1
|
Czarnota J, Masłoń A, Pajura R. Wastewater Treatment Plants as a Source of Malodorous Substances Hazardous to Health, Including a Case Study from Poland. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:5379. [PMID: 37047993 PMCID: PMC10093992 DOI: 10.3390/ijerph20075379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Using Poland as an example, it was shown that 41.6% of the requests for intervention in 2016-2021 by Environmental Protection Inspections were related to odour nuisance. Further analysis of the statistical data confirmed that approximately 5.4% of wastewater treatment plants in the group of municipal facilities were subject to complaints. Detailed identification of the subject of odour nuisance at wastewater treatment plants identified hydrogen sulphide (H2S), ammonia (NH3) and volatile organic compounds (VOCs) as the most common malodorous substances within these facilities. Moreover, the concentrations of hydrogen sulphide and ammonia exceed the reference values for some substances in the air (0.02 mg/m3 for H2S and 0.4 mg/m3 for NH3). A thorough assessment of the properties of these substances made it clear that even in small concentrations they have a negative impact on the human body and the environment, and their degree of nuisance is described as high. In the two WWTPs analysed in Poland (WWTP 1 and WWTP 2), hydrogen sulphide concentrations were in the range of 0-41.86 mg/m3 (Long-Term Exposure Limit for H2S is 7.0 mg/m3), ammonia 0-1.43 mg/m3 and VOCs 0.60-134.79 ppm. The values recognised for H2S cause lacrimation, coughing, olfactory impairment, psychomotor agitation, and swelling of the cornea with photophobia. Recognition of the methods used in practice at WWTPs to reduce and control malodorous emissions indicates the possibility of protecting the environment and human health, but these solutions are ignored in most facilities due to the lack of requirements specified in legislation.
Collapse
|
2
|
Abrosimova LA, Kuznetsov NA, Astafurova NA, Samsonova AR, Karpov AS, Perevyazova TA, Oretskaya TS, Fedorova OS, Kubareva EA. Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA. Biomolecules 2021; 11:1420. [PMID: 34680052 PMCID: PMC8533099 DOI: 10.3390/biom11101420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
Nicking endonucleases (NEs) are enzymes that incise only one strand of the duplex to produce a DNA molecule that is 'nicked' rather than cleaved in two. Since these precision tools are used in genetic engineering and genome editing, information about their mechanism of action at all stages of DNA recognition and phosphodiester bond hydrolysis is essential. For the first time, fast kinetics of the Nt.BspD6I interaction with DNA were studied by the stopped-flow technique, and changes of optical characteristics were registered for the enzyme or DNA molecules. The role of divalent metal cations was estimated at all steps of Nt.BspD6I-DNA complex formation. It was demonstrated that divalent metal ions are not required for the formation of a non-specific complex of the protein with DNA. Nt.BspD6I bound five-fold more efficiently to its recognition site in DNA than to a random DNA. DNA bending was confirmed during the specific binding of Nt.BspD6I to a substrate. The optimal size of Nt.BspD6I's binding site in DNA as determined in this work should be taken into account in methods of detection of nucleic acid sequences and/or even various base modifications by means of NEs.
Collapse
Affiliation(s)
- Liudmila A. Abrosimova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Natalia A. Astafurova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | | | - Andrey S. Karpov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | - Tatiana A. Perevyazova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya Str. 3, 142290 Puschino, Russia;
| | - Tatiana S. Oretskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (T.S.O.); (E.A.K.)
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (T.S.O.); (E.A.K.)
