1
|
Biswas S, Sen S, Im J, Biswas S, Krstic P, Ashcroft B, Borges C, Zhao Y, Lindsay S, Zhang P. Universal Readers Based on Hydrogen Bonding or π-π Stacking for Identification of DNA Nucleotides in Electron Tunnel Junctions. ACS NANO 2016; 10:11304-11316. [PMID: 28024337 DOI: 10.1021/acsnano.6b06466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A reader molecule, which recognizes all the naturally occurring nucleobases in an electron tunnel junction, is required for sequencing DNA by a recognition tunneling (RT) technique, referred to as a universal reader. In the present study, we have designed a series of heterocyclic carboxamides based on hydrogen bonding and a large-sized pyrene ring based on a π-π stacking interaction as universal reader candidates. Each of these compounds was synthesized to bear a thiolated linker for attachment to metal electrodes and examined for their interactions with naturally occurring DNA nucleosides and nucleotides by 1H NMR, ESI-MS, computational calculations, and surface plasmon resonance. RT measurements were carried out in a scanning tunnel microscope. All of these molecules generated electrical signals with DNA nucleotides in tunneling junctions under physiological conditions (phosphate buffered aqueous solution, pH 7.4). Using a support vector machine as a tool for data analysis, we found that these candidates distinguished among naturally occurring DNA nucleotides with the accuracy of pyrene (by π-π stacking interactions) > azole carboxamides (by hydrogen-bonding interactions). In addition, the pyrene reader operated efficiently in a larger tunnel junction. However, the azole carboxamide could read abasic (AP) monophosphate, a product from spontaneous base hydrolysis or an intermediate of base excision repair. Thus, we envision that sequencing DNA using both π-π stacking and hydrogen-bonding-based universal readers in parallel should generate more comprehensive genome sequences than sequencing based on either reader molecule alone.
Collapse
Affiliation(s)
| | | | | | | | - Predrag Krstic
- Institute for Advanced Computational Science, Stony Brook University , Stony Brook, New York 11794-5250, United States
| | | | | | | | | | | |
Collapse
|
2
|
Berdis AJ, McCutcheon D. The use of non-natural nucleotides to probe template-independent DNA synthesis. Chembiochem 2016; 8:1399-408. [PMID: 17607682 DOI: 10.1002/cbic.200700096] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The vast majority of DNA polymerases use the complementary templating strand of DNA to guide each nucleotide incorporation. There are instances, however, in which polymerases can efficiently incorporate nucleotides in the absence of templating information. This process, known as translesion DNA synthesis, can alter the proper genetic code of an organism. To further elucidate the mechanism of template-independent DNA synthesis, we monitored the incorporation of various nucleotides at the "blunt-end" of duplex DNA by the high-fidelity bacteriophage T4 DNA polymerase. Although natural nucleotides are not incorporated at the blunt-end, a limited subset of non-natural indolyl analogues containing extensive pi-electron surface areas are efficiently utilized by the T4 DNA polymerase. These analogues possess high binding affinities that are remarkably similar to those measured during incorporation opposite an abasic site. In contrast, the k(pol) values are significantly lower during blunt-end extension when compared to incorporation opposite an abasic site. These kinetic differences suggest that the single-stranded region of the DNA template plays an important role during polymerization through stacking interactions with downstream bases, interactions with key amino acid residues, or both. In addition, we demonstrate that terminal deoxynucleotide transferase, a template-independent enzyme, can efficiently incorporate many of these non-natural nucleotides. However, that this unique polymerase cannot extend large, bulky non-natural nucleotides suggests that elongation is limited by steric constraints imposed by structural features present within the polymerase. Regardless, the kinetic data obtained from using either DNA polymerase indicate that template-independent synthesis can occur without the contributions of hydrogen-bonding interactions and suggest that pi-electron interactions play an important role in polymerization efficiency when templating information is not present.
