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Deng J, Walther A. Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States. J Am Chem Soc 2020; 142:685-689. [DOI: 10.1021/jacs.9b11598] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jie Deng
- A3BMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- DFG Cluster of Excellence “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), 79110 Freiburg, Germany
- Freiburg Materials Research Center, University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Andreas Walther
- A3BMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- DFG Cluster of Excellence “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), 79110 Freiburg, Germany
- Freiburg Materials Research Center, University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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2
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Bauer RJ, Jurkiw TJ, Evans TC, Lohman GJS. Rapid Time Scale Analysis of T4 DNA Ligase-DNA Binding. Biochemistry 2017; 56:1117-1129. [PMID: 28165732 DOI: 10.1021/acs.biochem.6b01261] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA ligases, essential to both in vivo genome integrity and in vitro molecular biology, catalyze phosphodiester bond formation between adjacent 3'-OH and 5'-phosphorylated termini in dsDNA. This reaction requires enzyme self-adenylylation, using ATP or NAD+ as a cofactor, and AMP release concomitant with phosphodiester bond formation. In this study, we present the first fast time scale binding kinetics of T4 DNA ligase to both nicked substrate DNA (nDNA) and product-equivalent non-nicked dsDNA, as well as binding and release kinetics of AMP. The described assays utilized a fluorescein-dT labeled DNA substrate as a reporter for ligase·DNA interactions via stopped-flow fluorescence spectroscopy. The analysis revealed that binding to nDNA by the active adenylylated ligase occurs in two steps, an initial rapid association equilibrium followed by a transition to a second bound state prior to catalysis. Furthermore, the ligase binds and dissociates from nicked and nonsubstrate dsDNA rapidly with initial association affinities on the order of 100 nM regardless of enzyme adenylylation state. DNA binding occurs through a two-step mechanism in all cases, confirming prior proposals of transient binding followed by a transition to a productive ligase·nDNA (Lig·nDNA) conformation but suggesting that weaker nonproductive "closed" complexes are formed as well. These observations demonstrate the mechanistic underpinnings of competitive inhibition by rapid binding of nonsubstrate DNA, and of substrate inhibition by blocking of the self-adenylylation reaction through nick binding by deadenylylated ligase. Our analysis further reveals that product release is not the rate-determining step in turnover.
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Affiliation(s)
- Robert J Bauer
- DNA Enzymes Division, New England BioLabs, Inc. , Ipswich, Massachusetts 01938-2723, United States
| | - Thomas J Jurkiw
- University of Michigan Medical School , Ann Arbor, Michigan 48109-0600, United States
| | - Thomas C Evans
- DNA Enzymes Division, New England BioLabs, Inc. , Ipswich, Massachusetts 01938-2723, United States
| | - Gregory J S Lohman
- DNA Enzymes Division, New England BioLabs, Inc. , Ipswich, Massachusetts 01938-2723, United States
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3
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Characterization of the chandipura virus leader RNA–phosphoprotein interaction using single tryptophan mutants and its detection in viral infected cells. Biochimie 2013; 95:180-94. [DOI: 10.1016/j.biochi.2012.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 09/11/2012] [Indexed: 11/15/2022]
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Hili R, Niu J, Liu DR. DNA ligase-mediated translation of DNA into densely functionalized nucleic acid polymers. J Am Chem Soc 2013; 135:98-101. [PMID: 23256841 PMCID: PMC3544274 DOI: 10.1021/ja311331m] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Indexed: 01/09/2023]
Abstract
We developed a method to translate DNA sequences into densely functionalized nucleic acids by using T4 DNA ligase to mediate the DNA-templated polymerization of 5'-phosphorylated trinucleotides containing a wide variety of appended functional groups. This polymerization proceeds sequence specifically along a DNA template and can generate polymers of at least 50 building blocks (150 nucleotides) in length with remarkable efficiency. The resulting single-stranded highly modified nucleic acid is a suitable template for primer extension using deep vent (exo-) DNA polymerase, thereby enabling the regeneration of template DNA. We integrated these capabilities to perform iterated cycles of in vitro translation, selection, and template regeneration on libraries of modified nucleic acid polymers.
