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Egger M, Bereiter R, Mair S, Micura R. Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202207590. [PMID: 38505292 PMCID: PMC10946891 DOI: 10.1002/ange.202207590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 11/08/2022]
Abstract
Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.
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Affiliation(s)
- Michaela Egger
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Stefan Mair
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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2
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Egger M, Bereiter R, Mair S, Micura R. Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes. Angew Chem Int Ed Engl 2022; 61:e202207590. [PMID: 35982640 PMCID: PMC9826390 DOI: 10.1002/anie.202207590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 01/11/2023]
Abstract
Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.
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Affiliation(s)
- Michaela Egger
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Stefan Mair
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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3
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González‐Olvera JC, Fiala R, Pless RC. Protonation of Guanine:5‐Methylcytosine and Guanine:Cytosine Base Pairs in Duplex Oligodeoxyribonucleotides. ChemistrySelect 2022. [DOI: 10.1002/slct.202200835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Julio C. González‐Olvera
- Universidad Politécnica de Santa Rosa Jáuregui Carretera Federal 57 QRO-SLP km 31-150, Parque Industrial Querétaro, Santa Rosa Jáuregui Querétaro 76220 Mexico
| | - Radovan Fiala
- CEITEC-Central European Institute of Technology Masaryk University Kamenice 753/5 62500 Brno Czech Republic
| | - Reynaldo C. Pless
- Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada Instituto Politécnico Nacional Cerro Blanco 141 Querétaro Querétaro 76090 Mexico
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4
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Thakare P, Vasile F, Vallaro M, Visentin S, Caron G, Licandro E, Cauteruccio S. Acid-base and lipophilic properties of peptide nucleic acid derivatives. J Pharm Anal 2021; 11:638-645. [PMID: 34765277 PMCID: PMC8572665 DOI: 10.1016/j.jpha.2020.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/26/2022] Open
Abstract
The first combined experimental and theoretical study on the ionization and lipophilic properties of peptide nucleic acid (PNA) derivatives, including eleven PNA monomers and two PNA decamers, is described. The acidity constants (pKa) of individual acidic and basic centers of PNA monomers were measured by automated potentiometric pH titrations in water/methanol solution, and these values were found to be in agreement with those obtained by MoKa software. These results indicate that single nucleobases do not change their pKa values when included in PNA monomers and oligomers. In addition, immobilized artificial membrane chromatography was employed to evaluate the lipophilic properties of PNA monomers and oligomers, which showed the PNA derivatives had poor affinity towards membrane phospholipids, and confirmed their scarce cell penetrating ability. Overall, our study not only is of potential relevance to evaluate the pharmacokinetic properties of PNA, but also constitutes a reliable basis to properly modify PNA to obtain mimics with enhanced cell penetration properties. The first study on acid-base and lipophilic properties of peptide nucleic acids (PNA). pKa of acid-base centers of PNA evaluated by potentiometric method and MoKa prediction. NMR experiments provide additional information on the protonation of PNA monomers. Lipophilicity of PNA monomers and oligomers is investigated by IAM chromatography. This study can lay the basis of evaluating the pharmacokinetic properties of PNA.
