1
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Gao S, Guan H, Bloomer H, Wich D, Song D, Khirallah J, Ye Z, Zhao Y, Chen M, Xu C, Liu L, Xu Q. Harnessing non-Watson-Crick's base pairing to enhance CRISPR effectors cleavage activities and enable gene editing in mammalian cells. Proc Natl Acad Sci U S A 2024; 121:e2308415120. [PMID: 38150477 PMCID: PMC10786293 DOI: 10.1073/pnas.2308415120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/21/2023] [Indexed: 12/29/2023] Open
Abstract
Genomic DNA of the cyanophage S-2L virus is composed of 2-aminoadenine (Z), thymine (T), guanine (G), and cytosine (C), forming the genetic alphabet ZTGC, which violates Watson-Crick base pairing rules. The Z-base has an extra amino group on the two position that allows the formation of a third hydrogen bond with thymine in DNA strands. Here, we explored and expanded applications of this non-Watson-Crick base pairing in protein expression and gene editing. Both ZTGC-DNA (Z-DNA) and ZUGC-RNA (Z-RNA) produced in vitro show detectable compatibility and can be decoded in mammalian cells, including Homo sapiens cells. Z-crRNA can guide CRISPR-effectors SpCas9 and LbCas12a to cleave specific DNA through non-Watson-Crick base pairing and boost cleavage activities compared to A-crRNA. Z-crRNA can also allow for efficient gene and base editing in human cells. Together, our results help pave the way for potential strategies for optimizing DNA or RNA payloads for gene editing therapeutics and give insights to understanding the natural Z-DNA genome.
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Affiliation(s)
- Shuliang Gao
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Huiwen Guan
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Hanan Bloomer
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Douglas Wich
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Donghui Song
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Jennifer Khirallah
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Yu Zhao
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Mengting Chen
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Chutian Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Lihan Liu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
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2
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Zhang A, Kondhare D, Leonard P, Seela F. DNA Strand Displacement with Base Pair Stabilizers: Purine-2,6-Diamine and 8-Aza-7-Bromo-7-Deazapurine-2,6-Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction. Chemistry 2022; 28:e202202412. [PMID: 36178316 PMCID: PMC10100337 DOI: 10.1002/chem.202202412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Indexed: 12/30/2022]
Abstract
Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides (1 and 2) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA-dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single-stranded invaders with single and multiple incorporations of stabilizers. Displacement is driven by negative enthalpy changes between target and displaced duplex. Toeholds are not required. Two new environmental sensitive fluorescent pyrene sensors were developed to monitor the progress of displacement reactions. Pyrene was connected to the nucleobase in the invader or to a dendritic linker in the output strand. Both new sensors were constructed by click chemistry; phosphoramidites and oligonucleotides were prepared. Sensors show monomer or excimer emission. Fluorescence intensity changes when the displacement reaction progresses. Our work demonstrates that strand displacement with base pair stabilizers is applicable to DNA, RNA and to related biopolymers with applications in chemical biology, nanotechnology and medicinal diagnostics.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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3
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Mei H, Budow-Busse S, Kondhare D, Eickmeier H, Reuter H, Seela F. The 2′-deoxyribofuranoside of 3-phenyltetrahydropyrimido[4,5- c]pyridazin-7-one: a bicyclic nucleoside with sugar residues in N and S conformations, and its molecular recognition. ACTA CRYSTALLOGRAPHICA SECTION C STRUCTURAL CHEMISTRY 2022; 78:382-389. [PMID: 35788502 PMCID: PMC9255914 DOI: 10.1107/s2053229622005964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/02/2022] [Indexed: 11/10/2022]
Abstract