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Affiliation(s)
- Ryan Hili
- Howard Hughes
Medical Institute, Department of Chemistry
and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, 02138, United States
| | - Jia Niu
- Howard Hughes
Medical Institute, Department of Chemistry
and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, 02138, United States
| | - David R. Liu
- Howard Hughes
Medical Institute, Department of Chemistry
and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, 02138, United States
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5
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Gao F, Zhou H, Li W, Zhang X. Detection of ligation products of DNA linkers with 5'-OH ends by denaturing PAGE silver stain. PLoS One 2012; 7:e39251. [PMID: 22761747 PMCID: PMC3384673 DOI: 10.1371/journal.pone.0039251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 05/21/2012] [Indexed: 11/18/2022] Open
Abstract
To explore if DNA linkers with 5′-hydroxyl (OH) ends could be joined by commercial T4 and E. coli DNA ligase, these linkers were synthesized by using the solid-phase phosphoramidite method and joined by using commercial T4 and E. coli DNA ligases. The ligation products were detected by using denaturing PAGE silver stain and PCR method. About 0.5–1% of linkers A–B and E–F, and 0.13–0.5% of linkers C–D could be joined by T4 DNA ligases. About 0.25–0.77% of linkers A–B and E–F, and 0.06–0.39% of linkers C–D could be joined by E. coli DNA ligases. A 1-base deletion (-G) and a 5-base deletion (-GGAGC) could be found at the ligation junctions of the linkers. But about 80% of the ligation products purified with a PCR product purification kit did not contain these base deletions, meaning that some linkers had been correctly joined by T4 and E. coli DNA ligases. In addition, about 0.025–0.1% of oligo 11 could be phosphorylated by commercial T4 DNA ligase. The phosphorylation products could be increased when the phosphorylation reaction was extended from 1 hr to 2 hrs. We speculated that perhaps the linkers with 5′-OH ends could be joined by T4 or E. coli DNA ligase in 2 different manners: (i) about 0.025–0.1% of linkers could be phosphorylated by commercial T4 DNA ligase, and then these phosphorylated linkers could be joined to the 3′-OH ends of other linkers; and (ii) the linkers could delete one or more nucleotide(s) at their 5′-ends and thereby generated some 5′-phosphate ends, and then these 5′-phosphate ends could be joined to the 3′-OH ends of other linkers at a low efficiency. Our findings may probably indicate that some DNA nicks with 5′-OH ends can be joined by commercial T4 or E. coli DNA ligase even in the absence of PNK.
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Affiliation(s)
- Feng Gao
- Department of Anal and Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Huafu Zhou
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wei Li
- Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, China
- * E-mail:
| | - Xuerong Zhang
- Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, China
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Lohman GJS, Chen L, Evans TC. Kinetic characterization of single strand break ligation in duplex DNA by T4 DNA ligase. J Biol Chem 2011; 286:44187-44196. [PMID: 22027837 PMCID: PMC3243518 DOI: 10.1074/jbc.m111.284992] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 10/14/2011] [Indexed: 01/24/2023] Open
Abstract
T4 DNA ligase catalyzes phosphodiester bond formation between juxtaposed 5'-phosphate and 3'-hydroxyl termini in duplex DNA in three steps: 1) enzyme-adenylylate formation by reaction with ATP; 2) adenylyl transfer to a 5'-phosphorylated polynucleotide to generate adenylylated DNA; and 3) phosphodiester bond formation with release of AMP. This investigation used synthetic, nicked DNA substrates possessing either a 5'-phosphate or a 5'-adenylyl phosphate. Steady state experiments with a nicked substrate containing juxtaposed dC and 5'-phosphorylated dT deoxynucleotides (substrate 1) yielded kcat and kcat/Km values of 0.4±0.1 s(-1) and 150±50 μm(-1) s(-1), respectively. Under identical reaction conditions, turnover of an adenylylated version of this substrate (substrate 1A) yielded kcat and kcat/Km values of 0.64±0.08 s(-1) and 240±40 μm(-1) s(-1). Single turnover experiments utilizing substrate 1 gave fits for the forward rates of Step 2 (k2) and Step 3 (k3) of 5.3 and 38 s(-1), respectively, with the slowest step ∼10-fold faster than the rate of turnover seen under steady state conditions. Single turnover experiments with substrate 1A produced a Step 3 forward rate constant of 4.3 s(-1), also faster than the turnover rate of 1A. Enzyme self-adenylylation was confirmed to also occur on a fast time scale (∼6 s(-1)), indicating that the rate-limiting step for T4 DNA ligase nick sealing is not a chemical step but rather is most likely product release. Pre-steady state reactions displayed a clear burst phase, consistent with this conclusion.