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Affiliation(s)
- Pramod Thakare
- Department of Chemistry, University of Milan, 20133, Milan, Italy
| | - Francesca Vasile
- Department of Chemistry, University of Milan, 20133, Milan, Italy
| | - Maura Vallaro
- Molecular Biotechnology & Health Sciences Department, University of Turin, 10135, Turin, Italy
| | - Sonja Visentin
- Molecular Biotechnology & Health Sciences Department, University of Turin, 10135, Turin, Italy
| | - Giulia Caron
- Molecular Biotechnology & Health Sciences Department, University of Turin, 10135, Turin, Italy
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5
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Sun Y, Tsai M, Zhou W, Lu W, Liu J. Reaction Kinetics, Product Branching, and Potential Energy Surfaces of 1O 2-Induced 9-Methylguanine-Lysine Cross-Linking: A Combined Mass Spectrometry, Spectroscopy, and Computational Study. J Phys Chem B 2019; 123:10410-10423. [PMID: 31718186 DOI: 10.1021/acs.jpcb.9b08796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a kinetics and mechanistic study on the 1O2 oxidation of 9-methylguanine (9MG) and the cross-linking of the oxidized intermediate 2-amino-9-methyl-9H-purine-6,8-dione (9MOGOX) with Nα-acetyl-lysine-methyl ester (abbreviated as LysNH2) in aqueous solutions of different pH. Experimental measurements include the determination of product branching ratios and reaction kinetics using mass spectrometry and absorption spectroscopy, and the characterization of product structures by employing collision-induced dissociation. Strong pH dependence was revealed for both 9MG oxidation and the addition of nucleophiles (water and LysNH2) at the C5 position of 9MOGOX. The 1O2 oxidation rate constant of 9MG was determined to be 3.6 × 107 M-1·s-1 at pH 10.0 and 0.3 × 107 M-1·s-1 at pH 7.0, both of which were measured in the presence of 15 mM LysNH2. The ωB97XD density functional theory coupled with various basis sets and the SMD implicit solvation model was used to explore the reaction potential energy surfaces for the 1O2 oxidation of 9MG and the formation of C5-water and C5-LysNH2 adducts of 9MOGOX. Computational results have shed light on reaction pathways and product structures for the different ionization states of the reactants. The present work has confirmed that the initial 1O2 addition represents the rate-limiting step for the oxidative transformations of 9MG. All of the downstream steps are exothermic with respect to the starting reactants. The C5-cross-linking of 9MOGOX with LysNH2 significantly suppressed the formation of spiroiminodihydantoin (9MSp) resulting from the C5-water addition. The latter became dominant only at the low concentration (∼1 mM) of LysNH2.
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Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry , Queens College of the City University of New York , 65-30 Kissena Blvd. , Queens , New York 11367 , United States.,Ph.D. Program in Chemistry , The Graduate Center of the City University of New York , 365 5th Avenue , New York , New York 10016 , United States
| | - Midas Tsai
- Department of Natural Sciences , LaGuardia Community College , 31-10 Thomson Avenue , Long Island City , New York 11101 , United States
| | - Wenjing Zhou
- Department of Chemistry and Biochemistry , Queens College of the City University of New York , 65-30 Kissena Blvd. , Queens , New York 11367 , United States
| | - Wenchao Lu
- Department of Chemistry and Biochemistry , Queens College of the City University of New York , 65-30 Kissena Blvd. , Queens , New York 11367 , United States.,Ph.D. Program in Chemistry , The Graduate Center of the City University of New York , 365 5th Avenue , New York , New York 10016 , United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry , Queens College of the City University of New York , 65-30 Kissena Blvd. , Queens , New York 11367 , United States.,Ph.D. Program in Chemistry , The Graduate Center of the City University of New York , 365 5th Avenue , New York , New York 10016 , United States
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6
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González-Olvera JC, Durec M, Marek R, Fiala R, Morales-García MDRJ, González-Jasso E, Pless RC. Protonation of Nucleobases in Single- and Double-Stranded DNA. Chembiochem 2018; 19:2088-2098. [PMID: 30073767 DOI: 10.1002/cbic.201800310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Indexed: 01/05/2023]
Abstract
Single-stranded model oligodeoxyribonucleotides, each containing a single protonatable base-cytosine, adenine, guanine, or 5-methylcytosine-centrally located in a background of non-protonatable thymine residues, were acid-titrated in aqueous solution, with UV monitoring. The basicity of the central base was shown to depend on the type of the central base and its nearest neighbours and to rise with increasing oligonucleotide length and decreasing ionic strength of the solution. More complex model oligonucleotides, each containing a centrally located 5-methylcytosine base, were comparatively evaluated in single-stranded and double-stranded form, by UV spectroscopy and high-field NMR. The N3 protonation of the 5-methylcytosine moiety in the double-stranded case occurred at much lower pH, at which the duplex was already experiencing general dissociation, than in the single-stranded case. The central guanine:5-methylcytosine base pair remained intact up to this point, possibly due to an unusual alternative protonation on O2 of the 5-methylcytosine moiety, already taking place at neutral or weakly basic pH, as indicated by UV spectroscopy, thus suggesting that 5-methylcytosine sites in double-stranded DNA might be protonated to a significant extent under physiological conditions.
