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Gerecht K, Freund N, Liu W, Liu Y, Fürst MJLJ, Holliger P. The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics. Annu Rev Biophys 2023; 52:413-432. [PMID: 37159296 DOI: 10.1146/annurev-biophys-111622-091203] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this sense, biological sciences now follow the lead given by the chemical sciences. Synthesis can complement analytic studies but also allows novel approaches to answering fundamental biological questions and opens up vast opportunities for the exploitation of biological processes to provide solutions for global problems. In this review, we explore aspects of this synthesis paradigm as applied to the chemistry and function of nucleic acids in biological systems and beyond, specifically, in genome resynthesis, synthetic genetics (i.e., the expansion of the genetic alphabet, of the genetic code, and of the chemical make-up of genetic systems), and the elaboration of orthogonal biosystems and components.
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Affiliation(s)
- Karola Gerecht
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Wei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Yang Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Maximilian J L J Fürst
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
- Current address: Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
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2
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Ye Z, Du Y, Pan X, Zheng X, Xue J. Electron transfer from guanosine to the lowest triplet excited state of 4-nitroindole through hydrogen-bonded complex. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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3
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Hoff K, Halpain M, Garbagnati G, Edwards JS, Zhou W. Enzymatic Synthesis of Designer DNA Using Cyclic Reversible Termination and a Universal Template. ACS Synth Biol 2020; 9:283-293. [PMID: 31895546 DOI: 10.1021/acssynbio.9b00315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphoramidite chemistry remains the industry standard for DNA synthesis despite significant limitations on the length and yield of the oligonucleotide, time restrictions, and hazardous waste production. Herein, we demonstrate the synthesis of single-stranded oligos on a solid surface by DNA polymerases and reverse transcriptases. We report the extension of surface-bound oligonucleotides enabled by transient hybridization of as few as two bases to a neighboring strand. When multiple hybridization structures are possible, each templating a different base, a DNA polymerase or reverse transcriptase can extend the oligonucleotide with any of the complementary bases. Therefore, the sequence of the newly synthesized fragment can be controlled by adding only the desired base as a substrate to the reaction solution. We used this enzymatic approach to synthesize a 20 base oligonucleotide by incorporating reversible terminator dNTPs through a two-step cyclic reversible termination process with a corrected stepwise efficiency over 98%. In our approach, a nascent DNA strand that serves as both primer and template is extended through polymerase-controlled sequential addition of 3'-reversibly blocked nucleotides followed by subsequent cleavage of the 3'-capping group. This process enables oligonucleotide synthesis in an environment not permitted by traditional phosphoramidite methods, eliminates the need for hazardous chemicals, has the potential to provide faster and higher yield results, and synthesizes DNA on a solid support with a free 3' end.
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Affiliation(s)
- Kendall Hoff
- Department of Advanced Research and Development, Centrillion Biosciences, Palo Alto, California 94303, United States
| | - Michelle Halpain
- Department of Advanced Research and Development, Centrillion Biosciences, Palo Alto, California 94303, United States
| | - Giancarlo Garbagnati
- Department of Advanced Research and Development, Centrillion Biosciences, Palo Alto, California 94303, United States
| | - Jeremy S. Edwards
- Department of Advanced Research and Development, Centrillion Biosciences, Palo Alto, California 94303, United States
- Chemistry and Chemical Biology and Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
- Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
- University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico 87131, United States
| | - Wei Zhou
- Department of Advanced Research and Development, Centrillion Biosciences, Palo Alto, California 94303, United States
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4
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Passow KT, Harki DA. 4-Cyanoindole-2'-deoxyribonucleoside (4CIN): A Universal Fluorescent Nucleoside Analogue. Org Lett 2018; 20:4310-4313. [PMID: 29989830 PMCID: PMC6168291 DOI: 10.1021/acs.orglett.8b01746] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The synthesis and characterization of a universal and fluorescent nucleoside, 4-cyanoindole-2'-deoxyribonucleoside (4CIN), and its incorporation into DNA is described. 4CIN is a highly efficient fluorophore with quantum yields >0.90 in water. When incorporated into duplex DNA, 4CIN pairs equivalently with native nucleobases and has uniquely high quantum yields ranging from 0.15 to 0.31 depending on sequence and hybridization contexts, surpassing that of 2-aminopurine, the prototypical nucleoside fluorophore. 4CIN constitutes a new isomorphic nucleoside for diverse applications.
