1
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Wagh MA, Shinde DR, Gamidi RK, Sanjayan GJ. 2-Amino-5-methylene-pyrimidine-4,6-dione-based Janus G-C nucleobase as a versatile building block for self-assembly. Org Biomol Chem 2023; 21:6914-6918. [PMID: 37593940 DOI: 10.1039/d3ob01174g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
This communication reports a nature-inspired Janus G-C nucleobase featuring two recognition sites: DDA (G mimic) and DAA (C mimic), which is capable of forming a linear tape-like supramolecular polymer structure. As demonstrated herein, the amino group of this self-assembling system can be further modified to yield a highly stable quadruple H-bonding system as well as a masked self-assembling system cleavable upon exposure to light.
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Affiliation(s)
- Mahendra A Wagh
- Organic Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune-411008, India.
- Academy of Scientific and Innovative research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh-201002, India
| | - Dinesh R Shinde
- Organic Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune-411008, India.
- Academy of Scientific and Innovative research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh-201002, India
| | - Rama Krishna Gamidi
- Organic Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune-411008, India.
| | - Gangadhar J Sanjayan
- Organic Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune-411008, India.
- Academy of Scientific and Innovative research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh-201002, India
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2
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López-Tena M, Chen SK, Winssinger N. Supernatural: Artificial Nucleobases and Backbones to Program Hybridization-Based Assemblies and Circuits. Bioconjug Chem 2023; 34:111-123. [PMID: 35856656 DOI: 10.1021/acs.bioconjchem.2c00292] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The specificity and predictability of hybridization make oligonucleotides a powerful platform to program assemblies and networks with logic-gated responses, an area of research which has grown into a field of its own. While the field has capitalized on the commercial availability of DNA oligomers with its four canonical nucleobases, there are opportunities to extend the capabilities of the hardware with unnatural nucleobases and other backbones. This Topical Review highlights nucleobases that favor hybridizations that are empowering for assemblies and networks as well as two chiral XNAs than enable orthogonal hybridization networks.
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Affiliation(s)
- Miguel López-Tena
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Si-Kai Chen
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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3
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Schuster GB, Hud NV, Alenaizan A. Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions. J Phys Chem B 2022; 126:10758-10767. [PMID: 36502412 DOI: 10.1021/acs.jpcb.2c05934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.
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Affiliation(s)
- Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
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4
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Alenaizan A. Structural Analysis of the Poly(thymidine)-Melamine Assembly. J Phys Chem B 2022; 126:6948-6954. [PMID: 36027577 DOI: 10.1021/acs.jpcb.2c04665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bonding between the DNA nucleobases and small organic molecules, such as melamine, is a new strategy for the design of novel DNA materials. Poly(thymidine) DNA and melamine self-assemble into a duplex structure containing two antiparallel DNA strands hydrogen bonded to central melamine units. In this Article, molecular dynamics simulations rationalize the observed antiparallel duplex structure. Alternative duplex and triplex structures with parallel and antiparallel strand orientations are shown to be unstable because of the increase in unfavorable interactions between the DNA backbones.
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Affiliation(s)
- Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia 31261
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5
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Wagh MA, Maity R, Bhosale RJ, Semwal D, Tothadi S, Vaidhyanathan R, Sanjayan GJ. Three in One: Triple G-C-T Base-Coded Brahma Nucleobase Amino Acid: Synthesis, Peptide Formation, and Structural Features. J Org Chem 2021; 86:15689-15694. [PMID: 34623156 DOI: 10.1021/acs.joc.1c01228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This note reports the synthesis and peptide formation of a novel triple G-C-T nucleobase amino acid (NBA) building block featuring three recognition faces: DDA (G mimic), DAA (C mimic), and ADA (T mimic). Readily obtainable in multigram scale in a remarkably easy one-step reaction, this unique NBA building block offers scope for wide ranging applications for nucleic acid recognition and nucleic acid peptide/protein interaction studies.
