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Cornelis S, Tytgat O, Fauvart M, Gansemans Y, Vander Plaetsen AS, Wiederkehr RS, Deforce D, Van Nieuwerburgh F, Stakenborg T. Silicon µPCR Chip for Forensic STR Profiling with Hybeacon Probe Melting Curves. Sci Rep 2019; 9:7341. [PMID: 31089203 PMCID: PMC6517373 DOI: 10.1038/s41598-019-43946-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/01/2019] [Indexed: 11/09/2022] Open
Abstract
The demand to perform forensic DNA profiling outside of centralized laboratories and on the crime scene is increasing. Several criminal investigations would benefit tremendously from having DNA based information available in the first hours rather than days or weeks. However, due to the complexity and time-consuming nature of standard DNA fingerprinting methods, rapid and automated analyses are hard to achieve. We here demonstrate the implementation of an alternative DNA fingerprinting method in a single microchip. By combining PCR amplification and HyBeacon melting assays in a silicon Lab-on-a-chip (LoC), a significant step towards rapid on-site DNA fingerprinting is taken. The small form factor of a LoC reduces reagent consumption and increases portability. Additional miniaturization is achieved through an integrated heating element covering 24 parallel micro-reactors with a reaction volume of 0.14 µl each. The high level of parallelization allows the simultaneous analysis of 4 short tandem repeat (STR) loci and the amelogenin gender marker commonly included in forensic DNA analysis. A reference and crime scene sample can be analyzed simultaneously for direct comparison. Importantly, by using industry-standard semiconductor manufacturing processes, mass manufacturability can be guaranteed. Following assay design and optimization, complete 5-loci profiles could be robustly generated on-chip that are on par with those obtained using conventional benchtop real-time PCR thermal cyclers. Together, our results are an important step towards the development of commercial, mass-produced, portable devices for on-site testing in forensic DNA analysis.
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Affiliation(s)
- Senne Cornelis
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Olivier Tytgat
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Maarten Fauvart
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
| | | | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium.
| | | | - Tim Stakenborg
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
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2
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Vollmer S, Richert C. DNA Triplexes That Bind Several Cofactor Molecules. Chemistry 2015; 21:18613-22. [PMID: 26561335 DOI: 10.1002/chem.201503220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Indexed: 12/29/2022]
Abstract
Cofactors are critical for energy-consuming processes in the cell. Harnessing such processes for practical applications requires control over the concentration of cofactors. We have recently shown that DNA triplex motifs with a designed binding site can be used to capture and release nucleotides with low micromolar dissociation constants. In order to increase the storage capacity of such triplex motifs, we have explored the limits of ligand binding through designed cavities in the oligopurine tract. Oligonucleotides with up to six non-nucleotide bridges between purines were synthesized and their ability to bind ATP, cAMP or FAD was measured. Triplex motifs with several single-nucleotide binding sites were found to bind purines more tightly than triplexes with one large binding site. The optimized triplex consists of 59 residues and four C3-bridges. It can bind up to four equivalents of ligand with apparent Kd values of 52 µM for ATP, 9 µM for FAD, and 2 µM for cAMP. An immobilized version fuels bioluminescence via release of ATP at body temperature. These results show that motifs for high-density capture, storage and release of energy-rich biomolecules can be constructed from synthetic DNA.
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Affiliation(s)
- Sven Vollmer
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-685-64321
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-685-64321.
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3
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Kumari R, Banerjee SS, Bhowmick AK, Das P. DNA-melamine hybrid molecules: from self-assembly to nanostructures. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015. [PMID: 26199847 PMCID: PMC4505151 DOI: 10.3762/bjnano.6.148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Single-stranded DNA-melamine hybrid molecular building blocks were synthesized using a phosphoramidation cross-coupling reaction with a zero linker approach. The self-assembly of the DNA-organic hybrid molecules was achieved by DNA hybridization. Following self-assembly, two distinct types of nanostructures in the form of linear chains and network arrays were observed. The morphology of the self-assembled nanostructures was found to depend on the number of DNA strands that were attached to a single melamine molecule.
