Diagnostics, School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Martin Egli
- Department of Biochemistry, Center for Structural Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, School of Medicine, Nashville, TN 37232-0146, USA
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Stross AE, Iadevaia G, Hunter CA. Cooperative duplex formation by synthetic H-bonding oligomers. Chem Sci 2015; 7:94-101. [PMID: 29861969 PMCID: PMC5950798 DOI: 10.1039/c5sc03414k] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/15/2015] [Indexed: 01/12/2023] Open
Abstract
Flexible phenol-phosphine oxide oligomers show promise as a new class of synthetic information molecule.
A series of flexible oligomers equipped with phenol H-bond donors and phosphine oxide H-bond acceptors have been synthesised using reductive amination chemistry. H-bonding interactions between complementary oligomers leads to the formation of double-stranded complexes which were characterised using NMR titrations and thermal denaturation experiments. The stability of the duplex increases by one order of magnitude for every H-bonding group added to the chain. Similarly, the enthalpy change for duplex assembly and the melting temperature for duplex denaturation both increase with increasing chain length. These observations indicate that H-bond formation along the oligomers is cooperative despite the flexible backbone, and the effective molarity for intramolecular H-bond formation (14 mM) is sufficient to propagate the formation of longer duplexes using this approach. The product K EM, which is used to quantify chelate cooperativity is 5, which means that each H-bond is more than 80% populated in the assembled duplex. The modular design of these oligomers represents a general strategy for the design of synthetic information molecules that could potentially encode and replicate chemical information in the same way as nucleic acids.
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Affiliation(s)
- Alexander E Stross
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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Sugimura H, Endo S, Ishizuka K. Stereocontrolled approach for the syntheses of 3-isopurine nucleosides: 3-(2-deoxy-β-d-ribofuranosyl)xanthine and isoguanine by intramolecular glycosylation. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.09.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Shirato W, Chiba J, Inouye M. A firmly hybridizable, DNA-like architecture with DAD/ADA- and ADD/DAA-type nonnatural base pairs as an extracellular genetic candidate. Chem Commun (Camb) 2015; 51:7043-6. [PMID: 25806487 DOI: 10.1039/c4cc09486g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe artificial DNA molecules exclusively consisting of four types of alkynyl C-nucleotides with nonnatural bases. The artificial DNA exhibited almost the same characteristics as natural DNA, such as in regard to the stepwise duplex and triplex formation and the right-handed higher-order structure with an antiparallel alignment fashion.
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Affiliation(s)
- Wataru Shirato
- Graduate School of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.
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36
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Maruyama H, Furukawa K, Kamiya H, Minakawa N, Matsuda A. Transcription of 4′-thioDNA templates to natural RNA in vitro and in mammalian cells. Chem Commun (Camb) 2015; 51:7887-90. [DOI: 10.1039/c4cc08862j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Synthetic chemically modified nucleic acids, which are compatible with DNA/RNA polymerases, have great potential as a genetic material for synthetic biological studies.
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Affiliation(s)
- Hideto Maruyama
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Sapporo 060-0812
- Japan
| | - Kazuhiro Furukawa
- Graduate School of Pharmaceutical Sciences
- The University of Tokushima
- Tokushima 770-8505
- Japan
| | - Hiroyuki Kamiya
- Graduate School of Biomedical & Health Sciences
- Hiroshima University
- Hiroshima 734-8553
- Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Sciences
- The University of Tokushima
- Tokushima 770-8505
- Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Sapporo 060-0812
- Japan
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37
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Ding Y, Wu F, Tan C. Synthetic Biology: A Bridge between Artificial and Natural Cells. Life (Basel) 2014; 4:1092-116. [PMID: 25532531 PMCID: PMC4284483 DOI: 10.3390/life4041092] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/02/2014] [Accepted: 12/11/2014] [Indexed: 12/24/2022] Open
Abstract
Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation machinery that synthesize proteins based on genetic sequences; and (3) genetic modules that control the dynamics of the whole cell. Artificial cells are minimal and well-defined systems that can be more easily engineered and controlled when compared to natural cells. Artificial cells can be used as biomimetic systems to study and understand natural dynamics of cells with minimal interference from cellular complexity. However, there remain significant gaps between artificial and natural cells. How much information can we encode into artificial cells? What is the minimal number of factors that are necessary to achieve robust functioning of artificial cells? Can artificial cells communicate with their environments efficiently? Can artificial cells replicate, divide or even evolve? Here, we review synthetic biological methods that could shrink the gaps between artificial and natural cells. The closure of these gaps will lead to advancement in synthetic biology, cellular biology and biomedical applications.