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Affiliation(s)
- Mahendra A Wagh
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road Pashan, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Rahul Maity
- Department of Chemistry and Centre for Energy Science, Indian Institute of Science Education and Research, Dr Homi Bhabha Road Pashan, Pune 411008, India
| | - Rohit J Bhosale
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road Pashan, Pune 411008, India
| | - Divyam Semwal
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road Pashan, Pune 411008, India
| | - Srinu Tothadi
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road Pashan, Pune 411008, India
| | - Ramanathan Vaidhyanathan
- Department of Chemistry and Centre for Energy Science, Indian Institute of Science Education and Research, Dr Homi Bhabha Road Pashan, Pune 411008, India
| | - Gangadhar J Sanjayan
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road Pashan, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
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6
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Bhingardeve P, Jain P, Ganesh KN. Molecular Assembly of Triplex of Duplexes from Homothyminyl-Homocytosinyl Cγ( S/ R)-Bimodal Peptide Nucleic Acids with dA 8/dG 6 and the Cell Permeability of Bimodal Peptide Nucleic Acids. ACS OMEGA 2021; 6:19757-19770. [PMID: 34368563 PMCID: PMC8340421 DOI: 10.1021/acsomega.1c02451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/05/2021] [Indexed: 05/08/2023]
Abstract
Peptide nucleic acids (PNAs) are analogues of DNA with a neutral acyclic polyamide backbone containing nucleobases attached through a t-amide link on repeating units of aminoethylglycine (aeg). They bind to complementary DNA or RNA in a sequence-specific manner to form duplexes with higher stablity than DNA:DNA and DNA:RNA hybrids. We have recently explored a new type of PNA termed bimodal PNA (bm-PNA) designed with two nucleobases per aeg repeating unit of PNA oligomer and attached at Cα or Cγ of each aeg unit through a spacer sidechain. We demonstrated that Cγ-bimodal PNA oligomers with mixed nucleobase sequences bind concurrently two different complementary DNAs, forming double duplexes, one from each t-amide and Cγ face, sharing a common PNA backbone. In such bm-PNA:DNA ternary complexes, the two duplexes show higher thermal stability than individual duplexes. Herein, we show that Cγ(S/R)-bimodal PNAs with homothymines (T8) on a t-amide face and homocytosine (C6) on a Cγ-face form a conjoined pentameric complex consisting of a triplex (bm-PNA-T8)2:dA8 and two duplexes of bm-PNA-C6:dG6. The pentameric complex [dG6:Cγ(S/R)-bm-PNA:dA8:Cγ(S/R)-bm-PNA:dG6] exhibits higher thermal stability than the individual triplex and duplex, with Cγ(S)-bm-PNA complexes being more stable than Cγ(R)-bm-PNA complexes. The conjoined duplexes of Cγ-bimodal PNAs can be used to generate novel higher-order assemblies with DNA and RNA. The Cγ(S/R)-bimodal PNAs are shown to enter MCF7 and NIH 3T3 cells and exhibit low toxicity to cells.
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Affiliation(s)
- Pramod Bhingardeve
- Indian
Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Prashant Jain
- Indian
Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Krishna N. Ganesh
- Indian
Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Indian
Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
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7
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Miao S, Liang Y, Rundell S, Bhunia D, Devari S, Munyaradzi O, Bong D. Unnatural bases for recognition of noncoding nucleic acid interfaces. Biopolymers 2021; 112:e23399. [PMID: 32969496 PMCID: PMC7855516 DOI: 10.1002/bip.23399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022]
Abstract
The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Yufeng Liang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah Rundell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Debmalya Bhunia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Shekar Devari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Oliver Munyaradzi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
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8
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Gupta MK, Madhanagopal BR, Ganesh KN. Peptide Nucleic Acid with Double Face: Homothymine–Homocytosine Bimodal Cα-PNA (bm-Cα-PNA) Forms a Double Duplex of the bm-PNA2:DNA Triplex. J Org Chem 2020; 86:414-428. [DOI: 10.1021/acs.joc.0c02158] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Manoj Kumar Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Bharath Raj Madhanagopal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Krishna N. Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
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9
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Bhingardeve P, Madhanagopal BR, Ganesh KN. Cγ( S/ R)-Bimodal Peptide Nucleic Acids (Cγ- bm-PNA) Form Coupled Double Duplexes by Synchronous Binding to Two Complementary DNA Strands. J Org Chem 2020; 85:13680-13693. [PMID: 32985197 DOI: 10.1021/acs.joc.0c01853] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptide nucleic acids (PNAs) are linear equivalents of DNA with a neutral acyclic polyamide backbone that has nucleobases attached via tert-amide link on repeating units of aminoethylglycine. They bind complementary DNA or RNA with sequence specificity to form hybrids that are more stable than the corresponding DNA/RNA self-duplexes. A new type of PNA termed bimodal PNA [Cγ(S/R)-bm-PNA] is designed to have a second nucleobase attached via amide spacer to a side chain at Cγ on the repeating aeg units of PNA oligomer. Cγ-bimodal PNA oligomers that have two nucleobases per aeg unit are demonstrated to concurrently bind two different complementary DNAs, to form duplexes from both tert-amide side and Cγ side. In such PNA:DNA ternary complexes, the two duplexes share a common PNA backbone. The ternary DNA 1:Cγ(S/R)-bm-PNA:DNA 2 complexes exhibit better thermal stability than the isolated duplexes, and the Cγ(S)-bm-PNA duplexes are more stable than Cγ(R)-bm-PNA duplexes. Bimodal PNAs are first examples of PNA analogues that can form DNA2:PNA:DNA1 double duplexes via recognition through natural bases. The conjoined duplexes of Cγ-bimodal PNAs can be used to generate novel higher-level assemblies.