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Affiliation(s)
- Kellan T. Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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5
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Sato T, Sato Y, Nishizawa S. Optimization of the Alkyl Linker of TO Base Surrogate in Triplex-Forming PNA for Enhanced Binding to Double-Stranded RNA. Chemistry 2017; 23:4079-4088. [PMID: 27897343 DOI: 10.1002/chem.201604676] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Indexed: 12/24/2022]
Abstract
A series of triplex-forming peptide nucleic acid (TFP) probes carrying a thiazole orange (TO) base surrogate through an alkyl linker was synthesized, and the interactions between these so-called tFIT probes and purine-rich sequences within double-stranded RNA (dsRNA) were examined. We found that the TO base surrogate linker significantly affected both the binding affinity and the fluorescence response upon triplex formation with the target dsRNA. Among the probes examined, the TO base surrogate connected through the propyl linker in the tFIT probes increased the binding affinity by a factor of ten while maintaining its function as the fluorescent universal base. Isothermal titration calorimetry experiments revealed that the increased binding affinity resulted from the gain in the binding enthalpy, which could be explained by the enhanced π-stacking interaction between the TO base surrogate and the dsRNA part of the triplex. We expect that these results will provide a molecular basis for designing strong binding tFIT probes for fluorescence sensing of various kinds of purine-rich dsRNAs sequences including those carrying a pyrimidine-purine inversion. The obtained data also offers a new insight into further development of the universal bases incorporated in TFP.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
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6
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Spring-Connell AM, Evich MG, Debelak H, Seela F, Germann MW. Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog. Nucleic Acids Res 2016; 44:8576-8587. [PMID: 27566150 PMCID: PMC5062995 DOI: 10.1093/nar/gkw736] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/10/2016] [Indexed: 12/30/2022] Open
Abstract
A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2'deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications.
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Affiliation(s)
| | - Marina G Evich
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Harald Debelak
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück, Germany
| | - Frank Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück, Germany Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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7
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Abstract
Whole genome amplification (WGA) is a widely used molecular technique that is becoming increasingly necessary in genetic research on a range of sample types including individual cells, fossilized remains and entire ecosystems. Multiple methods of WGA have been developed, each with specific strengths and weaknesses, but with a common defect in that each method distorts the initial template DNA during the course of amplification. The type, extent, and circumstance of the bias vary with the WGA method and particulars of the template DNA. In this review, we endeavor to discuss the types of bias introduced, the susceptibility of common WGA techniques to these bias types, and the interdependence between bias and characteristics of the template DNA. Finally, we attempt to illustrate some of the criteria specific to the analytical platform and research application that should be considered to enable combination of the appropriate WGA method, template DNA, sequencing platform, and intended use for optimal results.
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Affiliation(s)
| | - John H Leamon
- CyVek Inc., 2 Barnes Industrial Road South, Wallingford, CT, 06492, USA.
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Vorobiev AV, Scarr NK, Belousov Y, Lukhtanov EA. 7-aminobutynyl-8-aza-7-deazahypoxanthine as a quasi-universal nucleobase. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 32:421-38. [PMID: 23895353 DOI: 10.1080/15257770.2013.806661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Several 7-(hydroxy, amino, methylureido, and guanidino)alkynyl-substituted 8-aza-7-deaza- hypoxanthine analogues were investigated as potential universal nucleobases. 7-Aminobutynyl-8-aza-7-deazahypoxanthine was found to be the most promising quasi-universal nucleobase with improved hybridization and polymerase chain reaction (PCR) enhancing properties as compared to commonly used hypoxanthine (the nucleobase of inosine). It demonstrated improved ambiguity for pairing with A, T, and C bases and its base pairing properties can be summarized as follows: X:C∼X:A∼X:T > X:G. The improvement in PCR performance directly correlated with primer's Tm. Primers containing multiple 7-aminobutynyl-8-aza-7-deazahypoxanthines were successfully used without noticeable inhibition of Taq polymerase activity provided the modifications are positioned more than two bases away from the 3' end.
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Affiliation(s)
- Alexei V Vorobiev
- Elitech Group, Epoch Biosciences, a Division of Wescor Inc., Bothell, Washington 98021, USA
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9
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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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10
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Pinheiro VB, Loakes D, Holliger P. Synthetic polymers and their potential as genetic materials. Bioessays 2012; 35:113-22. [PMID: 23281109 DOI: 10.1002/bies.201200135] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA and RNA are the only known natural genetic materials. Systematic modification of each of their chemical building blocks (nucleobase, sugar, and phosphate) has enabled the study of the key properties that make those nucleic acids genetic materials. All three moieties contribute to replication and, significantly, all three moieties can be replaced by synthetic analogs without loss of function. Synthetic nucleic acid polymers capable of storing and propagating information not only expand the central dogma, but also highlight that DNA and RNA are not unique chemical solutions for genetic information storage. By considering replication as a question of information transfer, we propose that any polymer that can be replicated could serve as a genetic material.
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Affiliation(s)
- Vitor B Pinheiro
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK.