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Affiliation(s)
- Rina Kumari
- Department of Chemistry, Indian Institute of Technology Patna, Patna 800013, India
| | - Shib Shankar Banerjee
- Department of Materials Science and Engineering, Indian Institute of Technology Patna, Patna 800013, India
| | - Anil K Bhowmick
- Rubber Technology Centre, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Patna 800013, India
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4
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Gerlach C, Claasen B, Richert C. High-fidelity recognition of RNA: solution structure of a DNA:RNA hybrid duplex with a molecular cap. Chembiochem 2014; 15:2584-9. [PMID: 25318665 DOI: 10.1002/cbic.201402409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Indexed: 11/08/2022]
Abstract
Binding RNA targets, such as microRNAs, with high fidelity is challenging, particularly when the nucleobases to be bound are located at the terminus of the duplex between probe and target. Recently, a peptidyl chain terminating in a quinolone, called ogOA, was shown to act as a cap that enhances affinity and fidelity for RNAs, stabilizing duplexes with Watson-Crick pairing at their termini. Here we report the three-dimensional structure of an intramolecular complex between a DNA strand featuring the ogOA cap and an RNA segment, solved by NMR and restrained torsion angle molecular dynamics. The quinolone stacks on the terminal base pair of the hybrid duplex, positioned by the peptidyl chain, whose prolinol residue induces a sharp bend between the 5' terminus of the DNA chain and the glycine linked to the oxolinic acid residue. The structure explains why canonical base pairing is favored over hard-to-suppress mismatched base combinations, such as T:G and A:A, and helps to design improved high-fidelity probes for RNA.
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Affiliation(s)
- Claudia Gerlach
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
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5
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Zhang L, Zhu H, Sajimon MC, Stütz JAR, Siegmund K, Richert C, Shafirovich V, Lewis FD. Stabilization of DNA Hairpins by Stilbene Capping of the Terminal Base Pair. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200600196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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6
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Egetenmeyer S, Richert C. Synthesis of oligodeoxynucleotides with 5'-caps binding RNA targets. ACTA ACUST UNITED AC 2013; Chapter 4:Unit4.53. [PMID: 23255203 DOI: 10.1002/0471142700.nc0453s51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protocols for the synthesis of oligodeoxynucleotides with a short peptidyl substituent linked to the 5'-O-terminus through a phosphodiester bond are presented. The example given is a peptidyl cap consisting of the residues of L-prolinol, glycine, and the acyl residue of oxolinic acid. DNA probes with this cap, also known as ogOA cap, give melting point increases for duplexes with RNA targets and improve mismatch discrimination at the terminus. The cap is either introduced in one step, using a newly developed phosphoramidite reagent, or assembled on the DNA chain. The step-wise assembly of the peptidyl chain is advantageous for combinatorial studies aimed at the optimization of a cap structure. The block coupling method, introducing the preassembled cap in one step, is attractive for routine use of a cap already optimized for a given application. Cap-bearing probes can increase fidelity of hybridization in a genomic context. They can be synthesized by automated DNA synthesis.
