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Ingale SA, Leonard P, Yang H, Seela F. 5-Nitroindole oligonucleotides with alkynyl side chains: universal base pairing, triple bond hydration and properties of pyrene "click" adducts. Org Biomol Chem 2015; 12:8519-32. [PMID: 25236942 DOI: 10.1039/c4ob01478b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Oligonucleotides with 3-ethynyl-5-nitroindole and 3-octadiynyl-5-nitroindole 2'-deoxyribonucleosides were prepared by solid-phase synthesis. To this end, nucleoside phosphoramidites with clickable side chains were synthesized. The 3-ethynylated 5-nitroindole nucleoside was hydrated during automatized DNA synthesis to 3-acetyl-5-nitroindole 2'-deoxyribonucleoside. Side product formation was circumvented by triisopropylsilyl protection of the ethynyl side chain and was removed with TBAF after oligonucleotide synthesis. All compounds with a clickable 5-nitroindole skeleton show universal base pairing and can be functionalized with almost any azide in any position of the DNA chain. Functionalization of the side chain with 1-azidomethylpyrene afforded click adducts in which the fluorescence was quenched by the 5-nitroindole moieties. However, fluorescence was slightly recovered during duplex formation. Oligonucleotides with a pyrene residue and a long linker arm are stabilized over those with non-functionalized side chains. From the UV red shift of the pyrene residue in oligonucleotides and modelling studies, pyrene intercalation was established for the long linker adduct showing increased duplex stability over those with a short side chain.
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Affiliation(s)
- Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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2
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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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3
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Nickens DG, Bardiya N, Patterson JT, Burke DH. Template-directed ligation of tethered mononucleotides by t4 DNA ligase for kinase ribozyme selection. PLoS One 2010; 5:e12368. [PMID: 20811490 PMCID: PMC2927549 DOI: 10.1371/journal.pone.0012368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 07/27/2010] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND In vitro selection of kinase ribozymes for small molecule metabolites, such as free nucleosides, will require partition systems that discriminate active from inactive RNA species. While nucleic acid catalysis of phosphoryl transfer is well established for phosphorylation of 5' or 2' OH of oligonucleotide substrates, phosphorylation of diffusible small molecules has not been demonstrated. METHODOLOGY/PRINCIPAL FINDINGS This study demonstrates the ability of T4 DNA ligase to capture RNA strands in which a tethered monodeoxynucleoside has acquired a 5' phosphate. The ligation reaction therefore mimics the partition step of a selection for nucleoside kinase (deoxy)ribozymes. Ligation with tethered substrates was considerably slower than with nicked, fully duplex DNA, even though the deoxynucleotides at the ligation junction were Watson-Crick base paired in the tethered substrate. Ligation increased markedly when the bridging template strand contained unpaired spacer nucleotides across from the flexible tether, according to the trends: A(2)>A(1)>A(3)>A(4)>A(0)>A(6)>A(8)>A(10) and T(2)>T(3)>T(4)>T(6) approximately T(1)>T(8)>T(10). Bridging T's generally gave higher yield of ligated product than bridging A's. ATP concentrations above 33 microM accumulated adenylated intermediate and decreased yields of the gap-sealed product, likely due to re-adenylation of dissociated enzyme. Under optimized conditions, T4 DNA ligase efficiently (>90%) joined a correctly paired, or TratioG wobble-paired, substrate on the 3' side of the ligation junction while discriminating approximately 100-fold against most mispaired substrates. Tethered dC and dG gave the highest ligation rates and yields, followed by tethered deoxyinosine (dI) and dT, with the slowest reactions for tethered dA. The same kinetic trends were observed in ligase-mediated capture in complex reaction mixtures with multiple substrates. The "universal" analog 5-nitroindole (dNI) did not support ligation when used as the tethered nucleotide. CONCLUSIONS/SIGNIFICANCE Our results reveal a novel activity for T4 DNA ligase (template-directed ligation of a tethered mononucleotide) and establish this partition scheme as being suitable for the selection of ribozymes that phosphorylate mononucleoside substrates.