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11
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Motea EA, Lee I, Berdis AJ. A non-natural nucleoside with combined therapeutic and diagnostic activities against leukemia. ACS Chem Biol 2012; 7:988-98. [PMID: 22390204 DOI: 10.1021/cb300038f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common type of childhood cancer, presenting with approximately 5,000 new cases each year in the United States. An interesting enzyme implicated in this disease is terminal deoxynucleotidyl transferase (TdT), a specialized DNA polymerase involved in V(D)J recombination. TdT is an excellent biomarker for ALL as it is overexpressed in ~90% of ALL patients, and these higher levels correlate with a poor prognosis. These collective features make TdT an attractive target to design new selective anti-cancer agents against ALL. In this report, we evaluate the anti-leukemia activities of two non-natural nucleotides designated 5-nitroindolyl-2'-deoxynucleoside triphosphate (5-NITP) and 3-ethynyl-5-nitroindolyl-2'-deoxynucleoside triphosphate (3-Eth-5-NITP). Using purified TdT, we demonstrate that both non-natural nucleotides are efficiently utilized as TdT substrates. However, 3-Eth-5-NITP is poorly elongated, and this observation validates its activity as a chain-terminator for blunt-end DNA synthesis. Cell-based experiments validate that the corresponding non-natural nucleoside produces robust cytostatic and cytotoxic effects against leukemia cells that overexpress TdT. The strategic placement of the ethynyl moiety allows the incorporated nucleoside triphosphate to be selectively tagged with an azide-containing fluorophore via "click" chemistry. This reaction allows the extent of nucleotide incorporation to be quantified such that the anti-cancer effects of the corresponding non-natural nucleoside can be self-assessed. The applications of this novel nucleoside are discussed, focusing on its use as a "theranostic" agent that can improve the accuracy of dosing regimens and accelerate clinical decisions regarding therapeutic intervention.
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Affiliation(s)
- Edward A. Motea
- Departments of †Chemistry and ‡Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Irene Lee
- Departments of †Chemistry and ‡Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Anthony J. Berdis
- Departments of †Chemistry and ‡Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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12
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Optimization of PCR amplification for sensitive capture of Methanopyrus isoleucyl-tRNA synthetase gene in environmental samples. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0097-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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13
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Ceballos C, Khiati S, Prata CAH, Zhang XX, Giorgio S, Marsal P, Grinstaff MW, Barthélémy P, Camplo M. Cationic Nucleoside Lipids Derived from Universal Bases: A Rational Approach for siRNA Transfection. Bioconjug Chem 2010; 21:1062-9. [DOI: 10.1021/bc100005k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Claire Ceballos
- Centre Interdisciplinaire de Nanoscience de Marseille CINaM, Upr-Cnrs 3118, Université Aix-Marseille II, Luminy, case 913, 13288 Marseille cedex 09, France, Inserm, U869, Université de Bordeaux, F-33076, Bordeaux, France, and Departments of Chemistry and Biomedical Engineering, Metcalf Center for Science and Engineering, Boston University, Boston, Massachusetts 02215
| | - Salim Khiati
- Centre Interdisciplinaire de Nanoscience de Marseille CINaM, Upr-Cnrs 3118, Université Aix-Marseille II, Luminy, case 913, 13288 Marseille cedex 09, France, Inserm, U869, Université de Bordeaux, F-33076, Bordeaux, France, and Departments of Chemistry and Biomedical Engineering, Metcalf Center for Science and Engineering, Boston University, Boston, Massachusetts 02215
| | - Carla A. H. Prata
- Centre Interdisciplinaire de Nanoscience de Marseille CINaM, Upr-Cnrs 3118, Université Aix-Marseille II, Luminy, case 913, 13288 Marseille cedex 09, France, Inserm, U869, Université de Bordeaux, F-33076, Bordeaux, France, and Departments of Chemistry and Biomedical Engineering, Metcalf Center for Science and Engineering, Boston University, Boston, Massachusetts 02215
| | - Xiao-Xiang Zhang
- Centre Interdisciplinaire de Nanoscience de Marseille CINaM, Upr-Cnrs 3118, Université Aix-Marseille II, Luminy, case 913, 13288 Marseille cedex 09, France, Inserm, U869, Université de Bordeaux, F-33076, Bordeaux, France, and Departments of Chemistry and Biomedical Engineering, Metcalf Center for Science and Engineering, Boston University, Boston, Massachusetts 02215