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Affiliation(s)
- Julio C González-Olvera
- Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Instituto Politécnico Nacional, Querétaro, Querétaro, 76090, Mexico.,Universidad Politécnica de Santa Rosa Jáuregui, Santa Rosa Jáuregui, Querétaro, 76220, Mexico
| | - Matúš Durec
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Radovan Fiala
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | | | - Eva González-Jasso
- Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Instituto Politécnico Nacional, Querétaro, Querétaro, 76090, Mexico
| | - Reynaldo C Pless
- Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Instituto Politécnico Nacional, Querétaro, Querétaro, 76090, Mexico
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7
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Pechlaner M, Dominguez-Martin A, Sigel RKO. Influence of pH and Mg(ii) on the catalytic core domain 5 of a bacterial group II intron. Dalton Trans 2018; 46:3989-3995. [PMID: 28265619 DOI: 10.1039/c6dt04784j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA molecules fold into complex structures that allow them to perform specific functions. To compensate the relative lack of diversity of functional groups within nucleotides, metal ions work as crucial co-factors. In addition, shifted pKas are observed in RNA, enabling acid-base reactions at ambient pH. The central catalytic domain 5 (D5) hairpin of the Azotobacter vinelandii group II intron undergoes both metal ion binding and pH dependence, presumably playing an important functional role in the ribozyme's reaction. By NMR spectroscopy we have here characterized the metal ion binding sites and affinities for the hairpin's internal G-A mismatch, bulge, and pentaloop. The influence of Mg(ii) and pH on the local conformation of the catalytically crucial region is also explored by fluorescence spectroscopy.
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Affiliation(s)
- M Pechlaner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.
| | - A Dominguez-Martin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.
| | - R K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.
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8
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Mandal S, Hebenbrock M, Müller J. A dinuclear silver(I)-mediated base pair in DNA formed from 1, N 6 -ethenoadenine and thymine. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.05.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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9
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Lu W, Sun Y, Zhou W, Liu J. pH-Dependent Singlet O2 Oxidation Kinetics of Guanine and 9-Methylguanine: An Online Mass Spectrometry and Spectroscopy Study Combined with Theoretical Exploration. J Phys Chem B 2017; 122:40-53. [DOI: 10.1021/acs.jpcb.7b09515] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Wenchao Lu
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Yan Sun
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Wenjing Zhou
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
| | - Jianbo Liu
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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10
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Müller J. Metal-mediated base pairs in parallel-stranded DNA. Beilstein J Org Chem 2017; 13:2671-2681. [PMID: 29564004 PMCID: PMC5753045 DOI: 10.3762/bjoc.13.265] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/29/2017] [Indexed: 01/03/2023] Open
Abstract
In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine-Ag(I)-cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.
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Affiliation(s)
- Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany
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11
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Jash B, Müller J. Application of a Metal-Mediated Base Pair to the Detection of Medicinally Relevant Single Nucleotide Polymorphisms. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700665] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstr. 28/30 48149 Münster Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstr. 28/30 48149 Münster Germany
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12
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Sigel A, Operschall BP, Griesser R, Song B, Okruszek A, Odani A, Katsuta T, Lippert B, Sigel H. (N7)-Platination and its effect on (N1)H-acidification in nucleoside phosphate derivatives. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.02.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Lu W, Teng H, Liu J. How protonation and deprotonation of 9-methylguanine alter its singlet O2 addition path: about the initial stage of guanine nucleoside oxidation. Phys Chem Chem Phys 2016; 18:15223-34. [DOI: 10.1039/c6cp01350c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protonated and deprotonated 9-methylguanine follow completely different oxidation routes.