Collapse
Affiliation(s)
- Anthony J Berdis
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | | |
Collapse
|
3
|
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
|
4
|
Rutledge LR, Wetmore SD. A computational proposal for the experimentally observed discriminatory behavior of hypoxanthine, a weak universal nucleobase. Phys Chem Chem Phys 2012; 14:2743-53. [PMID: 22270716 DOI: 10.1039/c2cp23600a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A computational model composed of six nucleobases was used to investigate why hypoxanthine does not yield duplexes of equal stability when paired opposite each of the natural DNA nucleobases. The magnitudes of all nearest-neighbor interactions in a DNA helix were calculated, including hydrogen-bonding, intra- and interstrand stacking interactions, as well as 1-3 intrastrand stacking interactions. Although the stacking interactions in DNA relevant arrangements are significant and account for at least one third of the total stabilization energy in our nucleobase complexes, the trends in the magnitude of the stacking interactions cannot explain the relative experimental melting temperatures previously reported in the literature. Furthermore, although the total hydrogen-bonding interactions explain why hypoxanthine preferentially pairs with cytosine, the experimental trend for the remaining nucleobases (A, T, G) is not explained. In fact, the calculated pairing preference of hypoxanthine matches that determined experimentally only when the sum of all types of nearest-neighbor interactions is considered. This finding highlights a strong correlation between the relative magnitude of the total nucleobase-nucleobase interactions and measured melting temperatures for DNA strands containing hypoxanthine despite the potential role of other factors (including hydration, temperature, sugar-phosphate backbone). By considering a large range of sequence combinations, we reveal that the binding preference of hypoxanthine is strongly dependent on the nucleobase sequence, which may explain the varied ability of hypoxanthine to universally bind to the natural bases. As a result, we propose that future work should closely examine the interplay between the dominant nucleobase-nucleobase interactions and the overall strand stability to fully understand how sequence context affects the universal binding properties of modified bases and to aid the design of new molecules with ambiguous pairing properties.
Collapse
Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | | |
Collapse
|
5
|
Lee I, Berdis AJ. Non-natural nucleotides as probes for the mechanism and fidelity of DNA polymerases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1064-80. [PMID: 19733263 DOI: 10.1016/j.bbapap.2009.08.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2009] [Revised: 08/17/2009] [Accepted: 08/19/2009] [Indexed: 11/25/2022]
Abstract
DNA is a remarkable macromolecule that functions primarily as the carrier of the genetic information of organisms ranging from viruses to bacteria to eukaryotes. The ability of DNA polymerases to efficiently and accurately replicate genetic material represents one of the most fundamental yet complex biological processes found in nature. The central dogma of DNA polymerization is that the efficiency and fidelity of this biological process is dependent upon proper hydrogen-bonding interactions between an incoming nucleotide and its templating partner. However, the foundation of this dogma has been recently challenged by the demonstration that DNA polymerases can effectively and, in some cases, selectively incorporate non-natural nucleotides lacking classic hydrogen-bonding capabilities into DNA. In this review, we describe the results of several laboratories that have employed a variety of non-natural nucleotide analogs to decipher the molecular mechanism of DNA polymerization. The use of various non-natural nucleotides has lead to the development of several different models that can explain how efficient DNA synthesis can occur in the absence of hydrogen-bonding interactions. These models include the influence of steric fit and shape complementarity, hydrophobicity and solvation energies, base-stacking capabilities, and negative selection as alternatives to rules invoking simple recognition of hydrogen-bonding patterns. Discussions are also provided regarding how the kinetics of primer extension and exonuclease proofreading activities associated with high-fidelity DNA polymerases are influenced by the absence of hydrogen-bonding functional groups exhibited by non-natural nucleotides.
Collapse
Affiliation(s)
- Irene Lee
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | | |
Collapse
|
6
|
Bergstrom DE. Unnatural nucleosides with unusual base pairing properties. ACTA ACUST UNITED AC 2009; Chapter 1:1.4.1-1.4.32. [PMID: 19488968 DOI: 10.1002/0471142700.nc0104s37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Synthetic modified nucleosides designed to pair in unusual ways with natural nucleobases have many potential applications in biology and biotechnology. This overview lays the foundation for future protocol units on synthesis and application of unnatural bases, with particular emphasis on unnatural base analogs that mimic natural bases in size, shape, and biochemical processing. Topics covered include base pairs with alternative H-bonding schemes, dimensionally expanded base pairs, hydrophobic base pairs, metal-ligated bases, degenerate bases, universal nucleosides, and triplex constituents.