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Affiliation(s)
- Simone Egetenmeyer
- Institute for Organic Chemistry, University of Stuttgart, Stuttgart, Germany
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7
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Lewis FD. Distance-Dependent Electronic Interactions Across DNA Base Pairs: Charge Transport, Exciton Coupling, and Energy Transfer. Isr J Chem 2013. [DOI: 10.1002/ijch.201300035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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8
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Carmieli R, Smeigh AL, Mickley Conron SM, Thazhathveetil AK, Fuki M, Kobori Y, Lewis FD, Wasielewski MR. Structure and Dynamics of Photogenerated Triplet Radical Ion Pairs in DNA Hairpin Conjugates with Anthraquinone End Caps. J Am Chem Soc 2012; 134:11251-60. [DOI: 10.1021/ja303721j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raanan Carmieli
- Department of Chemistry and Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Amanda L. Smeigh
- Department of Chemistry and Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Sarah M. Mickley Conron
- Department of Chemistry and Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Arun K. Thazhathveetil
- Department of Chemistry and Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Masaaki Fuki
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya Surugaku, Shizuoka 422-8529,
Japan
| | - Yasuhiro Kobori
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya Surugaku, Shizuoka 422-8529,
Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho
Kawaguchi, Saitama 332-0012, Japan
| | - Frederick D. Lewis
- Department of Chemistry and Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
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9
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Sargsyan G, Balaz M. Porphyrin-DNA conjugates: porphyrin induced adenine-guanine homoduplex stabilization and interduplex assemblies. Org Biomol Chem 2012; 10:5533-40. [PMID: 22692698 DOI: 10.1039/c2ob25710f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
DNA has found widespread uses as a nanosized scaffold for assembly of patterned multichomophoric nanostructures. Herein we report the synthesis, self-assembly, stability, and spectroscopic studies of short alternating non-self-complementary DNA sequences 5'-(dGdA)(4) and 5'-(dAdG)(4) with non-charged tetraarylporphyrins covalently linked to the 5' position of deoxyadenosine or deoxyguanosine via a phosphate or amide linker. The linker, the metal in the porphyrin coordination center, and the neighboring nucleobase have very distinct effects on the duplex formation of porphyrin-deoxyguanosine-deoxyadenosine oligodeoxynucleotides. At ionic strength between 5 mM and 40 mM, free base trispyridylphenylporphyrin appended to the 5' termini of 5'-(dAdG)(4) oligonucleotide via short non-polar amide linker served as a hydrophobic molecular cap inducing deoxyadenosine-deoxyguanosine antiparallel homoduplex. At ionic strength of ≥60 mM, the free base porphyrin functioned as a molecular 'glue' and induced the formation of porphyrin-DNA inter-homoduplex assemblies with characteristic tetrasignate CD Cotton effects in the porphyrin Soret band region. When the porphyrin cap was covalently attached to 5' position of deoxyguanosine or deoxyadenosine via charged phosphate linker, no significant deoxyadenosine-deoxyguanosine hybridization was observed even at elevated ionic strengths.
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Affiliation(s)
- Gevorg Sargsyan
- Department of Chemistry, University of Wyoming, 1000 E. University ave., Laramie, WY 82071, USA
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10
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Egetenmeyer S, Richert C. A 5'-cap for DNA probes binding RNA target strands. Chemistry 2011; 17:11813-27. [PMID: 21932288 DOI: 10.1002/chem.201101828] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Indexed: 11/09/2022]
Abstract
Detecting short RNA strands with high fidelity at any of the bases of their sequence, including the termini, can be challenging, since fraying, wobbling, and refolding all compete with canonical base pairing. We performed a search for 5'-substituents of oligodeoxynucleotides that increase base pairing fidelity at the terminus of duplexes with RNA target strands. From a total of over 70 caps, differing in stacking moiety and linker, a phosphodiester-linked sequence of the residues of L-prolinol, glycine, and oxolinic acid, dubbed ogOA, was identified as a 5'-cap that stabilizes any of the four canonical base pairs, with ΔT(m) values of up to +13.1 °C for an octamer. At the same time, the cap increases discrimination against any of the 12 possible terminal mismatches, including mismatches that are more stable than their perfectly matched counterparts in the control duplex, such as A:A. A probe with the cap also showed increased selectivity in the detection of two closely related microRNAs, let7c and let7a, with a ΔT(m) value of 9.2 °C. Melting curves also yielded thermodynamic data that shed light on the uniformity of molecular recognition in the sequence space of DNA:DNA and DNA:RNA duplexes. Hybridization probes with fidelity-enhancing caps should find applications in the individual and parallel detection of biologically active RNA species.