The title compound 3-phenyltetrahydropyrimido[4,5-c]pyridazine 2′-deoxyribonucleoside [systematic name: 6-(2-deoxy-β-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-3-phenylpyrimido[4,5-c]pyridazin-7-one monohydrate, C17H18N4O4·H2O, 1] shows two conformations in the crystalline state and the two conformers (1a and 1b) adopt different sugar puckers. The sugar residue of 1a shows a C2′-endo S-type conformation, while 1b displays a C3′-endo N-type sugar pucker. Both conformers adopt similar anti conformations around the N-glycosylic bonds, with χ = −97.5 (3)° for conformer 1a and χ = −103.8 (3)° for conformer 1b. The extended crystalline network is stabilized by several intermolecular hydrogen bonds involving nucleoside and water molecules. The nucleobases and phenyl substituents of the two conformers (1a and 1b) are stacked and display a reverse alignment. A Hirshfeld surface analysis supports the hydrogen-bonding pattern, while curvedness surfaces visualize the stacking interactions of neighbouring molecules. The recognition face of nucleoside 1 for base-pair formation mimics that of 2′-deoxythymidine. Nucleoside 1 shows two pK
a values: 1.8 for protonation and 11.2 for deprotonation. DNA oligonucleotides containing nucleoside 1 were synthesized and hybridized with complementary DNA strands. Nucleoside 1 forms a stable base pair with dA which is as stable as the canonical dA–dT pair. The bidentate 1–dA base pair is strengthened by a third hydrogen bond provided by the dA analogue 3-bromopyrazolo[3,4-d]pyrimidine-4,6-diamine 2′-deoxyribofuranoside (4). By this, duplex stability is increased and the suggested base-pairing patterns are supported.
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4
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Chai Y, Kondhare D, Zhang A, Leonard P, Seela F. The 2-Amino Group of 8-Aza-7-deaza-7-bromopurine-2,6-diamine and Purine-2,6-diamine as Stabilizer for the Adenine-Thymine Base Pair in Heterochiral DNA with Strands in Anomeric Configuration. Chemistry 2021; 27:2093-2103. [PMID: 33090562 PMCID: PMC7898646 DOI: 10.1002/chem.202004221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 02/05/2023]
Abstract
Stabilization of DNA is beneficial for many applications in the fields of DNA therapeutics, diagnostics, and materials science. Now, this phenomenon is studied on heterochiral DNA, an autonomous DNA recognition system with complementary strands in α-D and β-D configuration showing parallel strand orientation. The 12-mer heterochiral duplexes were constructed from anomeric (α/β-D) oligonucleotide single-strands. Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides having the capability to form tridentate base pairs with dT were used to strengthen the stability of the dA-dT base pair. Tm data and thermodynamic values obtained from UV melting profiles indicated that the 8-aza-7-deaza 2'-deoxyribonucleoside decorated with a bromo substituent is so far the most efficient stabilizer for heterochiral DNA. Compared with that, the stabilizing effect of the purine-2,6-diamine 2'-deoxyribonucleoside is low. Global changes of helix structures were identified by circular dichroism (CD) spectra during melting.
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Affiliation(s)
- Yingying Chai
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Department of RespiratoryCritical Care Medicine Targeted Tracer, Research and Development LaboratoryWest China HospitalSichuan610041P. R. China
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
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5
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E. coli Gyrase Fails to Negatively Supercoil Diaminopurine-Substituted DNA. J Mol Biol 2015; 427:2305-18. [PMID: 25902201 DOI: 10.1016/j.jmb.2015.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 03/06/2015] [Accepted: 04/10/2015] [Indexed: 12/18/2022]
Abstract
Type II topoisomerases modify DNA supercoiling, and crystal structures suggest that they sharply bend DNA in the process. Bacterial gyrases are a class of type II topoisomerases that can introduce negative supercoiling by creating a wrap of DNA before strand passage. Isoforms of these essential enzymes were compared to reveal whether they can bend or wrap artificially stiffened DNA. Escherichia coli gyrase and human topoisomerase IIα were challenged with normal DNA or stiffer DNA produced by polymerase chain reaction reactions in which diaminopurine (DAP) replaced adenine deoxyribonucleotide triphosphates. On single DNA molecules twisted with magnetic tweezers to create plectonemes, the rates or pauses during relaxation of positive supercoils in DAP-substituted versus normal DNA were distinct for both enzymes. Gyrase struggled to bend or perhaps open a gap in DAP-substituted DNA, and segments of wider DAP DNA may have fit poorly into the N-gate of the human topoisomerase IIα. Pauses during processive activity on both types of DNA exhibited ATP dependence consistent with two pathways leading to the strand-passage-competent state with a bent gate segment and a transfer segment trapped by an ATP-loaded and latched N-gate. However, E. coli DNA gyrase essentially failed to negatively supercoil 35% stiffer DAP DNA.