Collapse
|
7
|
Wu W, Bergstrom DE, Jo Davisson V. Chemoenzymatic preparation of nucleoside triphosphates. ACTA ACUST UNITED AC 2008; Chapter 13:Unit 13.2. [PMID: 18428922 DOI: 10.1002/0471142700.nc1302s16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The design and synthesis of alternative nucleoside triphosphate substrates for DNA and RNA polymerases holds continued promise to create biochemical probes and precursors for synthesis of nucleic acid mimics. The azole carboxamide nucleotides are of particular interest, as they display multiple conformations in the context of DNA replication. An efficient chemoenzymatic preparation of azole carboxamide deoxyribo- and ribonucleoside triphosphates is presented. Nucleoside diphosphate is prepared from nucleoside 5'-O-tosylate by displacement with tris(tetra-n-butylammonium) pyrophosphate. Enzymatic phosphorylation of the azole carboxamide deoxyribonucleoside diphosphate to its triphosphate is based on ATP as the phosphate donor and nucleoside diphosphate kinase as the catalyst, coupled with phospho(enol)pyruvate (PEP) and pyruvate kinase as an ATP regeneration system. Enzymatic phosphorylation of the azole carboxamide ribonucleoside diphosphate requires PEP as the phosphate donor and pyruvate kinase as the catalyst. The optimized purification uses boronate affinity gel to yield highly purified nucleoside triphosphate.
Collapse
Affiliation(s)
- Weidong Wu
- Purdue University, West Lafayette, Indiana, USA
| | | | | |
Collapse
|
8
|
Lambertucci C, Schepers G, Cristalli G, Herdewijn P, Aerschot AV. Synthesis and evaluation of hexitol nucleoside congeners as ambiguous nucleosides. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.01.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
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.
Collapse
Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, Canada E4L 1G8
| | | | | |
Collapse
|
10
|
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]
|
11
|
|
12
|
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.
Collapse
|
13
|
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]
|
14
|
Efficient incorporation of 1-(2-deoxy-β-d-ribofuranosyl)-2-oxo-imidazole-4-carboxamide into DNA via a suitable convertible phosphoramidite derivative. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.03.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
15
|
Grassi G, Foti F, Risitano F, Zona D. Efficient synthesis of 3-carboxylate pyrroles using microwave irradiation. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2004.12.102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
16
|
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]
|
17
|
Shionoya M, Tanaka K. Artificial metallo-DNA: a bio-inspired approach to metal array programming. Curr Opin Chem Biol 2004; 8:592-7. [PMID: 15556401 DOI: 10.1016/j.cbpa.2004.09.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The structure of DNA is such that the multi-array of functionalized units with desired numbers and sequences within the DNA is possible. In particular, to replace DNA bases, which are biologically important elements for gene expression, by alternative bases would provide powerful tools for programming molecular arrays in a pre-designed manner. This review focuses on recent chemical approaches to self-assembled metal arrays within DNA with metal-mediated base pairing.
Collapse
Affiliation(s)
- Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | | |
Collapse
|
18
|
Hirao I, Fujiwara T, Kimoto M, Yokoyama S. Unnatural base pairs between 2- and 6-substituted purines and 2-oxo(1H)pyridine for expansion of the genetic alphabet. Bioorg Med Chem Lett 2004; 14:4887-90. [PMID: 15341945 DOI: 10.1016/j.bmcl.2004.07.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2004] [Revised: 07/15/2004] [Accepted: 07/17/2004] [Indexed: 10/26/2022]
Abstract
An unnatural base pair between 2-amino-6-(2-thienyl)purine (denoted by s) and 2-oxo(1H)pyridine (denoted by y) shows high selectivity in transcription and translation. Toward the further development of unnatural base pairs that also have exclusive selectivity in replication, we examined the roles of the 2-amino and 6-thienyl groups of s using base pairs between y and purine-analogs, 6-thienylpurine and 2-amino-6-furanylpurine, as well as s. The results obtained from the thermal stability and DNA polymerase single-nucleotide insertion experiments suggest that the 2-amino group of s contributes toward the shape complementarity of the pairing with y, rather than the hydrogen bonding with the 2-keto group of y. In addition, the bulkiness of positions 2 and 6 of the unnatural purines cooperatively determines the selectivity of the noncanonical pairing with y or the natural pyrimidines in replication. This information is useful not only for the development of unnatural, orthogonal base pairs, but also for understanding the mechanisms of base pair formation in replication.