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Affiliation(s)
| | - Lixin Chen
- New England Biolabs Inc., Ipswich, Massachusetts 01938-2723
| | - Thomas C Evans
- New England Biolabs Inc., Ipswich, Massachusetts 01938-2723.
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Fedorova OS, Kuznetsov NA, Koval VV, Knorre DG. Conformational dynamics and pre-steady-state kinetics of DNA glycosylases. BIOCHEMISTRY (MOSCOW) 2011; 75:1225-39. [PMID: 21166640 DOI: 10.1134/s0006297910100044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Results of investigations of E. coli DNA glycosylases using pre-steady-state kinetics are considered. Special attention is given to the connection of conformational changes in the interacting biomolecules with kinetic mechanisms of the enzymatic processes.
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Affiliation(s)
- O S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
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Yu Z, Cui M, Yan C, Song F, Liu Z, Liu S, Zhang H. Gas phase isomeric differentiation of oleanolic and ursolic acids associated with heptakis-(2,6-di-O-methyl)-beta-cyclodextrin by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:444-50. [PMID: 20306522 DOI: 10.1002/jms.1733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Oleanolic acid (OA) and ursolic acid (UA) are isomeric triterpenoid compounds with similar pharmaceutical properties. Usually, modern chromatographic and electrophoretic methods are widely utilized to differentiate these two compounds. Compared with mass spectrometric (MS) methods, these modern separation methods are both time- and sample-consuming. Herein, we present a new method for structural differentiation of OA and UA by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with the association of heptakis-(2,6-di-O-methyl)-beta-cyclodextrin (DM-beta-CD). Exact MS and tandem MS (MS/MS) data showed that there is no perceptible difference between OA and UA, as well as their beta-cyclodextrin and gamma-cyclodextrin complexes. However, there is a remarkable difference in MS/MS spectra of DM-beta-CD complexes of OA and UA. The peak corresponding to the neutral loss of a formic acid and a water molecule could only be observed in the MS/MS spectrum of the complex of DM-beta-CD : OA. Molecular modeling calculations were also employed to further investigate the structural differences of DM-beta-CD : OA and DM-beta-CD : UA complexes. Therefore, by employing DM-beta-CD as a reference reagent, OA and UA could be differentiated with purely MS method.
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Affiliation(s)
- Zhan Yu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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Jaganathan H, Ivanisevic A. Circular dichroism study of enzymatic manipulation on magnetic and metallic DNA template nanowires. Colloids Surf B Biointerfaces 2008; 67:279-83. [DOI: 10.1016/j.colsurfb.2008.08.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Accepted: 08/29/2008] [Indexed: 11/26/2022]
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Yuan C, Lou XW, Rhoades E, Chen H, Archer LA. T4 DNA ligase is more than an effective trap of cyclized dsDNA. Nucleic Acids Res 2007; 35:5294-302. [PMID: 17686784 PMCID: PMC2018621 DOI: 10.1093/nar/gkm582] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
T4 DNA ligase is used in standard cyclization assays to trap double-stranded DNA (dsDNA) in low-probability, cyclic or highly bent conformations. The cyclization probability, deduced from the relative yield of cyclized product, can be used in conjunction with statistical mechanical models to extract the bending stiffness of dsDNA. By inserting the base analog 2-aminopurine (2-AP) at designated positions in 89 bp and 94 bp dsDNA fragments, we find that T4 DNA ligase can have a previously unknown effect. Specifically, we observe that addition of T4 ligase to dsDNA in proportions comparable to what is used in the cyclization assay leads to a significant increase in fluorescence from 2-AP. This effect is believed to originate from stabilization of local base-pair opening by formation of transient DNA-ligase complexes. Non-specific binding of T4 ligase to dsDNA is also confirmed using fluorescence correlation spectroscopy (FCS) experiments, which reveal a systematic reduction of dsDNA diffusivity in the presence of ligase. ATP competes with regular DNA for non-covalent binding to the T4 ligase and is found to significantly reduce DNA-ligase complexation. For short dsDNA fragments, however, the population of DNA-ligase complexes at typical ATP concentrations used in DNA cyclization studies is determined to be large enough to dominate the cyclization reaction.