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6
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Roles of the amino group of purine bases in the thermodynamic stability of DNA base pairing. Molecules 2014; 19:11613-27. [PMID: 25100254 PMCID: PMC6271411 DOI: 10.3390/molecules190811613] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 01/19/2023] Open
Abstract
The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I) and 2'-deoxyribo-2,6-diaminopurine (D) as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G•C > D•T ≈ I•C > A•T > G•T > I•T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.
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7
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Hughesman CB, Turner RFB, Haynes CA. Role of the heat capacity change in understanding and modeling melting thermodynamics of complementary duplexes containing standard and nucleobase-modified LNA. Biochemistry 2011; 50:5354-68. [PMID: 21548576 DOI: 10.1021/bi200223s] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Melting thermodynamic data obtained by differential scanning calorimetry (DSC) are reported for 43 duplexed oligonucleotides containing one or more locked nucleic acid (LNA) substitutions. The measured heat capacity change (ΔC(p)) for the helix-to-coil transition is used to compute the changes in enthalpy and entropy for melting of an LNA-bearing duplex at the T(m) of its corresponding isosequential unmodified DNA duplex to allow rigorous thermodynamic analysis of the stability enhancements provided by LNA substitutions. Contrary to previous studies, our analysis shows that the origin of the improved stability is almost exclusively a net reduction (ΔΔS° < 0) in the entropy gain accompanying the helix-to-coil transition, with the magnitude of the reduction dependent on the type of nucleobase and its base pairing properties. This knowledge and our average measured value for ΔC(p) of 42 ± 11 cal mol(-1) K(-1) bp(-1) are then used to derive a new model that accurately predicts melting thermodynamics and the increased melting temperature (ΔT(m)) of heteroduplexes formed between an unmodified DNA strand and a complementary strand containing any number and configuration of standard LNA nucleotides A, T, C, and G. This single-base thermodynamic (SBT) model requires only four entropy-related parameters in addition to ΔC(p). Finally, DSC data for 20 duplexes containing the nucleobase-modified LNAs 2-aminoadenine (D) and 2-thiothymine (H) are reported and used to determine SBT model parameters for D and H. The data and model suggest that along with the greater stability enhancement provided by D and H bases relative to their corresponding A and T analogues, the unique pseudocomplementary properties of D-H base pairs may make their use appealing for in vitro and in vivo applications.
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Affiliation(s)
- Curtis B Hughesman
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada
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8
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Koshkin AA. Syntheses and base-pairing properties of locked nucleic acid nucleotides containing hypoxanthine, 2,6-diaminopurine, and 2-aminopurine nucleobases. J Org Chem 2004; 69:3711-8. [PMID: 15153000 DOI: 10.1021/jo0303923] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Second generation 2'-O,4'-C-methylene-linked nucleotides 1-3 containing hypoxanthine, 2,6-diaminopurine, and 2-aminopurine nucleobases were synthesized and incorporated into locked nucleic acid (LNA) oligonucleotides by means of the automated phosphoramidite method. The required phosphoramidite monomeric units were efficiently prepared via convergent synthesis. The glycosyl donor 4 was stereoselectively coupled with hypoxanthine and 6-chloro-2-aminopurine to give the 4'-C-branched nucleosides 5 and 17. The methods for conversion of 5 and 17 into phosphoramidites 11, 25, and 29 were developed and described in full details for the first time. Hybridization properties of LNA octamers containing the new LNA nucleotides were assessed against perfect and singly mismatched DNA. The binding studies revealed that all LNA octamers hybridize very efficiently to DNA following Watson-Crick base-pairing rules with increased binding affinity compared to the DNA analogues. The unique properties of the nucleotides 1-3 make them very useful for further strengthening of the LNA technology.