Collapse
Affiliation(s)
- Ichiro Hirao
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
| | | | | | | |
Collapse
|
19
|
Paul N, Nashine VC, Hoops G, Zhang P, Zhou J, Bergstrom DE, Davisson VJ. DNA Polymerase Template Interactions Probed by Degenerate Isosteric Nucleobase Analogs. ACTA ACUST UNITED AC 2003; 10:815-25. [PMID: 14522052 DOI: 10.1016/j.chembiol.2003.08.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The development of novel artificial nucleobases and detailed X-ray crystal structures for primer/template/DNA polymerase complexes provide opportunities to assess DNA-protein interactions that dictate specificity. Recent results have shown that base pair shape recognition in the context of DNA polymerase must be considered a significant component. The isosteric azole carboxamide nucleobases (compounds 1-5; ) differ only in the number and placement of nitrogen atoms within a common shape and therefore present unique electronic distributions that are shown to dictate the selectivity of template-directed nucleotide incorporation by DNA polymerases. The results demonstrate how nucleoside triphosphate substrate selection by DNA polymerase is a complex phenomenon involving electrostatic interactions in addition to hydrogen bonding and shape recognition. These azole nucleobase analogs offer unique molecular tools for probing nonbonded interactions dictating substrate selection and fidelity of DNA polymerases.
Collapse
Affiliation(s)
- Natasha Paul
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | | | | | | | | | | | | |
Collapse
|
20
|
Ulrich SM, Sallee NA, Shokat KM. Conformational restraint is a critical determinant of unnatural nucleotide recognition by protein kinases. Bioorg Med Chem Lett 2002; 12:3223-7. [PMID: 12372539 DOI: 10.1016/s0960-894x(02)00616-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This report describes the synthesis of N(4)-(benzyl) AICAR triphosphate, a conformationally restrained analogue of N(4)-(benzyl) ribavirin triphosphate. Both of these nucleotides were evaluated as phosphodonors for wild-type p38MAP kinase and T106G p38MAP kinase, a designed mutant with expanded nucleotide specificity. The conformationally restrained nucleotide, N(4)-(benzyl) AICAR triphosphate, is orthogonal to (not accepted as a substrate by) wild-type p38MAP kinase, in contrast to N(4)-(benzyl) ribavirin triphosphate. Furthermore, N(4)-(benzyl) AICAR triphosphate, is accepted as a substrate by T106G p38MAP kinase, in contrast to N(4)-(benzyl) ribavirin triphosphate. We hypothesize that the presence of an internal hydrogen bond in N(4)-(benzyl) AICAR and its absence in N(4)-(benzyl) ribavirin triphosphate is the main determinant for their differing structure-activity relationships.
Collapse
Affiliation(s)
- Scott M Ulrich
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143-0450, USA.
| | | | | |
Collapse
|
21
|
Bergstrom DE. Unnatural Nucleosides with Unusual Base Pairing Properties. ACTA ACUST UNITED AC 2001; Chapter 1:Unit 1.4. [PMID: 18428819 DOI: 10.1002/0471142700.nc0104s05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
22
|
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.
Collapse
Affiliation(s)
- D Loakes
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
| |
Collapse
|
23
|
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.
Collapse
Affiliation(s)
- B P Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | | | | | |
Collapse
|
24
|
Abstract
The duplex-forming activities of oligonucleotides can be photomodulated by incorporation of an azobenzene unit. Upon isomerizing the trans-azobenzene to the cis form by irradiation with UV light, the T(m) value of the duplex (with the complementary DNA) is lowered so that the duplex is dissociated. The duplex is formed again when the cis-azobenzene is converted to the trans-azobenzene by irradiation with visible light. The photoregulation is successful irrespective of the position of the azobenzene unit in the oligonucleotides. The trans-azobenzene in the oligonucleotides intercalates between two DNA base pairs in the duplexes and stabilizes them because of a favorable enthalpy change. The nonplanar structure of a cis-azobenzene is unfavorable for such an interaction. These photoresponsive oligonucleotides are promising candidates for the regulation of various bioreactions.
Collapse
Affiliation(s)
- H Asanuma
- Research Center for Advanced Science and Technology The University of Tokyo Meguro-ku, Tokyo 153-8904 Japan
| | | | | | | |
Collapse
|
25
|
|
26
|
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.
Collapse
Affiliation(s)
- D A Klewer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | | | | | | | | | | |
Collapse
|
27
|
Berger M, Wu Y, Ogawa AK, McMinn DL, Schultz PG, Romesberg FE. Universal bases for hybridization, replication and chain termination. Nucleic Acids Res 2000; 28:2911-4. [PMID: 10908353 PMCID: PMC102677 DOI: 10.1093/nar/28.15.2911] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2000] [Revised: 06/13/2000] [Accepted: 06/13/2000] [Indexed: 11/13/2022] Open
Abstract
Several unnatural, predominantly hydrophobic nucleobases that pack efficiently in duplex DNA without hydrogen bonding functionalities are reported to circumvent the hydrogen bonding-based specificity, both during oligonucleotide hybridization and enzymatic DNA synthesis. The reported nucleoside analogs are efficient 'universal bases' for hybridization, template directed DNA synthesis and chain termination. Moreover, several of the universal bases function in their biological role, hybridization or replication, with an efficiency not significantly reduced relative to their natural counterparts.