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Affiliation(s)
- Chongli Yuan
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Xiong Wen Lou
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth Rhoades
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Huimin Chen
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Lynden A. Archer
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
- *To whom correspondence should be addressed. +1 607 254 8825+1 607 255 9166
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11
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Abstract
T4 DNA ligase is an Mg2+-dependent and ATP-dependent enzyme that seals DNA nicks in three steps: it covalently binds AMP, transadenylates the nick phosphate, and catalyses formation of the phosphodiester bond releasing AMP. In this kinetic study, we further detail the reaction mechanism, showing that the overall ligation reaction is a superimposition of two parallel processes: a 'processive' ligation, in which the enzyme transadenylates and seals the nick without dissociating from dsDNA, and a 'nonprocessive' ligation, in which the enzyme takes part in the abortive adenylation cycle (covalent binding of AMP, transadenylation of the nick, and dissociation). At low concentrations of ATP (<10 microM) and when the DNA nick is sealed with mismatching base pairs (e.g. five adjacent), this superimposition resolves into two kinetic phases, a burst ligation (approximately 0.2 min(-1)) and a subsequent slow ligation (approximately 2x10(-3) min(-1)). The relative rate and extent of each phase depend on the concentrations of ATP and Mg2+. The activation energies of self-adenylation (16.2 kcal.mol(-1)), transadenylation of the nick (0.9 kcal.mol(-1)), and nick-sealing (16.3-18.8 kcal.mol(-1)) were determined for several DNA substrates. The low activation energy of transadenylation implies that the transfer of AMP to the terminal DNA phosphate is a spontaneous reaction, and that the T4 DNA ligase-AMP complex is a high-energy intermediate. To summarize current findings in the DNA ligation field, we delineate a kinetic mechanism of T4 DNA ligase catalysis.
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Affiliation(s)
- Alexey V Cherepanov
- Kluyver Department of Biotechnology, Delft University of Technology, The Netherlands
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Cherepanov AV, de Vries S. Kinetic mechanism of the Mg2+-dependent nucleotidyl transfer catalyzed by T4 DNA and RNA ligases. J Biol Chem 2002; 277:1695-704. [PMID: 11687591 DOI: 10.1074/jbc.m109616200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mg(2+)-dependent adenylylation of the T4 DNA and RNA ligases was studied in the absence of a DNA substrate using transient optical absorbance and fluorescence spectroscopy. The concentrations of Mg(2+), ATP, and pyrophosphate were systematically varied, and the results led to the conclusion that the nucleotidyl transfer proceeds according to a two-metal ion mechanism. According to this mechanism, only the di-magnesium-coordinated form Mg(2)ATP(0) reacts with the enzyme forming the covalent complex E.AMP. The reverse reaction (ATP synthesis) occurs between the mono-magnesium-coordinated pyrophosphate form MgP(2)O(7)(2-) and the enzyme.MgAMP complex. The nucleotide binding rate decreases in the sequence ATP(4-) > MgATP(2-) > Mg(2)ATP(0), indicating that the formation of the non-covalent enzyme.nucleotide complex is driven by electrostatic interactions. T4 DNA ligase shows notably higher rates of ATP binding and of subsequent adenylylation compared with RNA ligase, in part because it decreases the K(d) of Mg(2+) for the enzyme-bound Mg(2)ATP(0) more than 10-fold. To elucidate the role of Mg(2+) in the nucleotidyl transfer catalyzed by T4 DNA and RNA ligases, we propose a transition state configuration, in which the catalytic Mg(2+) ion coordinates to both reacting nucleophiles: the lysyl moiety of the enzyme that forms the phosphoramidate bond and the alpha-beta-bridging oxygen of ATP.
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Affiliation(s)
- Alexei V Cherepanov
- Kluyver Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
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