| | - Suzanne Giorgio
- Centre Interdisciplinaire de Nanoscience de Marseille CINaM, Upr-Cnrs 3118, Université Aix-Marseille II, Luminy, case 913, 13288 Marseille cedex 09, France, Inserm, U869, Université de Bordeaux, F-33076, Bordeaux, France, and Departments of Chemistry and Biomedical Engineering, Metcalf Center for Science and Engineering, Boston University, Boston, Massachusetts 02215
| | - Philippe Marsal
- Centre Interdisciplinaire de Nanoscience de Marseille CINaM, Upr-Cnrs 3118, Université Aix-Marseille II, Luminy, case 913, 13288 Marseille cedex 09, France, Inserm, U869, Université de Bordeaux, F-33076, Bordeaux, France, and Departments of Chemistry and Biomedical Engineering, Metcalf Center for Science and Engineering, Boston University, Boston, Massachusetts 02215
| | - Mark W. Grinstaff
- Centre Interdisciplinaire de Nanoscience de Marseille CINaM, Upr-Cnrs 3118, Université Aix-Marseille II, Luminy, case 913, 13288 Marseille cedex 09, France, Inserm, U869, Université de Bordeaux, F-33076, Bordeaux, France, and Departments of Chemistry and Biomedical Engineering, Metcalf Center for Science and Engineering, Boston University, Boston, Massachusetts 02215
| | - Philippe Barthélémy
- Centre Interdisciplinaire de Nanoscience de Marseille CINaM, Upr-Cnrs 3118, Université Aix-Marseille II, Luminy, case 913, 13288 Marseille cedex 09, France, Inserm, U869, Université de Bordeaux, F-33076, Bordeaux, France, and Departments of Chemistry and Biomedical Engineering, Metcalf Center for Science and Engineering, Boston University, Boston, Massachusetts 02215
| | - Michel Camplo
- Centre Interdisciplinaire de Nanoscience de Marseille CINaM, Upr-Cnrs 3118, Université Aix-Marseille II, Luminy, case 913, 13288 Marseille cedex 09, France, Inserm, U869, Université de Bordeaux, F-33076, Bordeaux, France, and Departments of Chemistry and Biomedical Engineering, Metcalf Center for Science and Engineering, Boston University, Boston, Massachusetts 02215
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14
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Prunkl C, Berndl S, Wanninger-Weiß C, Barbaric J, Wagenknecht HA. Photoinduced short-range electron transfer in DNA with fluorescent DNA bases: lessons from ethidium and thiazole orange as charge donors. Phys Chem Chem Phys 2010; 12:32-43. [DOI: 10.1039/b914487k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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15
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Barbaric J, Wanninger-Weiß C, Wagenknecht HA. Indole in DNA: Comparison of a Nucleosidic with a Non-Nucleosidic DNA Base Substitution. European J Org Chem 2009. [DOI: 10.1002/ejoc.200800863] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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16
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Morgan JR, Lyon RP, Maeda DY, Zebala JA. Snap-to-it probes: chelate-constrained nucleobase oligomers with enhanced binding specificity. Nucleic Acids Res 2008; 36:3522-30. [PMID: 18448470 PMCID: PMC2441785 DOI: 10.1093/nar/gkn219] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe snap-to-it probes, a novel probe technology to enhance the hybridization specificity of natural and unnatural nucleic acid oligomers using a simple and readily introduced structural motif. Snap-to-it probes were prepared from peptide nucleic acid (PNA) oligomers by modifying each terminus with a coordinating ligand. The two coordinating ligands constrain the probe into a macrocyclic configuration through formation of an intramolecular chelate with a divalent transition metal ion. On hybridization with a DNA target, the intramolecular chelate in the snap-to-it probe dissociates, resulting in the probe 'snapping-to' and binding the target nucleic acid. Thermal transition analysis of snap-to-it probes with complementary and single-mismatch DNA targets revealed that the transition between free and target-bound probe conformations was a reversible equilibrium, and the intramolecular chelate provided a thermodynamic barrier to target binding that resulted in a significant increase in mismatch discrimination. A 4-6 degrees C increase in specificity (DeltaT(m)) was observed from snap-to-it probes bearing either terminal iminodiacetic acid ligands coordinated with Ni(2+), or terminal dihistidine and nitrilotriacetic acid ligands coordinated with Cu(2+). The difference in specificity of the PNA oligomer relative to DNA was more than doubled in snap-to-it probes. Snap-to-it probes labeled with a fluorophore-quencher pair exhibited target-dependent fluorescence enhancement upon binding with target DNA.