Collapse
Affiliation(s)
- M Berger
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | | | | | | | | |
Collapse
|
28
|
Asanuma H, Ito T, Yoshida T, Liang X, Komiyama M. Photoregulation der Bildung und Dissoziation eines DNA-Duplexes durchcis-trans-Isomerisierung einer Azobenzoleinheit. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19990816)111:16<2547::aid-ange2547>3.0.co;2-t] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
29
|
Day JP, Bergstrom D, Hammer RP, Barany F. Nucleotide analogs facilitate base conversion with 3' mismatch primers. Nucleic Acids Res 1999; 27:1810-8. [PMID: 10101188 PMCID: PMC148388 DOI: 10.1093/nar/27.8.1810] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We compared the efficiency of PCR amplification using primers containing either a nucleotide analog or a mismatch at the 3' base. To determine the distribution of bases inserted opposite eight different analogs, 3' analog primers were used to amplify four different templates. The products from the reactions with the highest amplification efficiency were sequenced. Analogs allowing efficient amplification followed by insertion of a new base at that position are herein termed 'convertides'. The three convertides with the highest amplification efficiency were used to convert sequences containing C, T, G and A bases into products containing the respective three remaining bases. Nine templates were used to generate conversion products, as well as non-conversion control products with no base change. We compared the ability of natural bases to convert specific sites with and without a preconversion step using nucleotide analog primers. Conversion products were identified by a ligation detection reaction using primers specific for the converted sequence. We found that conversions resulting in transitions were easier to accomplish than transversions and that sequence context influences conversion. Specifically, primer slippage appears to be an important mechanism for producing artifacts via polymerase extension of a 3' base or analog transiently base paired to neighboring bases of the template. Nucleotide analogs could often reduce conversion artifacts and increase the yield of the expected product. While new analogs are needed to reliably achieve transversions, the current set have proven effective for creating transition conversions.
Collapse
Affiliation(s)
- J P Day
- Department of Microbiology, Box 62, Hearst Microbiology Research Center, Strang Cancer Prevention Center, Joan and Sanford I. Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | | | | | | |
Collapse
|
30
|
Orson FM, Klysik J, Bergstrom DE, Ward B, Glass GA, Hua P, Kinsey BM. Triple helix formation: binding avidity of acridine-conjugated AG motif third strands containing natural, modified and surrogate bases opposed to pyrimidine interruptions in a polypurine target. Nucleic Acids Res 1999; 27:810-6. [PMID: 9889277 PMCID: PMC148251 DOI: 10.1093/nar/27.3.810] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A critical issue for the general application of triple-helix-forming oligonucleotides (TFOs) as modulators of gene expression is the dramatically reduced binding of short TFOs to targets that contain one or two pyrimidines within an otherwise homopurine sequence. Such targets are often found in gene regulatory regions, which represent desirable sites for triple helix formation. Using intercalator-conjugated AG motif TFOs, we compared the efficacy and base selectivity of 13 different bases or base surrogates in opposition to pyrimidines and purines substituted into selected positions within a paradigm 15-base polypurine target sequence. We found that substitutions closer to the intercalator end of the TFO (positions 4-6) had a more deleterious effect on the dissociation constant (K d) than those farther away (position 11). Opposite T residues at position 11, 3-nitropyrrole or cytosine in the TFO provided adequate binding avidity for useful triplex formation (K ds of 55 and 110 nM, respectively). However, 3-nitropyrrole was more base selective than cytosine, binding to T >/=4 times better than to A, G or C. None of the TFOs tested showed avid binding when C residues were in position 11, although the 3-nitropyrrole-containing TFO bound with a K d of 200 nM, significantly better than the other designs. Molecular modeling showed that the 3-nitropyrrole.T:A triad is isomorphous with the A.A:T triad, and suggests novel parameters for evaluating new base triad designs.
Collapse
Affiliation(s)
- F M Orson
- The Veterans Affairs Medical Center, Department of Internal Medicine, Baylor College of Medicine, Building 109, Room 226, VAMC, 2002 Holcombe, Houston, TX 77030, USA.
| | | | | | | | | | | | | |
Collapse
|