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Affiliation(s)
- Pramod Bhingardeve
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Bharath Raj Madhanagopal
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
| | - Krishna N Ganesh
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, India.,Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
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10
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Liang Y, Miao S, Mao J, DeSantis C, Bong D. Context-Sensitive Cleavage of Folded DNAs by Loop-Targeting bPNAs. Biochemistry 2020; 59:2410-2418. [PMID: 32519542 DOI: 10.1021/acs.biochem.0c00362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, we demonstrate context-dependent molecular recognition of DNA by synthetic bPNA iron and copper complexes, using oxidative backbone cleavage as a chemical readout for binding. Oligoethylenimine bPNAs displaying iron·EDTA or copper·phenanthroline sites were found to be efficient chemical nucleases for designed and native structured DNAs with T-rich single-stranded domains. Cleavage reactivity depends strongly on structural context, as strikingly demonstrated with DNA substrates of the form (GGGTTA)n. This repeat sequence from the human telomere is known to switch between parallel and antiparallel G-quadruplex (G4) topologies with a change from potassium to sodium buffer: notably, bPNA-copper complexes efficiently cleave long repeat sequences into ∼22-nucleotide portions in sodium, but not potassium, buffer. We hypothesize preferential cleavage of the antiparallel topology (Na+) over the parallel topology (K+) due to the greater accessibility of the TTA loop to bPNA in the antiparallel (Na+) form. Similar ion-sensitive telomere shortening upon treatment with bPNA nucleases can be observed in both isolated and intracellular DNA from PC3 cells by quantitative polymerase chain reaction. Live cell treatment was accompanied by accelerated cellular senescence, as expected for significant telomere shortening. Taken together, the loop-targeting approach of bPNA chemical nucleases complements prior intercalation strategies targeting duplex and quadruplex DNA. Structurally sensitive loop targeting enables discrimination between similar target sequences, thus expanding bPNA targeting beyond simple oligo-T sequences. In addition, bPNA nucleases are cell membrane permeable and therefore may be used to target native intracellular substrates. In addition, these data indicate that bPNA scaffolds can be a platform for new synthetic binders to particular nucleic acid structural motifs.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiqin Miao
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jie Mao
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Chris DeSantis
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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11
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Gupta MK, Madhanagopal BR, Datta D, Ganesh KN. Structural Design and Synthesis of Bimodal PNA That Simultaneously Binds Two Complementary DNAs To Form Fused Double Duplexes. Org Lett 2020; 22:5255-5260. [PMID: 32551691 DOI: 10.1021/acs.orglett.0c01950] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bimodal PNAs are new PNA constructs designed to bind two different cDNA sequences synchronously to form double duplexes. They are synthesized on solid phase using sequential coupling and click reaction to introduce a second base in each monomer at Cα via alkyltriazole linker. The ternary bimodal PNA:DNA complexes show stability higher than that of individual duplexes. Bimodal PNAs are appropriate to create higher-order fused nucleic acid assemblies.
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Affiliation(s)
- Manoj Kumar Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Bharath Raj Madhanagopal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Dhrubajyoti Datta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Krishna N Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India.,Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
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12
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Theoretical study of hydrogen bonds and electronic properties in hexagonal arrangements composed of self-assembled DNA analogues. Struct Chem 2020. [DOI: 10.1007/s11224-020-01545-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Miao S, Liang Y, Marathe I, Mao J, DeSantis C, Bong D. Duplex Stem Replacement with bPNA+ Triplex Hybrid Stems Enables Reporting on Tertiary Interactions of Internal RNA Domains. J Am Chem Soc 2019; 141:9365-9372. [PMID: 31094510 PMCID: PMC7043357 DOI: 10.1021/jacs.9b03435] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report herein the synthesis and DNA/RNA binding properties of bPNA+, a new variant of bifacial peptide nucleic acid (bPNA) that binds oligo T/U nucleic acids to form triplex hybrids. By virtue of a new bivalent side chain on bPNA+, similar DNA affinity and hybrid thermostability can be obtained with half the molecular footprint of previously reported bPNA. Lysine derivatives bearing two melamine bases (K2M) can be prepared on multigram scale by double reductive alkylation with melamine acetaldehyde, resulting in a tertiary amine side chain that affords both peptide solubility and selective base-triple formation with 4 T/U bases; the Fmoc-K2M derivative can be used directly in solid phase peptide synthesis, rendering bPNA+ conveniently accessible. A compact bPNA+binding site of two U6 domains can be genetically encoded to replace existing 6 bp stem elements at virtually any location within an RNA transcript. We thus replaced internal 6 bp RNA stems that supported loop regions with 6 base-triple hybrid stems using fluorophore-labeled bPNA+. As the loop regions engaged in RNA tertiary interactions, the labeled hybrid stems provided a fluorescent readout; bPNA+ enabled this readout without covalent chemical modification or introduction of new structural elements. This strategy was demonstrated to be effective for reporting on widely observed RNA tertiary interactions such as intermolecular RNA-RNA kissing loop dimerization, RNA-protein binding, and intramolecular RNA tetraloop-tetraloop receptor binding, illustrating the potential general utility of this method. The modest 6 bp stem binding footprint of bPNA+ makes the hybrid stem replacement method practical for noncovalent installation of synthetic probes of RNA interactions. We anticipate that bPNA+ structural probes will be useful for the study of tertiary interactions in long noncoding RNAs.