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Affiliation(s)
- David G. Nickens
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Nirmala Bardiya
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - James T. Patterson
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Donald H. Burke
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
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4
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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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Timofeev EN, Kolganova NA, Smirnov IP, Kochetkova SV, Florent'ev VL. [Oligodeoxynucleotides containing substituted 4-nitroindoles: synthesis and study of their DNA duplexes]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2008; 34:220-6. [PMID: 18522278 DOI: 10.1134/s106816200802009x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The synthesis of oligonucleotides containing 1-(2-deoxy-beta-D-ribofuranosyl)-2-methyl-4-nitroindole and 1-(2-deoxy-beta-D-ribofuranosyl)-2-phenyl-4-nitroindole is described. The synthesized modified oligonucleotides were used for studying the stability of intermolecular DNA duplexes with one unnatural strand and for evaluation of discriminating potential of 2-methyl- and 2-phenyl-4-nitroindoles toward nucleic bases. For comparison, an unmodified oligonucleotide and oligonucleotides bearing 5-nitroindole were used. It was shown that 2-methyl-4-nitroindole was only insignificantly inferior in stability to 5-nitroindole and characterized by a similar discriminating potential. 2-Phenyl-4-nitroindole provided a more pronounced duplex destabilization, the discrimination toward natural bases being decreased. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2008, vol. 34, no. 2; see also http:// www.maik.ru.
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Gallego J, Loakes D. Solution structure and dynamics of DNA duplexes containing the universal base analogues 5-nitroindole and 5-nitroindole 3-carboxamide. Nucleic Acids Res 2007; 35:2904-12. [PMID: 17438041 PMCID: PMC1888824 DOI: 10.1093/nar/gkm074] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Universal bases hybridize with all other natural DNA or RNA bases, and have applications in PCR and sequencing. We have analysed by nuclear magnetic resonance spectroscopy the structure and dynamics of three DNA oligonucleotides containing the universal base analogues 5-nitroindole and 5-nitroindole-3-carboxamide. In all systems studied, both the 5-nitroindole nucleotide and the opposing nucleotide adopt a standard anti conformation and are fully stacked within the DNA duplex. The 5-nitroindole bases do not base pair with the nucleotide opposite them, but intercalate between this base and an adjacent Watson–Crick pair. In spite of their smooth accommodation within the DNA double-helix, the 5-nitroindole-containing duplexes exist as a dynamic mixture of two different stacking configurations exchanging fast on the chemical shift timescale. These configurations depend on the relative intercalating positions of the universal base and the opposing base, and their exchange implies nucleotide opening motions on the millisecond time range. The structure of these nitroindole-containing duplexes explains the mechanism by which these artificial moieties behave as universal bases.
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Affiliation(s)
- José Gallego
- Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, 46013 Valencia, Spain.
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Loakes D, Hill F, Brown DM, Ball S, Reeve MA, Robinson PS. 5′-Tailed Octanucleotide Primers for Cycle Sequencing. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319908044634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- D. Loakes
- a Medical Research Council, Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
| | - F. Hill
- a Medical Research Council, Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
| | - D. M. Brown
- a Medical Research Council, Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
| | - S. Ball
- b Nycomed Amersham plc, Amersham Laboratories , White Lion Road, Amersham, Buckinghamshire , HP7 9LL , UK
| | - M. A. Reeve
- b Nycomed Amersham plc, Amersham Laboratories , White Lion Road, Amersham, Buckinghamshire , HP7 9LL , UK
| | - P. S. Robinson
- b Nycomed Amersham plc, Amersham Laboratories , White Lion Road, Amersham, Buckinghamshire , HP7 9LL , UK
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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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Berger M, Luzzi SD, Henry AA, Romesberg FE. Stability and selectivity of unnatural DNA with five-membered-ring nucleobase analogues. J Am Chem Soc 2002; 124:1222-6. [PMID: 11841290 DOI: 10.1021/ja012090t] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In an effort to develop an orthogonal third base pair for the storage of genetic information, thiophene and furan heterocycles have been examined as nucleobase analogues. The stability of the unnatural bases was evaluated in duplex DNA paired opposite other unnatural bases as well as opposite the natural bases. Several unnatural base pairs are identified that are both reasonably stable and strongly selective against mispairing with native bases. These results expand the potential nucleobase analogues with which the genetic alphabet may be expanded to include five-membered-ring heterocycles.