| |
Collapse
|
3
|
FRET probe-based antibacterial susceptibility testing (F-AST) by detection of bacterial nucleases released by antibiotic-induced lysis. Biosens Bioelectron 2019; 130:225-229. [DOI: 10.1016/j.bios.2019.01.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 11/21/2022]
|
4
|
Rosta E, Yang W, Hummer G. Calcium inhibition of ribonuclease H1 two-metal ion catalysis. J Am Chem Soc 2014; 136:3137-44. [PMID: 24499076 PMCID: PMC3985467 DOI: 10.1021/ja411408x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Indexed: 01/05/2023]
Abstract
Most phosphate-processing enzymes require Mg(2+) as a cofactor to catalyze nucleotide cleavage and transfer reactions. Ca(2+) ions inhibit many of these enzymatic activities, despite Ca(2+) and Mg(2+) having comparable binding affinities and overall biological abundances. Here we study the molecular details of the calcium inhibition mechanism for phosphodiester cleavage, an essential reaction in the metabolism of nucleic acids and nucleotides, by comparing Ca(2+)- and Mg(2+) catalyzed reactions. We study the functional roles of the specific metal ion sites A and B in enabling the catalytic cleavage of an RNA/DNA hybrid substrate by B. halodurans ribonuclease (RNase) H1 using hybrid quantum-mechanics/molecular mechanics (QM/MM) free energy calculations. We find that Ca(2+) substitution of either of the two active-site Mg(2+) ions substantially increases the height of the reaction barrier and thereby abolishes the catalytic activity. Remarkably, Ca(2+) at the A site is inactive also in Mg(2+)-optimized active-site structures along the reaction path, whereas Mg(2+) substitution recovers activity in Ca(2+)-optimized structures. Geometric changes resulting from Ca(2+) substitution at metal ion site A may thus be a secondary factor in the loss of catalytic activity. By contrast, at metal ion site B geometry plays a more important role, with only a partial recovery of activity after Mg(2+) substitution in Ca(2+)-optimized structures. Ca(2+)-substitution also leads to a change in mechanism, with deprotonation of the water nucleophile requiring a closer approach to the scissile phosphate, which in turn increases the barrier. As a result, Ca(2+) is less efficient in activating the water. As a likely cause for the different reactivities of Mg(2+) and Ca(2+) ions in site A, we identify differences in charge transfer to the ions and the associated decrease in the pKa of the oxygen nucleophile attacking the phosphate group.
Collapse
Affiliation(s)
- Edina Rosta
- Laboratory
of Chemical Physics, National Institute of
Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Wei Yang
- Laboratory
of Molecular Biology, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Gerhard Hummer
- Laboratory
of Chemical Physics, National Institute of
Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, 60438 Frankfurt am Main, Germany
| |
Collapse
|
5
|
Qing Z, He X, Qing T, Wang K, Shi H, He D, Zou Z, Yan L, Xu F, Ye X, Mao Z. Poly(thymine)-templated fluorescent copper nanoparticles for ultrasensitive label-free nuclease assay and its inhibitors screening. Anal Chem 2013; 85:12138-43. [PMID: 24236868 DOI: 10.1021/ac403354c] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Noble-metal fluorescent nanoparticles have attracted considerable interest on account of their excellent properties and potential applicable importance in many fields. Particularly, we recently found that poly(thymine) (poly T) could template the formation of fluorescent copper nanoparticles (CuNPs), offering admirable potential as novel functional biochemical probes. However, exploration of poly T-templated CuNPs for application is still at a very early stage. We report herein for the first example to develop a novel ultrasensitive label-free method for the nuclease (S1 nuclease as a model system) assay, and its inhibitors screening using the poly T-templated fluorescent CuNPs. In this assay, the signal reporter of poly T of 30 mer (T30) kept the original long state in the absence of nuclease, which could effectively template the formation of fluorescent CuNPs. In the presence of nuclease, poly T was digested to mono- or oligonucleotide fragments with decrease of fluorescence. The proposed method was low-cost and simple in its operation without requirement for complex labeling of probe DNA or sophisticated synthesis of the fluorescent compound. The assay process was very rapid with only 5 min for the formation of fluorescent CuNPs. The capabilities for target detection from complex fluids and screening of nuclease inhibitors were verified. A high sensitivity exhibited with a detectable minimum concentration of 5 × 10(-7) units μL(-1) S1 nuclease, which was about 1-4 orders of magnitude more sensitive than the developed approaches.
Collapse
Affiliation(s)
- Zhihe Qing
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, P. R. China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Khazanov N, Marcovitz A, Levy Y. Asymmetric DNA-search dynamics by symmetric dimeric proteins. Biochemistry 2013; 52:5335-44. [PMID: 23866074 DOI: 10.1021/bi400357m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We focus on dimeric DNA-binding proteins from two well-studied families: orthodox type II restriction endonucleases (REs) and transcription factors (TFs). Interactions of the protein's recognition sites with the DNA and, particularly, the contribution of each of the monomers to one-dimensional (1D) sliding along nonspecific DNA were studied using computational tools. Coarse-grained molecular dynamics simulations of DNA scanning by various TFs and REs provide insights into how the symmetry of a homodimer can be broken while they nonspecifically interact with DNA. The characteristics of protein sliding along DNA, such as the average sliding length, partitioning between 1D and 3D search, and the one-dimensional diffusion coefficient D1, strongly depend on the salt concentration, which in turn affects the probability of the two monomers adopting a cooperative symmetric sliding mechanism. Indeed, we demonstrate that maximal DNA search efficiency is achieved when the protein adopts an asymmetric search mode in which one monomer slides while its partner hops. We find that proteins classified as TFs have a higher affinity for the DNA, longer sliding lengths, and an increased probability of symmetric sliding in comparison with REs. Moreover, TFs can perform their biological function over a much wider range of salt concentrations than REs. Our results demonstrate that the different biological functions of DNA-binding proteins are related to the different nonspecific DNA search mechanisms they adopt.