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14
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Kashida H, Hattori Y, Tazoe K, Inoue T, Nishikawa K, Ishii K, Uchiyama S, Yamashita H, Abe M, Kamiya Y, Asanuma H. Bifacial Nucleobases for Hexaplex Formation in Aqueous Solution. J Am Chem Soc 2018; 140:8456-8462. [PMID: 29886741 DOI: 10.1021/jacs.8b02807] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although DNA can form triplex and quadruplex structures through hydrogen bonds, design and preparation of structures with more than five strands is difficult even when artificial nucleic acids are used. Herein we report a hexaplex formed by oligomers of artificial nucleic acids bearing bifacial molecules on d-threoninol. Aminopyrimidine and cyanuric acid derivatives were selected as bases because they have complementary hydrogen bonding patterns. The complex formed by aminopyrimidine and cyanuric acid decamers melted with large hysteresis. Hexaplex formation was indicated by gel electrophoresis, size exclusion chromatography and atomic force microscopy imaging, and proven directly through native mass spectrometry. CD measurements and molecular dynamics simulations indicated that the hexaplex adopts a helical structure. The hexaplex formation was highly dependent on pH and the presence of divalent cations. The hexaplex was stable in aqueous solution, and its unique structure and properties may lead to novel nanostructures, molecular assemblies, metal sensors, and ion channels.
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Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan.,PRESTO , Japan Science and Technology Agency , 4-1-8 Honcho, Kawaguchi , Saitama 332-0012 , Japan
| | - Yuhei Hattori
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
| | - Kaho Tazoe
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
| | - Tadashi Inoue
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
| | - Keiji Nishikawa
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
| | - Kentaro Ishii
- Okazaki Institute for Integrative Bioscience , National Institutes of Natural Sciences, Okazaki 444-8787 , Japan
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience , National Institutes of Natural Sciences, Okazaki 444-8787 , Japan.,Graduate School of Engineering , Osaka University , Suita , Osaka 565-0871 , Japan
| | - Hayato Yamashita
- PRESTO , Japan Science and Technology Agency , 4-1-8 Honcho, Kawaguchi , Saitama 332-0012 , Japan.,Graduate School of Engineering Science , Osaka University , Toyonaka , Osaka 560-8531 , Japan
| | - Masayuki Abe
- Graduate School of Engineering Science , Osaka University , Toyonaka , Osaka 560-8531 , Japan
| | - Yukiko Kamiya
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
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15
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Thadke SA, Perera JDR, Hridya VM, Bhatt K, Shaikh AY, Hsieh WC, Chen M, Gayathri C, Gil RR, Rule GS, Mukherjee A, Thornton CA, Ly DH. Design of Bivalent Nucleic Acid Ligands for Recognition of RNA-Repeated Expansion Associated with Huntington's Disease. Biochemistry 2018; 57:2094-2108. [PMID: 29562132 PMCID: PMC6091552 DOI: 10.1021/acs.biochem.8b00062] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report the development of a new class of nucleic acid ligands that is comprised of Janus bases and the MPγPNA backbone and is capable of binding rCAG repeats in a sequence-specific and selective manner via, inference, bivalent H-bonding interactions. Individually, the interactions between ligands and RNA are weak and transient. However, upon the installation of a C-terminal thioester and an N-terminal cystine and the reduction of disulfide bond, they undergo template-directed native chemical ligation to form concatenated oligomeric products that bind tightly to the RNA template. In the absence of an RNA target, they self-deactivate by undergoing an intramolecular reaction to form cyclic products, rendering them inactive for further binding. The work has implications for the design of ultrashort nucleic acid ligands for targeting rCAG-repeat expansion associated with Huntington's disease and a number of other related neuromuscular and neurodegenerative disorders.