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Affiliation(s)
- Simone Egetenmeyer
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart, Germany
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11
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Lucas R, Gómez-Pinto I, Aviñó A, Reina JJ, Eritja R, González C, Morales JC. Highly polar carbohydrates stack onto DNA duplexes via CH/π interactions. J Am Chem Soc 2011; 133:1909-16. [PMID: 21244028 DOI: 10.1021/ja108962j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbohydrate-nucleic acid contacts are known to be a fundamental part of some drug-DNA recognition processes. Most of these interactions occur through the minor groove of DNA, such as in the calicheamicin or anthracycline families, or through both minor and major groove binders such as in the pluramycins. Here, we demonstrate that carbohydrate-DNA interactions are also possible through sugar capping of a DNA double helix. Highly polar mono- and disaccharides are capable of CH/π stacking onto the terminal DNA base pair of a duplex as shown by NMR spectroscopy. The energetics of the carbohydrate-DNA interactions vary depending on the stereochemistry, polarity, and contact surface of the sugar involved and also on the terminal base pair. These results reveal carbohydrate-DNA base stacking as a potential recognition motif to be used in drug design, supramolecular chemistry, or biobased nanomaterials.
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Affiliation(s)
- Ricardo Lucas
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, Americo Vespucio, 49, 41092 Sevilla, Spain
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12
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Ng PS, Laing BM, Balasundarum G, Pingle M, Friedman A, Bergstrom DE. Synthesis and evaluation of new spacers for use as dsDNA end-caps. Bioconjug Chem 2011; 21:1545-53. [PMID: 20715857 DOI: 10.1021/bc100202y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of aliphatic and aromatic spacer molecules designed to cap the ends of DNA duplexes have been synthesized. The spacers were converted into dimethoxytrityl-protected phosphoramidites as synthons for oligonucleotides synthesis. The effect of the spacers on the stability of short DNA duplexes was assessed by melting temperature studies. End-caps containing amide groups were found to be less stabilizing than the hexaethylene glycol spacer. End-caps containing either a terthiophene or a naphthalene tetracarboxylic acid diimide were found to be significantly more stabilizing. The former showed a preference for stacking above an A*T base pair. Spacers containing only methylene (-CH(2)-) and amide (-CONH-) groups interact weakly with DNA and consequently may be optimal for applications that require minimal influence on DNA structure but require a way to hold the ends of double-stranded DNA together.
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Affiliation(s)
- Pei-Sze Ng
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Biological Sciences, and Bindley Bioscience Center, Purdue University, 1205 W State St., West Lafayette, IN 47907, USA
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13
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Daublain P, Thazhathveetil AK, Shafirovich V, Wang Q, Trifonov A, Fiebig T, Lewis FD. Dynamics and Efficiency of Electron Injection and Transport in DNA Using Pyrenecarboxamide as an Electron Donor and 5-Bromouracil as an Electron Acceptor. J Phys Chem B 2010; 114:14265-72. [DOI: 10.1021/jp9107393] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Pierre Daublain
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Arun K. Thazhathveetil
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Vladimir Shafirovich
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Qiang Wang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Anton Trifonov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Torsten Fiebig
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Frederick D. Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
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14
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Abstract
Binding target strands with single base selectivity at a terminal position is difficult with natural DNA or RNA hybridization probes. Nature uses a degenerate genetic code that is based on RNA:RNA codon:anticodon duplexes tolerating wobble base pairs at the terminus. The importance of short RNA strands in regulatory processes in the cell make it desirable to develop receptor-like approaches for high fidelity binding, even at the very 3'-terminus of a probe. Here, we report the three-dimensional structure of a DNA duplex with a 3'-terminal 2'-anthraquinoylamido-2'-deoxyuridine (Uaq) residue that was solved by NMR and restrained molecular dynamics. The Uaq residue binds the 5'-terminus of the target strand through a combination of pi-stacking, hydrogen bonding, and interactions in the minor groove. The acylated aminonucleoside is the best molecular cap for 3'-termini reported to date. The Uaq motif assists binding of DNA strands, but is particularly effective in enhancing the affinity for RNA target strands, with a DeltaT(m) in the UV melting point of up to +18.2 degrees C per residue. Increased base pairing selectivity is induced for all sequence motifs tested, even in cases where unmodified duplexes show no preference for the canonical base pair at all. A single mismatched nucleobase facing the 3'-terminus gives DeltaDeltaT(m) values as large as -23.9 degrees C (RNA) or -29.5 degrees C (DNA). The 5'-phosphoramidite of the Uaq cap reported here allows for routine incorporation during automated syntheses.