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Affiliation(s)
- Markus Berger
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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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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Kraltcheva AI, Hardin SH. Octamer-primed sequencing technology: effects of dNTP supplementation. Nucleic Acids Res 2001; 29:E48. [PMID: 11353093 PMCID: PMC55469 DOI: 10.1093/nar/29.10.e48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Octamer-primed sequencing is a directed DNA sequencing strategy that employs the use of a presynthesized octamer primer library. Together with electronic octamer sequencing technology (eOST) it provides a faster, less expensive way to obtain DNA sequence information and can be used as a valuable tool for gap closure in large-scale genomic sequencing. In this paper we discuss the effect of dGTP/TTP supplementation on octamer sequencing. We show that addition of 75 microM dGTP and 5 microM TTP can improve the sequencing success rate by increasing the length and accuracy of generated sequence information. We also discuss the effect of template base composition immediately downstream of the octamer primer on the outcome of octamer sequencing.
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Affiliation(s)
- A I Kraltcheva
- Department of Biology and Biochemistry and Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
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Zhang BP, Egholm M, Paul N, Pingle M, Bergstrom DE. Peptide nucleic acid-DNA duplexes containing the universal base 3-nitropyrrole. Methods 2001; 23:132-40. [PMID: 11181032 DOI: 10.1006/meth.2000.1114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A peptide nucleic acid (PNA) monomer containing the universal base 3-nitropyrrole was synthesized by coupling 1-carboxymethyl-3-nitropyrrole to ethyl N-[2-(tert-butoxycarbonylamino)ethyl]glycinate. The PNA sequence H-TGTACGTXACAACTA-NH2 (X = 3-nitropyrrole and C) and DNA sequence 5'-TGTACGTXACAACTA-3' were synthesized and thermal melting studies with the complementary DNA sequence 5'-TAGTTGTYACGTACA-3' (Y = A,C, G, T) compared. The T(m) data show that 3-nitropyrrole pairs indiscriminately with all four natural nucleobases as a constituent of either DNA or PNA. However, 3-nitropyrrole-containing PNA-DNA (average T(m) value = 51.1 degrees C) is significantly more thermally stable than 3-nitropyrrole-containing DNA-DNA (average T(m) value = 39.6 degrees C). From circular dichroism measurements, it is apparent that 3-nitropyrrole in the PNA strand causes a significant change in duplex structure.
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Affiliation(s)
- B P Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, USA
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Klewer DA, Hoskins A, Zhang P, Davisson VJ, Bergstrom DE, LiWang AC. NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control. Nucleic Acids Res 2000; 28:4514-22. [PMID: 11071940 PMCID: PMC113877 DOI: 10.1093/nar/28.22.4514] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The three-dimensional structures of two DNA duplexes d(CATGAGTAC). d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high resolution nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Good convergence was observed between final structures derived from A- and B-form starting geometries for both 1 and 2. Structures of 1 and 2 are right-handed duplexes within the B-form conformational regime. Furthermore, the structures of 1 and 2 are highly similar, with differences in the structures localized to the vicinity of residue 14 (X versus T). The pyrrole group of 1 is in the syn conformation and it is displaced towards the major groove. Furthermore, unlike T14 in 2, the base of X14 has reduced pi-pi stacking interactions with C13 and C15 and the nitro group of X14 is pointing out of the major groove. The structures presented here establish the basis of the thermal data of DNA duplexes containing X and should be informative during the design of improved wild card nucleobase analogs.
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Affiliation(s)
- D A Klewer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
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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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