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Affiliation(s)
- Shivaji A. Thadke
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - J. Dinithi R. Perera
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - V. M. Hridya
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India
| | - Kirti Bhatt
- Department of Neurology, Box 645, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Ashif Y. Shaikh
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Che Hsieh
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Mengshen Chen
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Chakicherla Gayathri
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Roberto R. Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Gordon S. Rule
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India
| | - Charles A. Thornton
- Department of Neurology, Box 645, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Danith H. Ly
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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16
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Liu H, Qi G, Song Q, Wang H. Benzene expansion Janus GC base analogues: A detailed theoretical study. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Abstract
An impressive array of antigene approaches has been developed for recognition of double helical DNA over the past three decades; however, few have exploited the 'Watson-Crick' base-pairing rules for establishing sequence-specific recognition. One approach employs peptide nucleic acid as a molecular reagent and strand invasion as a binding mode. However, even with integration of the latest conformationally-preorganized backbone design, such an approach is generally confined to sub-physiological conditions due to the lack of binding energy. Here we report the use of a class of shape-selective, bifacial nucleic acid recognition elements, namely Janus bases, for targeting double helical DNA or RNA. Binding occurs in a highly sequence-specific manner under physiologically relevant conditions. The work may provide a foundation for the design of oligonucleotides for targeting the secondary and tertiary structures of nucleic acid biopolymers.
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18
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Optical absorption and emission properties of benzene-expanded Janus AT nucleobase analogues: A DFT study. Struct Chem 2016. [DOI: 10.1007/s11224-016-0743-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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Avakyan N, Greschner AA, Aldaye F, Serpell CJ, Toader V, Petitjean A, Sleiman HF. Reprogramming the assembly of unmodified DNA with a small molecule. Nat Chem 2016; 8:368-76. [PMID: 27001733 DOI: 10.1038/nchem.2451] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 01/07/2016] [Indexed: 02/08/2023]
Abstract
The ability of DNA to store and encode information arises from base pairing of the four-letter nucleobase code to form a double helix. Expanding this DNA 'alphabet' by synthetic incorporation of new bases can introduce new functionalities and enable the formation of novel nucleic acid structures. However, reprogramming the self-assembly of existing nucleobases presents an alternative route to expand the structural space and functionality of nucleic acids. Here we report the discovery that a small molecule, cyanuric acid, with three thymine-like faces, reprogrammes the assembly of unmodified poly(adenine) (poly(A)) into stable, long and abundant fibres with a unique internal structure. Poly(A) DNA, RNA and peptide nucleic acid (PNA) all form these assemblies. Our studies are consistent with the association of adenine and cyanuric acid units into a hexameric rosette, which brings together poly(A) triplexes with a subsequent cooperative polymerization. Fundamentally, this study shows that small hydrogen-bonding molecules can be used to induce the assembly of nucleic acids in water, which leads to new structures from inexpensive and readily available materials.
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Affiliation(s)
- Nicole Avakyan
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Andrea A Greschner
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.,INRS: Centre Énergie Matériaux Télécommunications, 1650 Boul. Lionel-Boulet, Varennes Quebec J3X 1S2, Canada
| | - Faisal Aldaye
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Christopher J Serpell
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.,School of Physical Sciences, Ingram Building, University of Kent, Canterbury CT2 7NH, Kent, UK
| | - Violeta Toader
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Anne Petitjean
- Department of Chemistry, Queen's University, Chernoff Hall, 90 Bader Lane, Kingston Ontario K7L 3N6, Canada
| | - Hanadi F Sleiman
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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20
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Beingessner RL, Fan Y, Fenniri H. Molecular and supramolecular chemistry of rosette nanotubes. RSC Adv 2016. [DOI: 10.1039/c6ra16315g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthetic strategies used to tune the properties of a class of supramolecular 1D nanostructures, the rosette nanotubes, are reviewed herein.