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Affiliation(s)
- Joel R Morgan
- Syntrix Biosystems, Inc., 215 Clay St. NW Suite B-5, Auburn, WA 98001, USA
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17
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Harki DA, Graci JD, Edathil JP, Castro C, Cameron CE, Peterson BR. Synthesis of a universal 5-nitroindole ribonucleotide and incorporation into RNA by a viral RNA-dependent RNA polymerase. Chembiochem 2007; 8:1359-62. [PMID: 17600792 PMCID: PMC2194811 DOI: 10.1002/cbic.200700160] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel A. Harki
- Dr. D. A. Harki, J. P. Edathil, Prof. B. R. Peterson, Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802 (USA), Fax: (+1) 814-863-5319, E-mail:
| | - Jason D. Graci
- J. D. Graci, Dr. C. Castro, Prof. C. E. Cameron, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 (USA)
| | - Jocelyn P. Edathil
- Dr. D. A. Harki, J. P. Edathil, Prof. B. R. Peterson, Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802 (USA), Fax: (+1) 814-863-5319, E-mail:
| | - Christian Castro
- J. D. Graci, Dr. C. Castro, Prof. C. E. Cameron, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 (USA)
| | - Craig E. Cameron
- J. D. Graci, Dr. C. Castro, Prof. C. E. Cameron, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 (USA)
| | - Blake R. Peterson
- Dr. D. A. Harki, J. P. Edathil, Prof. B. R. Peterson, Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802 (USA), Fax: (+1) 814-863-5319, E-mail:
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18
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Rutledge LR, Wheaton CA, Wetmore SD. A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine. Phys Chem Chem Phys 2007; 9:497-509. [PMID: 17216066 DOI: 10.1039/b606388h] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine-cytosine pair is approximately 25 kJ mol(-1) stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences. However, our calculations suggest that the stacking interactions of hypoxanthine are similar in magnitude to the hydrogen-bonding interactions at all levels of theory (with the exception of B3LYP, which incorrectly predicts stacked dimers to be unstable). Therefore, stacking interactions should also be considered when analyzing the stability of DNA helices containing hypoxanthine and the use of larger models that account for both hydrogen-bonding and stacking within DNA duplexes will likely result in better agreement with experimental observations. For the majority of the dimers, PWB6K and AMBER provide reasonable binding strengths at reduced computational costs, and therefore will be useful techniques for considering larger models.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, Canada E4L 1G8
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19
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Nitrosubstituted aromatic molecules as universal nucleobases: Computational analysis of stacking interactions. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.07.051] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Valis L, Wang Q, Raytchev M, Buchvarov I, Wagenknecht HA, Fiebig T. Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer. Proc Natl Acad Sci U S A 2006; 103:10192-10195. [PMID: 16801552 PMCID: PMC1502433 DOI: 10.1073/pnas.0600957103] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 1999, Wan et al. [Proc. Natl. Acad. Sci. USA 96, 6014-6019] published a pioneering paper that established the entanglement between DNA base pair motions and the transfer time of the charge carrier. The DNA assemblies contained an ethidium covalently bound via a flexible alkyl chain to the 5' hydroxyl group of the DNA backbone. Although covalently attached, the loose way in which the ethidium was linked to DNA allowed for large degrees of conformational freedom and thus raised some concern with respect to conformational inhomogeneity. In this letter, we report studies on a different set of ethidium DNA conjugates. In contrast to the "Caltech systems," these conjugates contain ethidium tightly incorporated (as a base pair surrogate) into the DNA base stack, opposite to an abasic site analog. Despite the tight binding, we found that charge transfer from the photoexcited ethidium base pair surrogate across two or more base pairs is several orders of magnitude slower than in case of the DNA systems bearing the tethered ethidium. To further broaden the scope of this account, we compared (oxidative) electron hole transfer and (reductive) electron transfer using the same ethidium chromophore as a charge donor in combination with two different charge acceptors. We found that both electron and hole transfer are characterized by similar rates and distance dependencies. The results demonstrate the importance of nuclear motions and conformational flexibility and underline the presence of a base gating mechanism, which appears to be generic to electronic transfer processes through pi-stacked nucleic acids.
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Affiliation(s)
- Linda Valis
- Institute for Organic Chemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Qiang Wang
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
| | - Milen Raytchev
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
| | - Ivan Buchvarov
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
| | | | - Torsten Fiebig
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
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21
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Too K, Brown DM, Holliger P, Loakes D. Effect of a Hydrogen Bonding Carboxamide Group on Universal Bases. ACTA ACUST UNITED AC 2006. [DOI: 10.1135/cccc20060899] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A number of aromatic universal base analogues have been described in the literature, but most are non-hydrogen bonding. We have examined the effect of introducing hydrogen bonding carboxamide groups onto the pyrrole ring of 5-nitroindole. The modified analogues retain universal base features, but there are no overall effects on duplex stability. This leads to the suggestion that the nitro group is within the hydrogen bonding face of the duplex, and the hydrogen bonding carboxamide group is in the duplex major groove.