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Affiliation(s)
- Amritraj Patra
- Institute for Organic Chemistry, University of Karlsruhe (TH), 76131 Karlsruhe, Germany
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15
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Lewis FD, Thazhathveetil AK, Zeidan TA, Vura-Weis J, Wasielewski MR. Dynamics of Ultrafast Singlet and Triplet Charge Transfer in Anthraquinone−DNA Conjugates. J Am Chem Soc 2009; 132:444-5. [DOI: 10.1021/ja908470d] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Frederick D. Lewis
- Department of Chemistry and Argonne−Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113
| | - Arun K. Thazhathveetil
- Department of Chemistry and Argonne−Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113
| | - Tarek A. Zeidan
- Department of Chemistry and Argonne−Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113
| | - Josh Vura-Weis
- Department of Chemistry and Argonne−Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113
| | - Michael R. Wasielewski
- Department of Chemistry and Argonne−Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113
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16
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Siegmund K, Daublain P, Wang Q, Trifonov A, Fiebig T, Lewis FD. Structure and Photoinduced Electron Transfer in DNA Hairpin Conjugates Possessing a Tethered 5′-Pyrenecarboxamide. J Phys Chem B 2009; 113:16276-84. [DOI: 10.1021/jp907323d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Karsten Siegmund
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Pierre Daublain
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Qiang Wang
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Anton Trifonov
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Torsten Fiebig
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Frederick D. Lewis
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
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17
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Printz M, Richert C. Pyrenylmethyldeoxyadenosine: A 3′-Cap for Universal DNA Hybridization Probes. Chemistry 2009; 15:3390-402. [DOI: 10.1002/chem.200801587] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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18
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Gale N, French DJ, Howard RL, McDowell DG, Debenham PG, Brown T. Rapid typing of STRs in the human genome by HyBeacon melting. Org Biomol Chem 2008; 6:4553-9. [PMID: 19039363 DOI: 10.1039/b813431f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new method based on DNA melting has been developed for the rapid analysis of STRs in the human genome. The system is based on homogeneous PCR followed by fluorescence melting analysis and utilises a HyBeacon probe combined with a PCR primer-blocker oligonucleotide. The use of blockers of different length permits identification of the full range of common D16S539 repeats enabling detection of 99.8% of known alleles. The interrogation of STRs can be carried out on standard genetic analysis platforms and could be applied to other loci to form the basis of a bespoke high-throughput system for use in forensic analysis, particularly as fluorescent genetic analysis platforms are now available for high-resolution melting. This methodology may be suitable for rapid forensic DNA analysis at the point-of-arrest or in a custody suite where it is important to identify an individual from a small group of suspects/detainees.
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Affiliation(s)
- Nittaya Gale
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
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19
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Abstract
The high fidelity detection of multiple DNA sequences in multiplex assays calls for duplexes whose stability is independent of sequence (isostable DNA), forming under universally stringent conditions. Nature did not evolve DNA to form isostable duplexes. Here we report how probe strands can be modified so that an all-A/T target strand is bound with the same or slightly higher affinity than the corresponding all-G/C strand with the same sequence of purines and pyrimidines. We refer to these probes that feature covalently attached ligands as "decorated nucleic acids". Caps, intercalators, and locks were used to stabilize A/T duplexes, and N4-ethylcytosine residues were employed to tune down the stability of G/C duplexes without significantly affecting base pairing selectivity. Near-isostability was demonstrated in solution and on microarrays of high and low density. Further, it is shown that hybridization results involving decorated probes on microarrays can be predicted on the basis of thermodynamic data for duplex formation in solution. Predictable formation of isostable DNA not only benefits microarrays for gene expression analysis and genotyping, but may also improve the sequence-specificity of other applications that rely on the massively parallel formation of Watson-Crick duplexes.