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Affiliation(s)
| | - Yiwen Fan
- Department of Chemical Engineering
- Northeastern University
- 253 Snell Engineering Center
- Boston
- USA
| | - Hicham Fenniri
- Department of Chemical Engineering
- Northeastern University
- 253 Snell Engineering Center
- Boston
- USA
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21
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Takezawa Y, Nishiyama K, Mashima T, Katahira M, Shionoya M. Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination. Chemistry 2015; 21:14713-6. [DOI: 10.1002/chem.201502772] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 11/11/2022]
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22
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Piao X, Xia X, Mao J, Bong D. Peptide Ligation and RNA Cleavage via an Abiotic Template Interface. J Am Chem Soc 2015; 137:3751-4. [PMID: 25747470 DOI: 10.1021/jacs.5b00236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xijun Piao
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Xin Xia
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jie Mao
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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23
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Xia X, Piao X, Bong D. Bifacial peptide nucleic acid as an allosteric switch for aptamer and ribozyme function. J Am Chem Soc 2014; 136:7265-8. [PMID: 24796374 DOI: 10.1021/ja5032584] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We demonstrate herein that bifacial peptide nucleic acid (bPNA) hybrid triplexes functionally substitute for duplex DNA or RNA. Structure-function loss in three non-coding nucleic acids was inflicted by replacement of a duplex stem with unstructured oligo-T/U strands, which are bPNA binding sites. Functional rescue was observed on refolding of the oligo-T/U strands into bPNA triplex hybrid stems. Bifacial PNA binding was thus used to allosterically switch-on protein and small-molecule binding in DNA and RNA aptamers, as well as catalytic bond scission in a ribozyme. Duplex stems that support the catalytic site of a minimal type I hammerhead ribozyme were replaced with oligo-U loops, severely crippling or ablating the native RNA splicing function. Refolding of the U-loops into bPNA triplex stems completely restored splicing function in the hybrid system. These studies indicate that bPNA may have general utility as an allosteric trigger for a wide range of functions in non-coding nucleic acids.
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Affiliation(s)
- Xin Xia
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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24
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Largy E, Liu W, Hasan A, Perrin DM. A Pyrimidopyrimidine Janus-AT Nucleoside with Improved Base-Pairing Properties to both A and T within a DNA Duplex: The Stabilizing Effect of a Second Endocyclic Ring Nitrogen. Chemistry 2014; 20:1495-9. [DOI: 10.1002/chem.201303867] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Indexed: 12/18/2022]
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25
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Xia X, Piao X, Bong D. Bifacial PNA complexation inhibits enzymatic access to DNA and RNA. Chembiochem 2014; 15:31-6. [PMID: 24259287 PMCID: PMC3896088 DOI: 10.1002/cbic.201300536] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Indexed: 02/02/2023]
Abstract
FULL STOP: Herein we report the effective in vitro inhibition of transcription, reverse-transcription and exonuclease function by formation of synthetic bPNA-nucleic acid triplex structures. Selective bPNA targeting of both DNA and RNA substrates suggests possible application of bPNAs as synthetic regulators of nucleic acid function.
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Affiliation(s)
- Xin Xia
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH 43210 (USA)
| | - Xijun Piao
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH 43210 (USA)
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH 43210 (USA)
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26
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Liu M, Li J, Chen S, Huang D, Chai H, Zhang Q, Shi D. One-pot NHC-assisted access to 2,3-dihydropyrimido[4,5-d]pyrimidin-4(1H)-ones. RSC Adv 2014. [DOI: 10.1039/c4ra05346j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An efficient N-heterocyclic carbene-assisted one-pot reaction synthesis of 2,3-dihydropyrimido[4,5-d] pyrimidin-4(1H)-ones from 2-(ethoxymethylene)malononitrile, guanidines (or amidines) and ketones (or aldehyde) has been developed. The novel method provides a highly efficient synthesis of pyrimido[4,5-d]pyrimidinering from materials with no heterocyclic structures.
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Affiliation(s)
- Mingxing Liu
- School of Chemical Engineering and Environment
- Beijing Institute of Technology
- Beijing, China
| | - Jiarong Li
- School of Chemical Engineering and Environment
- Beijing Institute of Technology
- Beijing, China
| | - Shu Chen
- School of Chemical Engineering and Environment
- Beijing Institute of Technology
- Beijing, China
| | - Danfei Huang
- School of Chemical Engineering and Environment
- Beijing Institute of Technology
- Beijing, China
| | - Hongxin Chai
- School of Chemical Engineering and Environment
- Beijing Institute of Technology
- Beijing, China
| | - Qi Zhang
- School of Chemical Engineering and Environment
- Beijing Institute of Technology
- Beijing, China
| | - Daxin Shi
- School of Chemical Engineering and Environment
- Beijing Institute of Technology
- Beijing, China
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27
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Liu H, Song Q, Liu J, Li Y, Wang H. Theoretical study on absorption and emission spectra of size-expanded Janus-type AT nucleobases and effect of base pairing. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 121:670-677. [PMID: 24368287 DOI: 10.1016/j.saa.2013.11.100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 11/13/2013] [Accepted: 11/17/2013] [Indexed: 06/03/2023]
Abstract
Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we design benzo- and naphtha-expanded Janus AT base analogues, using DFT, TDDFT, and CIS methods to investigate the structural and optical properties of the Janus AT base analogues (termed as J-AT, xJ-AT, yyJ-AT, BF, xBF and yyBF), and also consider the effect of base pairing. The results show that the Janus AT base analogues can pair with T and A simultaneously to form stable H-bonded WC base pairs. The ground state structure of J-AT is similar to BF, the size expansion is 2.42Å for the x-Janus AT bases and 4.86Å for the yy-Janus AT bases. The excited state geometries of J-AT and BF change dramatically, while the other bases are similar to the ground state geometries. The lowest excited singlet transitions of the Janus AT base analogues are predicted to be of ππ(*) character and mainly dominated by the configuration HOMO-LUMO. The maximum absorption wavelengths of size expansion Janus AT base analogues are greatly red shifted compared with J-AT (or BF). BF, xBF and yyJ-AT have larger oscillator strengths than J-AT, xJ-AT and yyBF. The emission wavelengths of the Janus AT base analogues also exhibit red shifts from x-Janus AT bases to yy-Janus AT bases. However, the emission wavelengths of J-AT and BF change greatly, which are coincident with the structures observed in the excited state geometries. With regard to the WC base pairs, the B3LYP functional reveals that the lowest energy transitions of some base pairs are charge transfer excitation, while the other base pairs are local excitation. The CAM-B3LYP functional predicts that all the lowest transitions are localized on the Janus AT bases, and show good agreement with the results of the M062X functional.