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22
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LaPointe SM, Wetmore SD. Characterization of the binding interactions between a unique class of modified purines and the natural nucleobases. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.04.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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LaPointe SM, Wheaton CA, Wetmore SD. The degenerate properties of modified purine and pyrimidine DNA bases: a density functional study. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.10.104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Epstein JR, Ferguson JA, Lee KH, Walt DR. Combinatorial decoding: an approach for universal DNA array fabrication. J Am Chem Soc 2004; 125:13753-9. [PMID: 14599214 DOI: 10.1021/ja0365577] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A fiber optic microsphere-based oligonucleotide array is described that employs the sequence of the oligonucleotide probe attached to each microsphere as positional identifiers. Each microsphere serves as an immobilized array feature, functionalized with a unique single-stranded oligonucleotide sequence and randomly distributed into an array of microwells. To determine the sequences attached to individual microspheres, a series of fluorescently labeled combinatorial-pooled oligonucleotide target solutions was designed. Each combinatorial decoding solution is intended to identify the nucleotide at a particular position on every microsphere in the array. The combinatorial target solutions were synthesized by linking the four possible nucleotides at each position to four different fluorescent reporter dyes. As such, when the solutions were hybridized to the array, one of four possible fluorescent responses was generated for each position on a microsphere probe sequence. Adjusting the stringency of hybridization enabled single-base mismatch discrimination, and the signal with the highest intensity corresponded to the perfect nucleotide match. By consecutively exposing the array to a series of combinatorial decoding pool solutions, it was possible to simultaneously determine the sequence of every randomly positioned oligonucleotide-functionalized microsphere in the array. Once mapped, the microsphere array can be used for any typical genomic microarray experiment.
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Affiliation(s)
- Jason R Epstein
- Max Tishler Laboratory for Organic Chemistry, Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA
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25
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LaPointe SM, Wetmore SD. Striving to Understand the Properties of Universal Nucleobases: A Computational Study of Azole Carboxamides. J Phys Chem A 2003. [DOI: 10.1021/jp035000a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shenna M. LaPointe
- Department of Chemistry, Mount Allison University, 68C York Street, Sackville, New Brunswick, E4L 1G8 Canada
| | - Stacey D. Wetmore
- Department of Chemistry, Mount Allison University, 68C York Street, Sackville, New Brunswick, E4L 1G8 Canada
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26
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Lage JM, Leamon JH, Pejovic T, Hamann S, Lacey M, Dillon D, Segraves R, Vossbrinck B, González A, Pinkel D, Albertson DG, Costa J, Lizardi PM. Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res 2003; 13:294-307. [PMID: 12566408 PMCID: PMC420367 DOI: 10.1101/gr.377203] [Citation(s) in RCA: 212] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Structural genetic alterations in cancer often involve gene loss or gene amplification. With the advent of microarray approaches for the analysis of the genome, as exemplified by array-CGH (Comparative Genomic Hybridization), scanning for gene-dosage alterations is limited only by issues of DNA microarray density. However, samples of interest to the pathologist often comprise small clusters of just a few hundred cells, which do not provide sufficient DNA for array-CGH analysis. We sought to develop a simple method that would permit amplification of the whole genome without the use of thermocycling or ligation of DNA adaptors, because such a method would lend itself to the automated processing of a large number of tissue samples. We describe a method that permits the isothermal amplification of genomic DNA with high fidelity and limited sequence representation bias. The method is based on strand displacement reactions that propagate by a hyperbranching mechanism, and generate hundreds, or even thousands, of copies of the genome in a few hours. Using whole genome isothermal amplification, in combination with comparative genomic hybridization on cDNA microarrays, we demonstrate the ability to detect gene losses in yeast and gene dosage imbalances in human breast tumor cell lines. Although sequence representation bias in the amplified DNA presents potential problems for CGH analysis, these problems have been overcome by using amplified DNA in both control and tester samples. Gene-dosage alterations of threefold or more can be observed with high reproducibility with as few as 1000 cells of starting material.