Collapse
Affiliation(s)
- Netaly Khazanov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | |
Collapse
|
7
|
Kielkowski P, Brock NL, Dickschat JS, Hocek M. Nucleobase protection strategy for gene cloning and expression. Chembiochem 2013; 14:801-4. [PMID: 23532949 DOI: 10.1002/cbic.201300127] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Indexed: 12/20/2022]
Abstract
Protecting group chemistry meets molecular biology: Chemically modified dATP carrying a bulky triethylsilylethynyl group was used in a PCR-based synthesis of a gene internally protected against cleavage by restriction endonucleases. The unmodified flanking regions were cleaved for cloning into a plasmid which was replicated by E. coli, and used for protein production.
Collapse
Affiliation(s)
- Pavel Kielkowski
- Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | | | | | | |
Collapse
|
8
|
Kim S, Broströmer E, Xing D, Jin J, Chong S, Ge H, Wang S, Gu C, Yang L, Gao YQ, Su XD, Sun Y, Xie XS. Probing allostery through DNA. Science 2013; 339:816-9. [PMID: 23413354 DOI: 10.1126/science.1229223] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which-together with molecular dynamics simulations-suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.
Collapse
Affiliation(s)
- Sangjin Kim
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
A sequence-specific nicking endonuclease from streptomyces: purification, physical and catalytic properties. ISRN BIOCHEMISTRY 2013; 2013:287158. [PMID: 25937959 PMCID: PMC4392989 DOI: 10.1155/2013/287158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 07/17/2013] [Indexed: 11/18/2022]
Abstract
A sequence-specific nicking endonuclease from Streptomyces designated as DC13 was purified to near homogeneity. Starting with 30 grams of wet cells, the enzyme was purified by ammonium sulfate fractionation, DEAE cellulose, and phenyl-Sepharose chromatography. The purified protein had a specific activity 1000 units/mg and migrated on SDS-PAGE gel with an estimated molecular weight of 71 kDa. Determination of subunit composition by gel filtration chromatography indicated that the native enzyme is a monomer. When incubated with different DNA substrates including pBluescript II KS, pUC118, pET-15b, and pET-26b, the enzyme converted these supercoiled plasmids to a mixture of open circular and linear DNA products, with the open circular DNA as the major cleavage product. Analysis of the kinetic of DNA cleavage showed that the enzyme appeared to cleave super-coiled plasmid in two distinct steps: a rapid cleavage of super-coiled plasmid to an open circular DNA followed a much slower step to linear DNA. The DNA cleavage reaction of the enzyme required Mg(2+) as a cofactor. Based on the monomeric nature of the enzyme, the kinetics of DNA cleavage exhibited by the enzyme, and cofactor requirement, it is suggested here that the purified enzyme is a sequence-specific nicking endonuclease that is similar to type IIS restriction endonuclease.
Collapse
|
10
|
Smith RM, Jacklin AJ, Marshall JJT, Sobott F, Halford SE. Organization of the BcgI restriction-modification protein for the transfer of one methyl group to DNA. Nucleic Acids Res 2012; 41:405-17. [PMID: 23147004 PMCID: PMC3592466 DOI: 10.1093/nar/gks1000] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Type IIB restriction–modification protein BcgI contains A and B subunits in a
2:1 ratio: A has the active sites for both endonuclease and methyltransferase functions
while B recognizes the DNA. Like almost all Type IIB systems, BcgI needs two unmethylated
sites for nuclease activity; it cuts both sites upstream and downstream of the recognition
sequence, hydrolyzing eight phosphodiester bonds in a single synaptic complex. This
complex may incorporate four A2B protomers to give the eight catalytic centres
(one per A subunit) needed to cut all eight bonds. The BcgI recognition sequence contains
one adenine in each strand that can be N6-methylated. Although most DNA
methyltransferases operate at both unmethylated and hemi-methylated sites, BcgI
methyltransferase is only effective at hemi-methylated sites, where the nuclease component
is inactive. Unlike the nuclease, the methyltransferase acts at solitary sites,
functioning catalytically rather than stoichiometrically. Though it transfers one methyl
group at a time, presumably through a single A subunit, BcgI methyltransferase can be
activated by adding extra A subunits, either individually or as part of A2B
protomers, which indicates that it requires an assembly containing at least two
A2B units.