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Affiliation(s)
- Hongxia Liu
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Chemical and Biological Engineering College, Yancheng Institute of Technology, Yancheng, Jiangsu 214122, China
| | - Qixia Song
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianhua Liu
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yan Li
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Haijun Wang
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China.
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28
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Artigas G, Marchán V. Synthesis of Janus compounds for the recognition of G-U mismatched nucleobase pairs. J Org Chem 2013; 78:10666-77. [PMID: 24087986 DOI: 10.1021/jo401684j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The design and synthesis of two Janus-type heterocycles with the capacity to simultaneously recognize guanine and uracyl in G-U mismatched pairs through complementary hydrogen bond pairing is described. Both compounds were conveniently functionalized with a carboxylic function and efficiently attached to a tripeptide sequence by using solid-phase methodologies. Ligands based on the derivatization of such Janus compounds with a small aminoglycoside, neamine, and its guanidinylated analogue have been synthesized, and their interaction with Tau RNA has been investigated by using several biophysical techniques, including UV-monitored melting curves, fluorescence titration experiments, and (1)H NMR. The overall results indicated that Janus-neamine/guanidinoneamine showed some preference for the +3 mutated RNA sequence associated with the development of some tauopathies, although preliminary NMR studies have not confirmed binding to G-U pairs. Moreover, a good correlation has been found between the RNA binding affinity of such Janus-containing ligands and their ability to stabilize this secondary structure upon complexation.
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Affiliation(s)
- Gerard Artigas
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona Martí i Franquès 1-11, E-08028 Barcelona, Spain
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29
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Largy E, Liu W, Hasan A, Perrin DM. Base-pairing behavior of a carbocyclic Janus-AT nucleoside analogue capable of recognizing A and T within a DNA duplex. Chembiochem 2013; 14:2199-208. [PMID: 24115365 DOI: 10.1002/cbic.201300250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Indexed: 01/18/2023]
Abstract
Janus-type nucleosides are heterocycles with two faces, each of which is designed to complement the H-bonding interactions of natural nucleosides comprising a canonical Watson-Crick base pair. By intercepting all of the hydrogen bonds contained within the base pair, oligomeric Janus nucleosides are expected to achieve sequence-specific DNA recognition through the formation of J-loops that will be more stable than D-loops, which simply replaces one base-pair with another. Herein, we report the synthesis of a novel Janus-AT nucleoside analogue, JAT , affixed on a carbocyclic analogue of deoxyribose that was converted to the corresponding phosphoramidite. A single JAT was successfully incorporated into a DNA strand by solid phase for targeting both A and T bases, and characterized through biophysical and computational methods. Experimental UV-melting and circular dichroism data demonstrated that within the context of a standard duplex, JAT associates preferentially with T over A, and much more poorly with C and G. Density functional theory calculations confirm that the JAT structure is well suited to associate only with A and T thereby highlighting the importance of the electronic structure in terms of H-bonding. Finally, molecular dynamics simulations validated the observation that JAT can substitute more effectively as an A-analogue than as a T-analogue without substantial distortion of the B-helix. Overall, this new Janus nucleotide is a promising tool for the targeting of A-T base pairs in DNA, and will lead to the development of oligo-Janus-nucleotide strands for sequence-specific DNA recognition.