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Affiliation(s)
- Yunfeng Ding
- Department of Biomedical Engineering, University of California Davis, One Shields Ave., Davis, CA 95616-5270, USA.
| | - Fan Wu
- Department of Biomedical Engineering, University of California Davis, One Shields Ave., Davis, CA 95616-5270, USA.
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, One Shields Ave., Davis, CA 95616-5270, USA.
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38
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Hernández D, Boto A. Nucleoside Analogues: Synthesis and Biological Properties of Azanucleoside Derivatives. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301731] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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39
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Kim EK, Switzer C. Polymerase Recognition of a Watson-Crick-Like Metal-Mediated Base Pair: Purine-2,6-Dicarboxylate⋅Copper(II)⋅ Pyridine. Chembiochem 2013; 14:2403-7. [DOI: 10.1002/cbic.201300634] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Indexed: 11/09/2022]
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Abstract
RNA molecules are highly modular components that can be used in a variety of contexts for building new metabolic, regulatory and genetic circuits in cells. The majority of synthetic RNA systems to date predominately rely on two-dimensional modularity. However, a better understanding and integration of three-dimensional RNA modularity at structural and functional levels is critical to the development of more complex, functional bio-systems and molecular machines for synthetic biology applications.
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Affiliation(s)
- Wade Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University3307 Third Avenue West, Seattle, WA 98119USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Bio-Molecular Science and Engineering Program, University of CaliforniaSanta Barbara, CA 93106-9510USA
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41
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Abstract
For over 20 years, laboratories around the world have been applying the principles of Darwinian evolution to isolate DNA and RNA molecules with specific ligand-binding or catalytic activities. This area of synthetic biology, commonly referred to as in vitro genetics, is made possible by the availability of natural polymerases that can replicate genetic information in the laboratory. Moving beyond natural nucleic acids requires organic chemistry to synthesize unnatural analogues and polymerase engineering to create enzymes that recognize artificial substrates. Progress in both of these areas has led to the emerging field of synthetic genetics, which explores the structural and functional properties of synthetic genetic polymers by in vitro evolution. This review examines recent advances in the Darwinian evolution of artificial genetic polymers and their potential downstream applications in exobiology, molecular medicine, and synthetic biology.
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Affiliation(s)
- John C Chaput
- Center for Evolutionary Medicine and Informatics in the Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5301, USA.
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42
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Nakano SI, Oka H, Yamaguchi D, Fujii M, Sugimoto N. Base-pairing selectivity of a ureido-linked phenyl-2'-deoxycytidine derivative. Org Biomol Chem 2012; 10:9664-70. [PMID: 23147647 DOI: 10.1039/c2ob26897c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Incorporation of modified nucleotides into nucleic acid strands often produces conformational constraints and steric hindrances that may change the property of base pairing. In this study, we investigated a 2'-deoxycytidine derivative that tethers a phenyl moiety to the exocyclic amino group of cytosine linked through a ureido group. This derivative compound is structurally similar to the carbamoylated DNA base lesions produced in cells. The thermodynamic and structural studies showed that the modified dC formed the base pair with dG in the complementary strand, but the base-pairing selectivity toward dG was decreased under poly(ethylene glycol)-mediated osmotic stress. The phenyl group and the ureido linker attached to dC provided selectivity for the formation of base pairing exclusively with dG in a wide range of pH conditions, whereas unmodified dC stabilized the pairings with dA or dC in acidic solutions. Moreover, this modified base could not form self-pairing through intermolecular hydrogen bonds. We suggest that formation of weak pairing and protonation of the cytosine base are hindered due to the base modification. These data provide insights into the pairing selectivity of carbamoylated cytosine lesions produced in cells, and suggest applications of the 2'-deoxycytidine derivatives in medical technologies, molecular biology experiments, and synthesis of a supramolecular network of DNA strands.
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Affiliation(s)
- Shu-ichi Nakano
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Kobe 650-0047, Japan.
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43
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D'Alonzo D, Guaragna A, Palumbo G. Exploring the role of chirality in nucleic acid recognition. Chem Biodivers 2012; 8:373-413. [PMID: 21404424 DOI: 10.1002/cbdv.201000303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.
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Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, via Cinthia, 4, I-80126 Napoli.