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Affiliation(s)
- José M Lage
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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27
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Pascaly M, Yoo J, Barton JK. DNA mediated charge transport: characterization of a DNA radical localized at an artificial nucleic acid base. J Am Chem Soc 2002; 124:9083-92. [PMID: 12149012 DOI: 10.1021/ja0202210] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA assemblies containing 4-methylindole incorporated as an artificial base provide a chemically well-defined system in which to explore the oxidative charge transport process in DNA. Using this artificial base, we have combined transient absorption and EPR spectroscopies as well as biochemical methods to test experimentally current mechanisms for DNA charge transport. The 4-methylindole radical cation intermediate has been identified using both EPR and transient absorption spectroscopies in oxidative flash-quench studies using a dipyridophenazine complex of ruthenium as the intercalating oxidant. The 4-methylindole radical cation intermediate is particularly amenable to study given its strong absorptivity at 600 nm and EPR signal measured at 77 K with g = 2.0065. Both transient absorption and EPR spectroscopies show that the 4-methylindole is well incorporated in the duplex; the data also indicate no evidence of guanine radicals, given the low oxidation potential of 4-methylindole relative to the nucleic acid bases. Biochemical studies further support the irreversible oxidation of the indole moiety and allow the determination of yields of irreversible product formation. The construction of these assemblies containing 4-methylindole as an artificial base is also applied in examining long-range charge transport mediated by the DNA base pair stack as a function of intervening distance and sequence. The rate of formation of the indole radical cation is >/=10(7) s(-)(1) for different assemblies with the ruthenium positioned 17-37 A away from the methylindole and with intervening A-T base pairs primarily composing the bridge. In these assemblies, methylindole radical formation at a distance is essentially coincident with quenching of the ruthenium excited state to form the Ru(III) oxidant; charge transport is not rate limiting over this distance regime. The measurements here of rates of radical cation formation establish that a model of G-hopping and AT-tunneling is not sufficient to account for DNA charge transport. Instead, these data are viewed mechanistically as charge transport through the DNA duplex primarily through hopping among well stacked domains of the helix defined by DNA sequence and dynamics.
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Affiliation(s)
- Matthias Pascaly
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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28
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Kuznetsov SV, Shen Y, Benight AS, Ansari A. A semiflexible polymer model applied to loop formation in DNA hairpins. Biophys J 2001; 81:2864-75. [PMID: 11606297 PMCID: PMC1301751 DOI: 10.1016/s0006-3495(01)75927-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A statistical mechanical "zipper" model is applied to describe the equilibrium melting of short DNA hairpins with poly(dT) loops ranging from 4 to 12 bases in the loop. The free energy of loop formation is expressed in terms of the persistence length of the chain. This method provides a new measurement of the persistence length of single-stranded DNA, which is found to be approximately 1.4 nm for poly(dT) strands in 100 mM NaCl. The free energy of the hairpin relative to the random coil state is found to scale with the loop size with an apparent exponent of > or = 7, much larger than the exponent of approximately 1.5-1.8 expected from considerations of loop entropy alone. This result indicates a strong dependence of the excess stability of the hairpins, from stacking interactions of the bases within the loop, on the size of the loop. We interpret this excess stability as arising from favorable hydrophobic interactions among the bases in tight loops and which diminish as the loops get larger. Free energy profiles along a generalized reaction coordinate are calculated from the equilibrium zipper model. The transition state for hairpin formation is identified as an ensemble of looped conformations with one basepair closing the loop, and with a lower enthalpy than the random coil state. The equilibrium model predicts apparent activation energy of approximately -11 kcal/mol for the hairpin closing step, in remarkable agreement with the value obtained from kinetics measurements.
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Affiliation(s)
- S V Kuznetsov
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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29
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Loakes D. Survey and summary: The applications of universal DNA base analogues. Nucleic Acids Res 2001; 29:2437-47. [PMID: 11410649 PMCID: PMC55727 DOI: 10.1093/nar/29.12.2437] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2001] [Revised: 04/18/2001] [Accepted: 04/18/2001] [Indexed: 11/13/2022] Open
Abstract
A universal base analogue forms 'base pairs' with each of the natural DNA/RNA bases with little discrimination between them. A number of such analogues have been prepared and their applications as biochemical tools investigated. Most of these analogues are non-hydrogen bonding, hydrophobic, aromatic 'bases' which stabilise duplex DNA by stacking interactions. This review of the literature of universal bases (to 2000) details the analogues investigated, and their uses and limitations are discussed.