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Affiliation(s)
- Alexei A Koshkin
- Department of Chemistry, Exiqon A/S, Bygstubben 9, DK-2950 Vedbaek, Denmark.
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9
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8-Aza-7-deazapurine–pyrimidine base pairs: the contribution of 2- and 7-substituents to the stability of duplex DNA. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00406-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Timofeev E, Mirzabekov A. Binding specificity and stability of duplexes formed by modified oligonucleotides with a 4096-hexanucleotide microarray. Nucleic Acids Res 2001; 29:2626-34. [PMID: 11410672 PMCID: PMC55729 DOI: 10.1093/nar/29.12.2626] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The binding of oligodeoxynucleotides modified with adenine 2'-O-methyl riboside, 2,6-diaminopurine 2'-O-methyl riboside, cytosine 2'-O-methyl riboside, 2,6-diaminopurine deoxyriboside or 5-bromodeoxyuridine was studied with a microarray containing all possible (4096) polyacrylamide-bound hexadeoxynucleotides (a generic microchip). The generic microchip was manufactured by using reductive immobilization of aminooligonucleotides in the activated copolymer of acrylamide, bis-acrylamide and N-(2,2-dimethoxyethyl) acrylamide. The binding of the fluorescently labeled modified octanucleotides to the array was analyzed with the use of both melting profiles and the fluorescence distribution at selected temperatures. Up to three substitutions of adenosines in the octamer sequence by adenine 2'-O-methyl ribosides (A(m)), 2,6-diaminopurine 2'-O-methyl ribosides (D(m)) or 2,6-diaminopurine deoxyribosides (D) resulted in increased mismatch discrimination measured at the melting temperature of the corresponding perfect duplex. The stability of complexes formed by 2'-O-methyl-adenosine-modified oligodeoxynucleotides was slightly decreased with every additional substitution, yielding approximately 4 degrees C of total loss in melting temperature for three modifications, as followed from microchip thermal denaturation experiments. 2,6-Diaminopurine 2'-O-methyl riboside modifications led to considerable duplex stabilization. The cytosine 2'-O-methyl riboside and 5-bromodeoxyuridine modifications generally did not change either duplex stability or mismatch resolution. Denaturation experiments conducted with selected perfect duplexes on microchips and in solution showed similar results on thermal stabilities. Some hybridization artifacts were observed that might indicate the formation of parallel DNA.
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Affiliation(s)
- E Timofeev
- Engelhardt Institute of Molecular Biology, 32 Vavilov Str., B-334, Moscow 117984, Russia
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11
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Herdewijn P. Heterocyclic modifications of oligonucleotides and antisense technology. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2000; 10:297-310. [PMID: 10984123 DOI: 10.1089/108729000421475] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Modification of the heterocyclic moiety of oligonucleotides has led to the discovery of potent antisense compounds. This review describes the physicochemical factors that are responsible for duplex stabilization through base modification. A summary is given of the different heterocyclic modifications that can be used to beneficially influence this duplex stability. The biologic activity of base-modified oligonucleotides is described, and the different factors that are important for obtaining in vivo antisense activity with heterocyclic-modified oligonucleotides are summarized.