Collapse
Affiliation(s)
- Rachel M Smith
- The DNA-protein Interactions Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | | | | | | | | |
Collapse
|
11
|
Smith RM, Marshall JJT, Jacklin AJ, Retter SE, Halford SE, Sobott F. Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA. Nucleic Acids Res 2012; 41:391-404. [PMID: 23147005 PMCID: PMC3592470 DOI: 10.1093/nar/gks1023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Type IIB restriction-modification systems, such as BcgI, feature a single protein with
both endonuclease and methyltransferase activities. Type IIB nucleases require two
recognition sites and cut both strands on both sides of their unmodified sites. BcgI cuts
all eight target phosphodiester bonds before dissociation. The BcgI protein contains A and
B polypeptides in a 2:1 ratio: A has one catalytic centre for each activity; B recognizes
the DNA. We show here that BcgI is organized as A2B protomers, with B at its
centre, but that these protomers self-associate to assemblies containing several
A2B units. Moreover, like the well known FokI nuclease, BcgI bound to its
site has to recruit additional protomers before it can cut DNA. DNA-bound BcgI can
alternatively be activated by excess A subunits, much like the activation of FokI by its
catalytic domain. Eight A subunits, each with one centre for nuclease activity, are
presumably needed to cut the eight bonds cleaved by BcgI. Its nuclease reaction may thus
involve two A2B units, each bound to a recognition site, with two more
A2B units bridging the complexes by protein–protein interactions
between the nuclease domains.
Collapse
Affiliation(s)
- Rachel M Smith
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | | | | | | | | | | |
Collapse
|
12
|
Crouzier L, Dubois C, Wengel J, Veedu RN. Cleavage and protection of locked nucleic acid-modified DNA by restriction endonucleases. Bioorg Med Chem Lett 2012; 22:4836-8. [PMID: 22727669 DOI: 10.1016/j.bmcl.2012.05.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/10/2012] [Accepted: 05/10/2012] [Indexed: 01/30/2023]
Abstract
Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far. We herein for the first time report cleavage by restriction endonuclease of LNA-modified DNA oligonucleotides. The experiments revealed that RsaI is an efficient enzyme capable of recognizing and cleaving LNA-modified DNA oligonucleotides. Furthermore, introduction of LNA nucleotides protects against cleavage by the restriction endonucleases PvuII, PstI, SacI, KpnI and EcoRI.
Collapse
Affiliation(s)
- Lucile Crouzier
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | | | | | | |
Collapse
|
13
|
Kleinstiver BP, Bérubé-Janzen W, Fernandes AD, Edgell DR. Divalent metal ion differentially regulates the sequential nicking reactions of the GIY-YIG homing endonuclease I-BmoI. PLoS One 2011; 6:e23804. [PMID: 21887323 PMCID: PMC3161791 DOI: 10.1371/journal.pone.0023804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 07/26/2011] [Indexed: 01/30/2023] Open
Abstract
Homing endonucleases are site-specific DNA endonucleases that function as mobile genetic elements by introducing double-strand breaks or nicks at defined locations. Of the major families of homing endonucleases, the modular GIY-YIG endonucleases are least understood in terms of mechanism. The GIY-YIG homing endonuclease I-BmoI generates a double-strand break by sequential nicking reactions during which the single active site of the GIY-YIG nuclease domain must undergo a substantial reorganization. Here, we show that divalent metal ion plays a significant role in regulating the two independent nicking reactions by I-BmoI. Rate constant determination for each nicking reaction revealed that limiting divalent metal ion has a greater impact on the second strand than the first strand nicking reaction. We also show that substrate mutations within the I-BmoI cleavage site can modulate the first strand nicking reaction over a 314-fold range. Additionally, in-gel DNA footprinting with mutant substrates and modeling of an I-BmoI-substrate complex suggest that amino acid contacts to a critical GC-2 base pair are required to induce a bottom-strand distortion that likely directs conformational changes for reaction progress. Collectively, our data implies mechanistic roles for divalent metal ion and substrate bases, suggesting that divalent metal ion facilitates the re-positioning of the GIY-YIG nuclease domain between sequential nicking reactions.