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Affiliation(s)
- Wenchao Lu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- Ph.D. Program in Chemistry, the Graduate Center of the City University of New York
| | - Huayu Teng
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- Ph.D. Program in Chemistry, the Graduate Center of the City University of New York
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14
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González-Olvera JC, Martínez-Reyes J, González-Jasso E, Pless RC. Determination of pKa values for deprotonable nucleobases in short model oligonucleotides. Biophys Chem 2015; 206:58-65. [PMID: 26188860 DOI: 10.1016/j.bpc.2015.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/01/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
Abstract
The deprotonation of ionizable nucleobases centrally placed in short model oligonucleotides was examined under different physical conditions, using UV absorption spectroscopy. The oligonucleotide sequences were designed so that only the central base would be ionized over the pH range examined. pKa values of 9.90±0.01 and 9.34±0.04 were determined for the guanine group in the oligomer d-ACAGCAC and 2'-deoxyguanosine, respectively, both at 25°C and 0.1M NaCl. Lengthening the oligonucleotide up to the tridecamer stage further increases the pKa of the central guanine moiety. Electrolyte concentration, temperature, and mixed water-ethanol solvents affect the acidity of the central base. Changes in the sequence surrounding the central guanine can also have a significant effect, especially in the case of strongly stacking sequences. The pKa values were also determined for the hepta(2'-O-methyl)ribonucleotide and the heptamer PNA of identical sequence, as well as for oligodeoxyribonucleotides with different deprotonable bases, viz. thymine, uracil, or hypoxanthine, in the central position. The results are interpreted in terms of the electric-field effect exerted on the departing proton by the negative electric charges located on the internucleotide phosphate groups, and calculations show this effect to approximately explain the magnitude of the pKa difference observed between the deoxyriboheptanucleotide and its electroneutral PNA analogue.
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Affiliation(s)
- Julio C González-Olvera
- Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Instituto Politécnico Nacional, Querétaro, Querétaro 76090, Mexico
| | - José Martínez-Reyes
- Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Instituto Politécnico Nacional, Querétaro, Querétaro 76090, Mexico
| | - Eva González-Jasso
- Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Instituto Politécnico Nacional, Querétaro, Querétaro 76090, Mexico
| | - Reynaldo C Pless
- Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Instituto Politécnico Nacional, Querétaro, Querétaro 76090, Mexico.
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15
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Pechlaner M, Donghi D, Zelenay V, Sigel RKO. Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial Group II Intron. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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16
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Pechlaner M, Donghi D, Zelenay V, Sigel RKO. Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial Group II Intron. Angew Chem Int Ed Engl 2015; 54:9687-90. [PMID: 26119804 DOI: 10.1002/anie.201504014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Indexed: 11/05/2022]
Abstract
NMR spectroscopy has revealed pH-dependent structural changes in the highly conserved catalytic domain 5 of a bacterial group II intron. Two adenines with pK(a) values close to neutral pH were identified in the catalytic triad and the bulge. Protonation of the adenine opposite to the catalytic triad is stabilized within a G(syn)-AH(+) (anti) base pair. The pH-dependent anti-to-syn flipping of this G in the catalytic triad modulates the known interaction with the linker region between domains 2 and 3 (J23) and simultaneously the binding of the catalytic Mg(2+) ion to its backbone. Hence, this here identified shifted pK(a) value controls the conformational change between the two steps of splicing.
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Affiliation(s)
- Maria Pechlaner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch/rna
| | - Daniela Donghi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch/rna
| | - Veronika Zelenay
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch/rna
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch/rna.
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17
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König SLB, Huppert JL, Sigel RKO, Evans AC. Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences. Nucleic Acids Res 2013; 41:7453-61. [PMID: 23771141 PMCID: PMC3753619 DOI: 10.1093/nar/gkt476] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 05/04/2013] [Accepted: 05/08/2013] [Indexed: 01/29/2023] Open
Abstract
G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions.
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Affiliation(s)
- Sebastian L. B. König
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK, Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland and University of Nice-Sophia Antipolis, UMR 7272 CNRS, Institut de 40 Chimie de Nice, 28 Avenue Valrose, 06108 Nice, France
| | - Julian L. Huppert
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK, Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland and University of Nice-Sophia Antipolis, UMR 7272 CNRS, Institut de 40 Chimie de Nice, 28 Avenue Valrose, 06108 Nice, France
| | - Roland K. O. Sigel
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK, Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland and University of Nice-Sophia Antipolis, UMR 7272 CNRS, Institut de 40 Chimie de Nice, 28 Avenue Valrose, 06108 Nice, France
| | - Amanda C. Evans
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK, Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland and University of Nice-Sophia Antipolis, UMR 7272 CNRS, Institut de 40 Chimie de Nice, 28 Avenue Valrose, 06108 Nice, France
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