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44
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45
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Johnson AT, Schlegel MK, Meggers E, Essen LO, Wiest O. On the structure and dynamics of duplex GNA. J Org Chem 2011; 76:7964-74. [PMID: 21838272 DOI: 10.1021/jo201469b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycol nucleic acid (GNA), with a nucleotide backbone comprising of just three carbons and the stereocenter derived from propylene glycol (1,2-propanediol), is a structural analog of nucleic acids with intriguing biophysical properties, such as formation of highly stable antiparallel duplexes with high Watson-Crick base pairing fidelity. Previous crystallographic studies of double stranded GNA (dsGNA) indicated two forms of backbone conformations, an elongated M-type (containing metallo-base pairs) and the condensed N-type (containing brominated base pairs). A herein presented new crystal structure of a GNA duplex at 1.8 Å resolution from self-complementary 3'-CTC(Br)UAGAG-2' GNA oligonucleotides reveals an N-type conformation with alternating gauche-anti torsions along its (O3'-C3'-C2'-O2') backbone. To elucidate the conformational state of dsGNA in solution, molecular dynamic simulations over a period of 20 ns were performed with the now available repertoire of structural information. Interestingly, dsGNA adopts conformational states in solution intermediate between experimentally observed backbone conformations: simulated dsGNA shows the all-gauche conformation characteristic of M-type GNA with the higher helical twist common to N-type GNA structures. The so far counterintuitive, smaller loss of entropy upon duplex formation as compared to DNA can be traced back to the conformational flexibility inherent to dsGNA but missing in dsDNA. Besides extensive interstrand base stacking and conformational preorganization of single strands, this flexibility contributes to the extraordinary thermal stability of GNA.
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Affiliation(s)
- Andrew T Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670, United States
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46
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Sasaki S, Onizuka K, Taniguchi Y. The oligodeoxynucleotide probes for the site-specific modification of RNA. Chem Soc Rev 2011; 40:5698-706. [PMID: 21647493 DOI: 10.1039/c1cs15066a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As the knowledge of the biological functions of RNA expands, the demand for research tools to investigate intracellular RNA is increasing. Oligonucleotides can be rationally designed for the target RNA sequence, and therefore, have become a reliable platform for the development of specific molecules for RNA. The chemical modification of RNA has a strong impact on RNA research; the fluorescent labeling of RNA is useful to monitor RNA production, processing, relocation in the cell, interaction with other intracellular components and degradation, etc. Chemical modification may affect the RNA function through a variety of pathways, and therefore, would be potentially useful for biological research, therapeutic approach and artificial manipulation of the RNA function. This tutorial review starts with an introduction of the biological relevance of modified RNA, and focuses on the recent progress of the oligodeoxynucleotide probes for the covalent modifications of RNA. The prospects of this new technology are also discussed.
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Affiliation(s)
- Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan.
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47
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Liang J, Luo Y, Zhao H. Synthetic biology: putting synthesis into biology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 3:7-20. [PMID: 21064036 PMCID: PMC3057768 DOI: 10.1002/wsbm.104] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself—encompassing many branches of science and across many scales of application. New DNA synthesis and assembly techniques have made routine customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery—a self‐replicating organism—is being pursued at this moment. The aim of this article is to dissect and organize these various components of synthetic biology into a coherent picture. WIREs Syst Biol Med 2011 3 7–20 DOI: 10.1002/wsbm.104 This article is categorized under:
Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Laboratory Methods and Technologies > Metabolomics
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Affiliation(s)
- Jing Liang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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48
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Fekry MI, Tipton PA, Gates KS. Kinetic consequences of replacing the internucleotide phosphorus atoms in DNA with arsenic. ACS Chem Biol 2011; 6:127-30. [PMID: 21268588 DOI: 10.1021/cb2000023] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It was claimed in a recent publication that a strain of Halomonadacea bacteria (GFAJ-1) isolated from the arsenic-rich waters of Mono Lake, California is able to substitute arsenic for phosphorus in its macromolecules and small molecule metabolites. In this short Perspective, we consider chemical and biochemical issues surrounding the central claim that Halomonadacea GFAJ-1 is able to survive while incorporating kinetically labile arsenodiester linkages into the backbone of its DNA. Chemical precedents suggest that arsenodiester linkages in the putative arsenic-containing DNA of GFAJ-1 would undergo very rapid hydrolytic cleavage in water at 25 °C with an estimated half-life of 0.06 s. In contrast, the phosphodiester linkages of native DNA undergo spontaneous hydrolysis with a half-life of approximately 30,000,000 y at 25 °C. Overcoming such dramatic kinetic instability in its genetic material would present serious challenges to Halomonadacea GFAJ-1.
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Affiliation(s)
- Mostafa I. Fekry
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini, Cairo, Egypt 11562
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49
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Kashida H, Murayama K, Toda T, Asanuma H. Control of the chirality and helicity of oligomers of serinol nucleic acid (SNA) by sequence design. Angew Chem Int Ed Engl 2011; 50:1285-8. [PMID: 21290494 DOI: 10.1002/anie.201006498] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Indexed: 11/06/2022]
Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Japan
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50
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Kashida H, Murayama K, Toda T, Asanuma H. Control of the Chirality and Helicity of Oligomers of Serinol Nucleic Acid (SNA) by Sequence Design. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006498] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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