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Affiliation(s)
- Carolin Ahlborn
- Institut für Organische Chemie, Universität Karlsruhe (TH), Karlsruhe, Germany
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20
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Jayawickramarajah J, Tagore D, Tsou L, Hamilton A. Allosteric Control of Self-Assembly: Modulating the Formation of Guanine Quadruplexes through Orthogonal Aromatic Interactions. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701883] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Jayawickramarajah J, Tagore DM, Tsou LK, Hamilton AD. Allosteric Control of Self-Assembly: Modulating the Formation of Guanine Quadruplexes through Orthogonal Aromatic Interactions. Angew Chem Int Ed Engl 2007; 46:7583-6. [PMID: 17823899 DOI: 10.1002/anie.200701883] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Rojas Stütz JA, Richert C. Tuning the reaction site for enzyme-free primer-extension reactions through small molecule substituents. Chemistry 2007; 12:2472-81. [PMID: 16402399 DOI: 10.1002/chem.200501008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The replication of genetic information relies on the template-directed extension of DNA primers catalyzed by polymerases. The active sites of polymerases accept four different substrates and ensure fidelity and processivity for each of them. Because of the pivotal role of catalyzed primer extension for life, it is important to better understand this reaction on a molecular level. Here we present results from primer-extension reactions performed with chemical systems that show high reactivity in the absence of polymerases. Small molecular caps linked to the 5'-terminus of templates are shown to enhance the rate and selectivity of primer extension driven by 2-methylimidazolides as activated monomers for any of the four different templating bases (A, C, G, and T). The most consistent effect is provided by a stilbene carboxamide residue, rather than larger aromatic or aliphatic substituents. Up to 20-fold rate enhancements were achieved for the reactions at the terminus of the template. The preference for a medium size cap can be explained by competing interactions with both the oligonucleotides and the incoming deoxynucleotide. The data also show that there is no particularly intractable problem in combining promiscuity with fidelity. Exploratory experiments involving a longer template and a downstream-binding strand with a 5'-cap show up to 38-fold rate acceleration over the same reaction templated by a single overhanging nucleotide.
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Affiliation(s)
- Jan A Rojas Stütz
- Institut für Organische Chemie, Universität Karlsruhe TH, 76131 Karlsruhe, Germany
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23
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Balaz M, Li BC, Jockusch S, Ellestad GA, Berova N. Tetraarylporphyrin as a selective molecular cap for non-Watson-Crick guanine-adenine base-pair sequences. Angew Chem Int Ed Engl 2007; 45:3530-3. [PMID: 16625664 DOI: 10.1002/anie.200504431] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Milan Balaz
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA.
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24
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Printz M, Richert C. Optimizing the stacking moiety and linker of 2'-acylamido caps of DNA duplexes with 3'-terminal adenine residues. ACTA ACUST UNITED AC 2007; 9:306-20. [PMID: 17266381 DOI: 10.1021/cc060142a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reported here is the synthesis of oligodeoxynucleotides with a 3'-terminal 2'-acylamido-2'-deoxyadenosine residue. The route to these oligonucleotides employs an N,O-Alloc-protected 5'-phosphoramidite of 2'-amino-2'-deoxyadenosine that was prepared in 11 steps from arabinoadenosine. Small combinatorial libraries of oligonucleotides were generated via acylation with a mixture of linker amino acids and subsequent acylation of their amino groups. Mass spectrometrically monitored nuclease selection assays led to oligonucleotides whose 2'-substituent increases the thermal stability of the DNA duplexes. A linker with three methylene groups between a perylene stacking moiety and the amido group gives a UV-melting point increase of up to 27.9 degrees C for the DNA sequence (TGCGCA*)2, where A* denotes the 2'-acylamidoadenosine residue. The same acylamido group improves mismatch discrimination at the terminal position with a melting point depression of >or=7 degrees C for any of the three mismatches in the target sequence of the octamer 5'-AGGTTGAA-3'. These results demonstrate how even a very weakly base-pairing nucleotide at the 3'-terminus of a DNA probe strand can be enforced to engage in strong and highly sequence-selective base-pairing interactions.