Collapse
Affiliation(s)
- Benjamin P. Kleinstiver
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Wesley Bérubé-Janzen
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Andrew D. Fernandes
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, Canada
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada
| | - David R. Edgell
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, Canada
- * E-mail:
| |
Collapse
|
14
|
Kielkowski P, Macíčková-Cahová H, Pohl R, Hocek M. Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102898] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
15
|
Kielkowski P, Macíčková-Cahová H, Pohl R, Hocek M. Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases. Angew Chem Int Ed Engl 2011; 50:8727-30. [DOI: 10.1002/anie.201102898] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 06/30/2011] [Indexed: 12/13/2022]
|
16
|
The reaction mechanism of FokI excludes the possibility of targeting zinc finger nucleases to unique DNA sites. Biochem Soc Trans 2011; 39:584-8. [PMID: 21428944 DOI: 10.1042/bst0390584] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The FokI endonuclease is a monomeric protein with discrete DNA-recognition and catalytic domains. The latter has only one active site so, to cut both strands, the catalytic domains from two monomers associate to form a dimer. The dimer involving a monomer at the recognition site and another from free solution is less stable than that from two proteins tethered to the same DNA. FokI thus cleaves DNA with two sites better than one-site DNA. The two sites can be immediately adjacent, but they can alternatively be many hundreds of base pairs apart, in either inverted or repeated orientations. The catalytic domain of FokI is often a component of zinc finger nucleases. Typically, the zinc finger domains of two such nucleases are designed to recognize two neighbouring DNA sequences, with the objective of cutting the DNA exclusively between the target sequences. However, this strategy fails to take account of the fact that the catalytic domains of FokI can dimerize across distant sites or even at a solitary site. Additional copies of either target sequence elsewhere in the chromosome must elicit off-target cleavages.
Collapse
|
17
|
Marshall JJT, Smith RM, Ganguly S, Halford SE. Concerted action at eight phosphodiester bonds by the BcgI restriction endonuclease. Nucleic Acids Res 2011; 39:7630-40. [PMID: 21653548 PMCID: PMC3177199 DOI: 10.1093/nar/gkr453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The BcgI endonuclease exemplifies a subset of restriction enzymes, the Type IIB class, which make two double-strand breaks (DSBs) at each copy of their recognition sequence, one either side of the site, to excise the sequence from the remainder of the DNA. In this study, we show that BcgI is essentially inactive when bound to a single site and that to cleave a DNA with one copy of its recognition sequence, it has to act in trans, bridging two separate DNA molecules. We also show that BcgI makes the two DSBs at an individual site in a highly concerted manner. Intermediates cut on one side of the site do not accumulate during the course of the reaction: instead, the DNA is converted straight to the final products cut on both sides. On DNA with two sites, BcgI bridges the sites in cis and then generally proceeds to cut both strands on both sides of both sites without leaving the DNA. The BcgI restriction enzyme can thus excise two DNA segments together, by cleaving eight phosphodiester bonds within a single-DNA binding event.
Collapse
|
18
|
Abstract
The endonucleases from the Type IIB restriction–modification systems differ from all other restriction enzymes. The Type IIB enzymes cleave both DNA strands at specified locations distant from their recognition sequences, like Type IIS nucleases, but they are unique in that they do so on both sides of the site, to liberate the site from the remainder of the DNA on a short duplex. The fact that these enzymes cut DNA at specific locations mark them as Type II systems, as opposed to the Type I enzymes that cut DNA randomly, but in terms of gene organization and protein assembly, most Type IIB restriction–modification systems have more in common with Type I than with other Type II systems. Our current knowledge of the Type IIB systems is reviewed in the present paper.