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Affiliation(s)
- P Herdewijn
- Rega Institute for Medical Research, K.U. Leuven, Laboratory for Medicinal Chemistry, Belgium
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12
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Tomasz M, Das A, Tang KS, Ford MGJ, Minnock A, Musser SM, Waring MJ. The Purine 2-Amino Group as the Critical Recognition Element for Sequence-Specific Alkylation and Cross-Linking of DNA by Mitomycin C. J Am Chem Soc 1998. [DOI: 10.1021/ja9824019] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Maria Tomasz
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Arunangshu Das
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Kit S. Tang
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Marjin G. J. Ford
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Andrew Minnock
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Steven M. Musser
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Michael J. Waring
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
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13
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Bifulco G, Galeone A, Nicolaou KC, Chazin WJ, Gomez-Paloma L. Solution Structure of the Complex between the Head-to-Tail Dimer of Calicheamicin γ1I Oligosaccharide and a DNA Duplex Containing d(ACCT) and d(TCCT) High-Affinity Binding Sites. J Am Chem Soc 1998. [DOI: 10.1021/ja973910y] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giuseppe Bifulco
- Contribution from the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, and Dipartimento di Chimica delle Sostanze Naturali, Universita' degli studi di Napoli “Federico II”, via D. Montesano 49, Napoli 80131, Italy
| | - Aldo Galeone
- Contribution from the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, and Dipartimento di Chimica delle Sostanze Naturali, Universita' degli studi di Napoli “Federico II”, via D. Montesano 49, Napoli 80131, Italy
| | - K. C. Nicolaou
- Contribution from the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, and Dipartimento di Chimica delle Sostanze Naturali, Universita' degli studi di Napoli “Federico II”, via D. Montesano 49, Napoli 80131, Italy
| | - Walter J. Chazin
- Contribution from the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, and Dipartimento di Chimica delle Sostanze Naturali, Universita' degli studi di Napoli “Federico II”, via D. Montesano 49, Napoli 80131, Italy
| | - Luigi Gomez-Paloma
- Contribution from the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, and Dipartimento di Chimica delle Sostanze Naturali, Universita' degli studi di Napoli “Federico II”, via D. Montesano 49, Napoli 80131, Italy
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14
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Luyten I, Herdewijn P. Hybridization properties of base-modified oligonucleotides within the double and triple helix motif. Eur J Med Chem 1998. [DOI: 10.1016/s0223-5234(98)80016-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Allan BW, Beechem JM, Lindstrom WM, Reich NO. Direct real time observation of base flipping by the EcoRI DNA methyltransferase. J Biol Chem 1998; 273:2368-73. [PMID: 9442083 DOI: 10.1074/jbc.273.4.2368] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
DNA methyltransferases are excellent prototypes for investigating DNA distortion and enzyme specificity because catalysis requires the extrahelical stabilization of the target base within the enzyme active site. The energetics and kinetics of base flipping by the EcoRI DNA methyltransferase were investigated by two methods. First, equilibrium dissociation constants (KDDNA) were determined for the binding of the methyltransferase to DNA containing abasic sites or base analogs incorporated at the target base. Consistent with a base flipping mechanism, tighter binding to oligonucleotides containing destabilized target base pairs was observed. Second, total intensity stopped flow fluorescence measurements of DNA containing 2-aminopurine allowed presteady-state real time observation of the base flipping transition. Following the rapid formation of an enzyme-DNA collision complex, a biphasic increase in total intensity was observed. The fast phase dominated the total intensity increase with a rate nearly identical to k(methylation) determined by rapid chemical quench-flow techniques (Reich, N. O., and Mashoon, N. (1993) J. Biol. Chem. 268, 9191-9193). The restacking of the extrahelical base also revealed biphasic kinetics with the recovered amplitudes from these off-rate experiments matching very closely to those observed during the base unstacking process. These results provide the first direct and continuous observation of base flipping and show that at least two distinct conformational transitions occurred at the flipped base subsequent to complex formation. Furthermore, our results suggest that the commitment to catalysis during the methylation of the target site is not determined at the level of the chemistry step but rather is mediated by prior intramolecular isomerization within the enzyme-DNA complex.