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Affiliation(s)
- Michael Printz
- Institute for Organic Chemistry, University of Karlsruhe (TH), 76131 Karlsruhe, Germany
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25
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Zhang L, Long H, Schatz GC, Lewis FD. Synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having stilbenedicarboxamide linkers. Org Biomol Chem 2006; 5:450-6. [PMID: 17252127 DOI: 10.1039/b614572h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having A-tract base pair domains connected by rod-like stilbenedicarboxamide linkers are reported. The nicked dumbbells have one to eight dA-dT base pairs and are missing a sugar-phosphate bond either between the linker and a thymine nucleoside residue or between two thymine residues. Chemical ligation of all of the nicked dumbbells with cyanogen bromide affords the dumbbell conjugates in good yield, providing the smallest mini-dumbbells prepared to date. The dumbbells have exceptionally high thermal stability, whereas the nicked dumbbells are only marginally more stable than the hairpin structures on either side of the nick. The structures of the nicked dumbbells and dumbbells have been investigated using a combination of circular dichroism spectroscopy and molecular modeling. The base pair domains are found to adopt normal B'-DNA geometry and thus provide a helical ruler for studies of the distance and angular dependence of electronic interactions between the chromophore linkers.
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Affiliation(s)
- Ligang Zhang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA
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26
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Balaz M, Li BC, Jockusch S, Ellestad GA, Berova N. Tetraarylporphyrin as a Selective Molecular Cap for Non-Watson–Crick Guanine–Adenine Base-Pair Sequences. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504431] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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27
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Jähnchen J, Purwanto MGM, Weisz K. NMR studies on self-complementary oligonucleotides conjugated with methylene blue. Biopolymers 2006; 79:335-43. [PMID: 16130129 DOI: 10.1002/bip.20363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A carboxyl-functionalized methylene blue (MB) derivative was synthesized and covalently coupled to three CG-rich self-complementary 2'-deoxyoligonucleotides at their 5'-end. Thermodynamic and structural details about the interactions between the dye and oligonucleotide duplexes were investigated employing ultraviolet (UV) melting and (1)H nuclear magnetic resonance (NMR) experiments. In contrast to previous findings on MB binding, no specific intercalation or binding in the minor or major groove of the double helix was found in a 100 mM NaCl buffer. Rather, proton chemical shift changes in the conjugates provide ample evidence for weak dye-DNA interactions largely through external MB stacking on the terminal base pairs.
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Affiliation(s)
- Judith Jähnchen
- Institut für Chemie und Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Soldmannstrasse 16, D-17489 Greifswald, Germany
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28
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Lewis FD, Zhang L, Liu X, Zuo X, Tiede DM, Long H, Schatz GC. DNA as Helical Ruler: Exciton-Coupled Circular Dichroism in DNA Conjugates. J Am Chem Soc 2005; 127:14445-53. [PMID: 16218640 DOI: 10.1021/ja0539387] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure and properties of oligonucleotide conjugates possessing stilbenedicarboxamide chromophores at both ends of a poly(dA):poly(dT) base-pair domain of variable length have been investigated using a combination of spectroscopic and computational methods. These conjugates form capped hairpin structures in which one stilbene serves as a hairpin linker and the other as a hydrophobic end-cap. The capping stilbene stabilizes the hairpin structures by ca. 2 kcal/mol, making possible the formation of a stable folded structure containing a single A:T base pair. Exciton coupling between the stilbene chromophores has little effect on the absorption bands of capped hairpins. However, exciton-coupled circular dichroism (EC-CD) can be observed for capped hairpins possessing as many as 11 base pairs. Both the sign and intensity of the EC-CD spectrum are sensitive to the number of base pairs separating the stilbene chromophores, as a consequence of the distance and angular dependence of exciton coupling. Calculated spectra obtained using a static vector model based on canonical B-DNA are in good agreement with the experimental spectra. Molecular dynamics simulations show that conformational fluctuations of the capped hairpins result in large deviations of the averaged spectra in both the positive and negative directions. These results demonstrate for the first time the ability of B-DNA to serve as a helical ruler for the study of electronic interactions between aligned chromophores. Furthermore, they provide important tests for atomistic theoretical models of DNA.
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Affiliation(s)
- Frederick D Lewis
- Department of Chemistry, Northwestern University, Evanston, IL 60208-3113, USA.