Collapse
|
19
|
Macíčková-Cahová H, Hocek M. Cleavage of adenine-modified functionalized DNA by type II restriction endonucleases. Nucleic Acids Res 2009; 37:7612-22. [PMID: 19820117 PMCID: PMC2794189 DOI: 10.1093/nar/gkp845] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 09/22/2009] [Accepted: 09/22/2009] [Indexed: 12/31/2022] Open
Abstract
A set of 6 base-modified 2'-deoxyadenosine derivatives was incorporated to diverse DNA sequences by primer extension using Vent (exo-) polymerase and the influence of the modification on cleavage by diverse restriction endonucleases was studied. While 8-substituted (Br or methyl) adenine derivatives were well tolerated by the restriction enzymes and the corresponding sequences were cleaved, the presence of 7-substituted 7-deazaadenine in the recognition sequence resulted in blocking of cleavage by some enzymes depending on the nature and size of the 7-substituent. All sequences with modifications outside of the recognition sequence were perfectly cleaved by all the restriction enzymes. The results are useful both for protection of some sequences from cleavage and for manipulation of functionalized DNA by restriction cleavage.
Collapse
Affiliation(s)
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic
| |
Collapse
|
20
|
Imhof P, Fischer S, Smith JC. Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis. Biochemistry 2009; 48:9061-75. [DOI: 10.1021/bi900585m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Petra Imhof
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Stefan Fischer
- Computational Biochemistry, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Jeremy C. Smith
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
- Oak Ridge National Laboratory, P.O. Box 2008 MS 6309, Oak Ridge, Tennessee 37831-6309
| |
Collapse
|
21
|
Bellamy SRW, Kovacheva YS, Zulkipli IH, Halford SE. Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping. Nucleic Acids Res 2009; 37:5443-53. [PMID: 19596810 PMCID: PMC2760798 DOI: 10.1093/nar/gkp569] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many enzymes acting on DNA require Mg(2+) ions not only for catalysis but also to bind DNA. Binding studies often employ Ca(2+) as a substitute for Mg(2+), to promote DNA binding whilst disallowing catalysis. The SfiI endonuclease requires divalent metal ions to bind DNA but, in contrast to many systems where Ca(2+) mimics Mg(2+), Ca(2+) causes SfiI to bind DNA almost irreversibly. Equilibrium binding by wild-type SfiI cannot be conducted with Mg(2+) present as the DNA is cleaved so, to study the effect of Mg(2+) on DNA binding, two catalytically-inactive mutants were constructed. The mutants bound DNA in the presence of either Ca(2+) or Mg(2+) but, unlike wild-type SfiI with Ca(2+), the binding was reversible. With both mutants, dissociation was slow with Ca(2+) but was in one case much faster with Mg(2+). Hence, Ca(2+) can affect DNA binding differently from Mg(2+). Moreover, SfiI is an archetypal system for DNA looping; on DNA with two recognition sites, it binds to both sites and loops out the intervening DNA. While the dynamics of looping cannot be measured with wild-type SfiI and Ca(2+), it becomes accessible with the mutant and Mg(2+).
Collapse
Affiliation(s)
- Stuart R W Bellamy
- The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | | | | | | |
Collapse
|
22
|
Laurens N, Bellamy SRW, Harms AF, Kovacheva YS, Halford SE, Wuite GJL. Dissecting protein-induced DNA looping dynamics in real time. Nucleic Acids Res 2009; 37:5454-64. [PMID: 19586932 PMCID: PMC2760800 DOI: 10.1093/nar/gkp570] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many proteins that interact with DNA perform or enhance their specific functions by binding simultaneously to multiple target sites, thereby inducing a loop in the DNA. The dynamics and energies involved in this loop formation influence the reaction mechanism. Tethered particle motion has proven a powerful technique to study in real time protein-induced DNA looping dynamics while minimally perturbing the DNA-protein interactions. In addition, it permits many single-molecule experiments to be performed in parallel. Using as a model system the tetrameric Type II restriction enzyme SfiI, that binds two copies of its recognition site, we show here that we can determine the DNA-protein association and dissociation steps as well as the actual process of protein-induced loop capture and release on a single DNA molecule. The result of these experiments is a quantitative reaction scheme for DNA looping by SfiI that is rigorously compared to detailed biochemical studies of SfiI looping dynamics. We also present novel methods for data analysis and compare and discuss these with existing methods. The general applicability of the introduced techniques will further enhance tethered particle motion as a tool to follow DNA-protein dynamics in real time.