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Affiliation(s)
- D Loakes
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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30
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Rueda M, Luque FJ, López JM, Orozco M. Amino−Imino Tautomerism in Derivatives of Cytosine: Effect on Hydrogen-Bonding and Stacking Properties. J Phys Chem A 2001. [DOI: 10.1021/jp010838o] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manuel Rueda
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain
| | - F. Javier Luque
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain
| | - Josep Maria López
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain
| | - Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain
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31
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32
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Guckian KM, Schweitzer BA, Ren RXF, Sheils CJ, Tahmassebi DC, Kool ET. Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA. J Am Chem Soc 2000; 122:2213-2222. [PMID: 20865137 DOI: 10.1021/ja9934854] [Citation(s) in RCA: 343] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We report the use of thermodynamic measurements in a self-complementary DNA duplex (5'-dXCGCGCG)(2), where X is an unpaired natural or nonnatural deoxynucleoside, to study the forces that stabilize aqueous aromatic stacking in the context of DNA. Thermal denaturation experiments show that the core duplex (lacking X) is formed with a free energy (37 °C) of -8.1 kcal·mol(-1) in a pH 7.0 buffer containing 1 M Na(+). We studied the effects of adding single dangling nucleosides (X) where the aromatic "base" is adenine, guanine, thymine, cytosine, pyrrole, benzene, 4-methylindole, 5-nitroindole, trimethylbenzene, difluorotoluene, naphthalene, phenanthrene, and pyrene. Adding these dangling residues is found to stabilize the duplex by an additional -0.8 to -3.4 kcal·mol(-1). At 5 μM DNA concentration, T(m) values range from 41.7 °C (core sequence) to 64.1 °C (with dangling pyrene residues). For the four natural bases, the order of stacking ability is A > G ≥ T = C. The nonpolar analogues stack more strongly in general than the more polar natural bases. The stacking geometry was confirmed in two cases (X = adenine and pyrene) by 2-D NOESY experiments. Also studied is the effect of ethanol cosolvent on the stacking of natural bases and pyrene. Stacking abilities were compared to calculated values for hydrophobicity, dipole moment, polarizability, and surface area. In general, hydrophobic effects are found to be larger than other effects stabilizing stacking (electrostatic effects, dispersion forces); however, the natural DNA bases are found to be less dependent on hydrophobic effects than are the more nonpolar compounds. The results also point out strategies for the design nucleoside analogues that stack considerably more strongly than the natural bases; such compounds may be useful in stabilizing designed DNA structures and complexes.
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Affiliation(s)
- Kevin M Guckian
- Contribution from the Department of Chemistry, University of Rochester, Rochester, New York 14627
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33
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Abstract
[formula: see text] The syntheses of PNA oligomers containing potential ambiguous nucleobase analogues, namely 3-nitropyrrole and 5-nitroindole, have been accomplished. Hybridization properties of these PNAs with complementary oligodeoxynucleotides were evaluated by thermal denaturation experiments. Both novel residues exhibited little variation in Tm (< or = 1.5 degrees C) when positioned against any of the four nucleoside bases. The capability to incorporate degenerate sites should further expand the utility of PNA in applications where precise sequence information is not available.
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Affiliation(s)
- H Challa
- Department of Chemistry and Coalition for Biomolecular Products, University of Alabama, Tuscaloosa 35487-0336, USA
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34
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Vallone PM, Benight AS. Melting studies of short DNA hairpins containing the universal base 5-nitroindole. Nucleic Acids Res 1999; 27:3589-96. [PMID: 10446251 PMCID: PMC148605 DOI: 10.1093/nar/27.17.3589] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Effects of the universal base 5-nitroindole on the thermodynamic stability of DNA hairpins having a 6 bp stem and four base loops were investigated by optical absorbance and differential scanning calorimetry techniques. Melting studies were conducted in buffer containing 115 mM Na(+). Five different modified versions of DNA hairpins containing a 5-nitroindole base or bases substituted at different positions in the stem and loop regions were examined. Thermo-dynamic parameters of the melting transitions estimated from a two-state analysis of optical melting curves and measured directly by calorimetry revealed that the presence of 5-nitroindole bases in the duplex stem or loop regions of short DNA hairpins significantly affects both their enthalpic and entropic melting components in a compensating manner, while the transition free energy varies linearly with the transition temperature. The calorimetrically determined enthalpy and entropy values of the modified hairpins were considerably smaller (43-53%) than the two-state optical parameters, suggesting that solvent effects may be significant in the melting processes of these hairpins. Results of circular dichroism measurements also revealed slight differences between the modified hairpins and the control in both the duplex and melted states, suggesting subtle structural differences between the control and DNA hairpins containing a 5-nitroindole base or bases.
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Affiliation(s)
- P M Vallone
- Department of Chemistry, 845 West Taylor Street, Room 4500, University of Illinois at Chicago, Chicago, IL 60607, USA
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35
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Ball S, Reeve MA, Robinson PS, Hill F, Brown DM, Loakes D. The use of tailed octamer primers for cycle sequencing. Nucleic Acids Res 1998; 26:5225-7. [PMID: 9801324 PMCID: PMC147975 DOI: 10.1093/nar/26.22.5225] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Studies have been carried out on the use of octamer oligonucleotides tailed with different base analogues as primers in cycle sequencing reactions. 5-Nitroindole tails improved the performance as primers of a number of octamers. A tail length of three or four 5-nitroindole residues significantly increased the sequencing signal intensity for almost all primers. The use of incomplete libraries of tailed octamer primers for primer walking is discussed.
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Affiliation(s)
- S Ball
- Nycomed Amersham plc, Amersham Laboratories, White Lion Road, Amersham, Buckinghamshire HP7 9LL, UK
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36
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Luyten I, Herdewijn P. Hybridization properties of base-modified oligonucleotides within the double and triple helix motif. Eur J Med Chem 1998. [DOI: 10.1016/s0223-5234(98)80016-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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