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Affiliation(s)
- Eric Largy
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 (Canada)
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30
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Piao X, Xia X, Bong D. Bifacial peptide nucleic acid directs cooperative folding and assembly of binary, ternary, and quaternary DNA complexes. Biochemistry 2013; 52:6313-23. [PMID: 23964711 DOI: 10.1021/bi4008963] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report herein the structuring of single-stranded thymine-rich DNA sequences into peptide-DNA hairpin triplex structures via designed melamine-thymine nucleobase recognition. Melamine-displaying α-peptides were synthesized with the general form (EM*)n, where M* denotes a lysine residue side chain derivatized with melamine, a bifacial hydrogen bond complement for thymine. We have found that (EM*)n peptides, which we term bifacial peptide nucleic acid (bPNA), function as a noncovalent template for thymine-rich DNA tracts. Unstructured DNA of the general form dTnCmTn are bound to (EM*)n peptides and fold into cooperatively melting 1:1 bPNA-DNA hairpin complexes with dissociation constants in the submicromolar to low nanomolar range for n = 4-10. As the length of the interface (n) is decreased, the melting temperature of the bPNA-DNA complex drops significantly, though Kd increases are less substantial, suggestive of strong enthalpy-entropy compensation. This is borne out by differential scanning calorimetry analysis, which indicates enthalpically driven bPNA-DNA base-stacking that becomes markedly less exothermic as the recognition surface n decreases in size. The recognition interface tolerates a high number of "mismatches" and indicates half-site, or monofacial, recognition between melamine and thymine may occur if only 1 complementary nucleobase is available. Association correlates directly with fractional thymine content, with optimal binding when the number of T-T sites match the number of melamine units. Interestingly, when a DNA host has more T-T sites than melamine sites on bPNA, two or three bPNAs can bind to a single DNA, resulting in ternary and quaternary complexes that have higher thermal stability than the binary (1:1) bPNA-DNA complex, suggestive of cooperative multisite binding. In contrast, when two bPNAs of different lengths bind to the same DNA host, a ternary complex is formed with two melting transitions, corresponding to independent melting of each bPNA component from the complex. These data demonstrate that melamine-displaying bPNA recognize thymine-rich DNA in predictable and multifaceted ways that allow binding affinity, structure stability, and stoichiometry to be tuned through simple bPNA length modification and matching with DNA length. Synthetic bPNA structuring elements may be useful tools for biotechnology.
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Affiliation(s)
- Xijun Piao
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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31
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Bonnac LF, Mansky LM, Patterson SE. Structure–Activity Relationships and Design of Viral Mutagens and Application to Lethal Mutagenesis. J Med Chem 2013; 56:9403-14. [DOI: 10.1021/jm400653j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Laurent F. Bonnac
- Center for Drug Design, Academic
Health Center, University of Minnesota,
Minneapolis, Minnesota 55455, United States
| | - Louis M. Mansky
- Institute for Molecular Virology,
Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Steven E. Patterson
- Center for Drug Design, Academic
Health Center, University of Minnesota,
Minneapolis, Minnesota 55455, United States
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32
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Liang F, Liu YZ, Zhang P. Universal base analogues and their applications in DNA sequencing technology. RSC Adv 2013. [DOI: 10.1039/c3ra41492b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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33
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Wong CH, Richardson SL, Ho YJ, Lucas AMH, Tuccinardi T, Baranger AM, Zimmerman SC. Investigating the binding mode of an inhibitor of the MBNL1·RNA complex in myotonic dystrophy type 1 (DM1) leads to the unexpected discovery of a DNA-selective binder. Chembiochem 2012; 13:2505-9. [PMID: 23097190 DOI: 10.1002/cbic.201200602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Indexed: 01/12/2023]
Affiliation(s)
- Chun-Ho Wong
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
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34
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Mata G, Luedtke NW. Stereoselective N-Glycosylation of 2-Deoxythioribosides for Fluorescent Nucleoside Synthesis. J Org Chem 2012; 77:9006-17. [DOI: 10.1021/jo3014929] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Guillaume Mata
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich,
Switzerland
| | - Nathan W. Luedtke
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich,
Switzerland
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35
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Zhao H, Huang W, Wu X, Xing Z, He Y, Chen Q. Different superstructures formed by Janus-type nucleosides. Chem Commun (Camb) 2012; 48:6097-9. [DOI: 10.1039/c2cc31036h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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36
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Zeng Y, Pratumyot Y, Piao X, Bong D. Discrete Assembly of Synthetic Peptide–DNA Triplex Structures from Polyvalent Melamine–Thymine Bifacial Recognition. J Am Chem Soc 2011; 134:832-5. [PMID: 22201288 DOI: 10.1021/ja2099326] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yingying Zeng
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Yaowalak Pratumyot
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Xijun Piao
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Dennis Bong
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
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