Collapse
Affiliation(s)
- Niels Laurens
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stuart R. W. Bellamy
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - August F. Harms
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Yana S. Kovacheva
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stephen E. Halford
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Gijs J. L. Wuite
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
- *To whom correspondence should be addressed. Tel: +31 20 5987987; Fax: +31 205987991;
| |
Collapse
|
23
|
Sanders KL, Catto LE, Bellamy SRW, Halford SE. Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands. Nucleic Acids Res 2009; 37:2105-15. [PMID: 19223323 PMCID: PMC2673415 DOI: 10.1093/nar/gkp046] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Many restriction endonucleases are dimers that act symmetrically at palindromic DNA sequences, with each active site cutting one strand. In contrast, FokI acts asymmetrically at a non-palindromic sequence, cutting ‘top’ and ‘bottom’ strands 9 and 13 nucleotides downstream of the site. FokI is a monomeric protein with one active site and a single monomer covers the entire recognition sequence. To cut both strands, the monomer at the site recruits a second monomer from solution, but it is not yet known which DNA strand is cut by the monomer bound to the site and which by the recruited monomer. In this work, mutants of FokI were used to show that the monomer bound to the site made the distal cut in the bottom strand, whilst the recruited monomer made in parallel the proximal cut in the top strand. Procedures were also established to direct FokI activity, either preferentially to the bottom strand or exclusively to the top strand. The latter extends the range of enzymes for nicking specified strands at specific sequences, and may facilitate further applications of FokI in gene targeting.
Collapse
Affiliation(s)
- Kelly L Sanders
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, UK
| | | | | | | |
Collapse
|
24
|
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]
|
25
|
Bellamy SRW, Mina P, Retter SE, Halford SE. Fidelity of DNA sequence recognition by the SfiI restriction endonuclease is determined by communications between its two DNA-binding sites. J Mol Biol 2008; 384:557-63. [PMID: 18848951 DOI: 10.1016/j.jmb.2008.09.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 09/18/2008] [Accepted: 09/19/2008] [Indexed: 10/21/2022]
Abstract
The SfiI restriction endonuclease is a tetramer in which two subunits form a dimeric unit that contains one DNA binding cleft and the other two subunits contain a second cleft on the opposite side of the protein. Full activity requires both clefts to be filled with its recognition sequence: SfiI has low activity when bound to one site. The ability of SfiI to cleave non-cognate sites, one base pair different from the true site, was initially tested on substrates that lacked specific sites but which contained either one or multiple non-cognate sites. No cleavage of the DNA with one non-cognate site was detected, while a small fraction of the DNA with multiple sites was nicked. The alternative sequences were, however, cleaved in both strands, albeit at low levels, when the DNA also carried either a recognition site for SfiI or the termini generated by SfiI. Further tests employed a mutant of SfiI, altered at the dimer interface, which was known to be more active than wild-type SfiI when bound to a single site. This mutant similarly failed to cleave DNA with one non-cognate site, but cleaved the substrates with multiple non-cognate sites more readily than did the native enzyme. To cleave additional sites, SfiI thus needs to interact concurrently with either two non-cognate sites or one non-cognate and one cognate site (or the termini thereof), yet this arrangement is still restrained from cleaving the alternative site unless the communication pathway between the two DNA-binding clefts is disrupted.
Collapse
Affiliation(s)
- Stuart R W Bellamy
- The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | | | | | | |
Collapse
|
26
|
Catto LE, Bellamy SRW, Retter SE, Halford SE. Dynamics and consequences of DNA looping by the FokI restriction endonuclease. Nucleic Acids Res 2008; 36:2073-81. [PMID: 18276642 PMCID: PMC2346600 DOI: 10.1093/nar/gkn051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Genetic events often require proteins to be activated by interacting with two DNA sites, trapping the intervening DNA in a loop. While much is known about looping equilibria, only a few studies have examined DNA-looping dynamics experimentally. The restriction enzymes that cut DNA after interacting with two recognition sites, such as FokI, can be used to exemplify looping reactions. The reaction pathway for FokI on a supercoiled DNA with two sites was dissected by fast kinetics to reveal, in turn: the initial binding of a protein monomer to each site; the protein–protein association to form the dimer, trapping the loop; the subsequent phosphodiester hydrolysis step. The DNA motion that juxtaposes the sites ought on the basis of Brownian dynamics to take ∼2 ms, but loop capture by FokI took 230 ms. Hence, DNA looping by FokI is rate limited by protein association rather than DNA dynamics. The FokI endonuclease also illustrated activation by looping: it cut looped DNA 400 times faster than unlooped DNA.