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Affiliation(s)
- B W Allan
- Department of Chemistry, University of California, Santa Barbara 93106-6081, USA
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Sun W, Hattman S, Kool E. Interaction of the bacteriophage Mu transcriptional activator protein, C, with its target site in the mom promoter. J Mol Biol 1997; 273:765-74. [PMID: 9367769 DOI: 10.1006/jmbi.1997.1349] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The bacteriophage Mu C gene encodes a 16.5 kDa site-specific DNA binding protein that is a transcriptional activator of the four "late" promoters, Pmom, Plys, PI and PP. A symmetrical consensus C recognition sequence, TTAT[N5-6]ATAA, containing an inverted tetrad repeat separated by a spacer of five to six G+C-rich nucleotides, has been proposed. To investigate this, we used oligonucleotide mutagenesis to introduce random substitutions within and flanking the proposed C-target region; each variant site was tested for C recognition by an in vivo functional transactivation assay. We observed that all single mutations, in either tetrad, reduced C activation. Although two out of ten substitutions within the spacer reduced activation, the spacer region does not appear to make specific contact with C. We also used in vitro chemical-protection and -interference to study C contacts with Pmom. The results indicate that C contacts Pmom DNA on only one face of the helix through interactions within two adjacent major grooves; this conclusion was supported by gel shift analyses using synthetic oligonucleotide duplexes containing I.C or other base-pair substitutions. Evidence is also presented that C-Pmom contacts are asymmetrical, and that they extend two nucleotides 3' to the promoter-proximal tetrad. We also show that C binding induces a deformation, possibly a bend, in Pmom DNA.
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Affiliation(s)
- W Sun
- Department of Biology, University of Rochester, NY 14627, USA
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17
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Eis PS, Smith JA, Rydzewski JM, Case DA, Boger DL, Chazin WJ. High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA. J Mol Biol 1997; 272:237-52. [PMID: 9299351 DOI: 10.1006/jmbi.1997.1223] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The three-dimensional solution structure of duocarmycin SA in complex with d-(G1ACTAATTGAC11).d-(G12TCATTAGTC22) has been determined by restrained molecular dynamics and relaxation matrix calculations using experimental NOE distance and torsion angle constraints derived from 1H NMR spectroscopy. The final input data consisted of a total of 858 distance and 189 dihedral angle constraints, an average of 46 constraints per residue. In the ensemble of 20 final structures, there were no distance constraint violations >0.06 A or torsion angle violations >0.8 degrees. The average pairwise root mean square deviation (RMSD) over all 20 structures for the binding site region is 0.57 A (average RMSD from the mean: 0.39 A). Although the DNA is very B-like, the sugar-phosphate backbone torsion angles beta, epsilon, and zeta are distorted from standard values in the binding site region. The structure reveals site-specific bonding of duocarmycin SA at the N3 position of adenine 19 in the AT-rich minor groove of the duplex and binding stabilization via hydrophobic interactions. Comparisons have been made to the structure of a closely related complex of duocarmycin A bound to an AT-rich DNA duplex. These results provide insights into critical aspects of the alkylation site selectivity and source of catalysis of the DNA alkylating agents, and the unusual stability of the resulting adducts.
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Affiliation(s)
- P S Eis
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Rydzewski JM, Leupin W, Chazin W. The width of the minor groove affects the binding of the bisquaternary heterocycle SN-6999 to duplex DNA. Nucleic Acids Res 1996; 24:1287-93. [PMID: 8614632 PMCID: PMC145775 DOI: 10.1093/nar/24.7.1287] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A complex between d(GGGAAAAACGG).d(CCGTTTTTCCC) and the minor groove binding drug SN-6999 has been studied by 1H nuclear magnetic resonance spectroscopy. The drug is found to bind in the d(A)5 tract, but with interactions extending one residue in the 3'-direction along each strand. Doubling of resonances in the complex indicates slow to intermediate exchange between two binding modes. An orientational preference (7:3) is found, the first such example in an SN-6999 complex. Furthermore, the upper limit of the lifetime for the major species is longer than was found for SN-6999 with other DNA duplexes. The preferred orientation of SN-6999 has the pyridinium ring near the 5'-end of the (+) strand; the minor binding mode has the reverse orientation. The orientational preference and slower exchange rate relative to other SN-6999 complexes is attributed to increased stabilization from van der Waals interactions due to better shape complementarity between the DNA duplex and ligand. The comparison of these results with studies of SN-6999 complexed to other DNA duplexes reveals the sensitivity of the binding properties to the delicate interplay between the molecular structure of the ligand and the specific characteristics of the DNA minor groove.
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Affiliation(s)
- J M Rydzewski
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Beaucage SL, Iyer RP. The synthesis of modified oligonucleotides by the phosphoramidite approach and their applications. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)87958-8] [Citation(s) in RCA: 277] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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