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Siegmund K, Maheshwary S, Narayanan S, Connors W, Riedrich M, Printz M, Richert C. Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. Nucleic Acids Res 2005; 33:4838-48. [PMID: 16126848 PMCID: PMC1192833 DOI: 10.1093/nar/gki795] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Quinolones are antibacterial drugs that are thought to bind preferentially to disturbed regions of DNA. They do not fall into the classical categories of intercalators, groove binders or electrostatic binders to the backbone. We solved the 3D structure of the DNA duplex (ACGCGU-NA)2, where NA denotes a nalidixic acid residue covalently linked to the 2′-position of 2′-amino-2′-deoxyuridine, by NMR and restrained torsion angle molecular dynamics (MD). In the complex, the quinolones stack on G:C base pairs of the core tetramer and disrupt the terminal A:U base pair. The displaced dA residues can stack on the quinolones, while the uracil rings bind in the minor groove. The duplex-bridging interactions of the drugs and the contacts of the displaced nucleotides explain the high UV-melting temperature for d(ACGCGU-NA)2 of up to 53°C. Further, non-covalently linked complexes between quinolones and DNA of the sequence ACGCGT can be generated via MD using constraints obtained for d(ACGCGU-NA)2. This is demonstrated for unconjugated nalidixic acid and its 6-fluoro derivative. The well-ordered and tightly packed structures thus obtained are compatible with a published model for the quinolone–DNA complex in the active site of gyrases.
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Affiliation(s)
- Karsten Siegmund
- Institute for Organic Chemistry, University of Karlsruhe (TH)D-76131 Karlsruhe, Germany
| | - Shruti Maheshwary
- Department of Chemistry, University of ConstanceD-78457-Konstanz, Germany
| | - Sukunath Narayanan
- Institute for Organic Chemistry, University of Karlsruhe (TH)D-76131 Karlsruhe, Germany
| | - William Connors
- Department of Chemistry, University of ConstanceD-78457-Konstanz, Germany
| | - Matthias Riedrich
- Department of Chemistry, University of ConstanceD-78457-Konstanz, Germany
| | - Michael Printz
- Institute for Organic Chemistry, University of Karlsruhe (TH)D-76131 Karlsruhe, Germany
| | - Clemens Richert
- Institute for Organic Chemistry, University of Karlsruhe (TH)D-76131 Karlsruhe, Germany
- Department of Chemistry, University of ConstanceD-78457-Konstanz, Germany
- To whom correspondence should be addressed. Tel: +49 721 608 2091; Fax: +49 721 608 4825;
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30
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Zhao Y, Truhlar DG. How well can new-generation density functional methods describe stacking interactions in biological systems? Phys Chem Chem Phys 2005; 7:2701-5. [PMID: 16189582 DOI: 10.1039/b507036h] [Citation(s) in RCA: 226] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson-Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA
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31
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Koepler O, Mazzini S, Bellucci MC, Mondelli R, Baro A, Laschat S, Hotfilder M, Viseur C, Frey W. Synthesis and DNA binding properties of novel benzo[b]isoquino[2,3-h]-naphthyridines. Org Biomol Chem 2005; 3:2848-58. [PMID: 16032363 DOI: 10.1039/b503281d] [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] [Indexed: 11/21/2022]
Abstract
Several benzo[b]isoquino[2,3-h]-naphthyridines have been prepared via formal hetero-Diels Alder reaction of N-aryl imines as a key step. These compounds have different side chains at C-11, and a cis or trans configuration at the C-8a,C-14a ring junction. Binding constants for the interaction with oligonucleotides and polynucleotides were determined by UV absorption and melting experiments. NMR experiments (NOE) revealed that the cis isomers, showing a slightly folded structure, preferentially bind to the minor groove of AT-rich oligomers. In contrast, the trans isomers prefer the CG-rich sequences, leading to cap-complexes with the isoquinoline moiety stacked at the top of the double helix, in agreement with the flatter shape, and with a preference for the 3'-terminals, as found for camptothecins. Models of the complexes were built up by molecular dynamics (MD) calculations, by using the inter-proton distances derived from the NOE values. Cytotoxicity assays against human Ewing sarcoma cell lines RD-ES and CAD-ES1 were performed.
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Affiliation(s)
- Oliver Koepler
- Institut für Organische Chemie, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig, Germany
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