Collapse
Affiliation(s)
- Lucy E Catto
- The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | | | | | | |
Collapse
|
27
|
Bellamy SRW, Milsom SE, Kovacheva YS, Sessions RB, Halford SE. A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease. J Mol Biol 2007; 373:1169-83. [PMID: 17870087 PMCID: PMC2082129 DOI: 10.1016/j.jmb.2007.08.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 08/10/2007] [Accepted: 08/14/2007] [Indexed: 11/29/2022]
Abstract
While many Type II restriction enzymes are dimers with a single DNA-binding cleft between the subunits, SfiI is a tetramer of identical subunits. Two of its subunits (a dimeric unit) create one DNA-binding cleft, and the other two create a second cleft on the opposite side of the protein. The two clefts bind specific DNA cooperatively to give a complex of SfiI with two recognition sites. This complex is responsible for essentially all of the DNA-cleavage reactions by SfiI: virtually none is due to the complex with one site. The communication between the DNA-binding clefts was examined by disrupting one of the very few polar interactions in the otherwise hydrophobic interface between the dimeric units: a tyrosine hydroxyl was removed by mutation to phenylalanine. The mutant protein remained tetrameric in solution and could bind two DNA sites. But instead of being activated by binding two sites, like wild-type SfiI, it showed maximal activity when bound to a single site and had a lower activity when bound to two sites. This interaction across the dimer interface thus enforces in wild-type SfiI a cooperative transition between inactive and active states in both dimers, but without this interaction as in the mutant protein, a single dimer can undergo the transition to give a stable intermediate with one inactive dimer and one active dimer.
Collapse
Affiliation(s)
- Stuart R W Bellamy
- The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK.
| | | | | | | | | |
Collapse
|
28
|
|
29
|
Reinhard BM, Sheikholeslami S, Mastroianni A, Alivisatos AP, Liphardt J. Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes. Proc Natl Acad Sci U S A 2007; 104:2667-72. [PMID: 17307879 PMCID: PMC1815239 DOI: 10.1073/pnas.0607826104] [Citation(s) in RCA: 249] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pairs of Au nanoparticles have recently been proposed as "plasmon rulers" based on the dependence of their light scattering on the interparticle distance. Preliminary work has suggested that plasmon rulers can be used to measure and monitor dynamic distance changes over the 1- to 100-nm length scale in biology. Here, we substantiate that plasmon rulers can be used to measure dynamical biophysical processes by applying the ruler to a system that has been investigated extensively by using ensemble kinetic measurements: the cleavage of DNA by the restriction enzyme EcoRV. Temporal resolutions of up to 240 Hz were obtained, and the end-to-end extension of up to 1,000 individual dsDNA enzyme substrates could be simultaneously monitored for hours. The kinetic parameters extracted from our single-molecule cleavage trajectories agree well with values obtained in bulk through other methods and confirm well known features of the cleavage process, such as DNA bending before cleavage. Previously unreported dynamical information is revealed as well, for instance, the degree of softening of the DNA just before cleavage. The unlimited lifetime, high temporal resolution, and high signal/noise ratio make the plasmon ruler a unique tool for studying macromolecular assemblies and conformational changes at the single-molecule level.
Collapse
Affiliation(s)
- Björn M. Reinhard
- Departments of *Physics and
- Chemistry, University of California, Berkeley, CA 94720; and
- Divisions of Physical Biosciences and
| | - Sassan Sheikholeslami
- Chemistry, University of California, Berkeley, CA 94720; and
- Materials Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Alexander Mastroianni
- Chemistry, University of California, Berkeley, CA 94720; and
- Materials Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - A. Paul Alivisatos
- Chemistry, University of California, Berkeley, CA 94720; and
- Materials Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Jan Liphardt
- Departments of *Physics and
- Divisions of Physical Biosciences and
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
30
|
Abstract
Direct and straightforward methods to follow nucleic acid cleavage are needed. A spectrophotometric quadruplex formation assay (QFA) was developed, which allows real-time monitoring of site-specific cleavage of nucleic acids. QFA was applied to study both protein and nucleic acid restriction enzymes, and was demonstrated to accurately determine Michaelis–Menten parameters for the cleavage reaction catalyzed by EcoRI. QFA can be used to study the mechanisms of protein–nucleic acid recognition. QFA is also a useful tool for dissecting individual nicking rates of a double-stranded cleavage.
Collapse
Affiliation(s)
- Besik I Kankia
- Department of Chemistry, University of Minnesota, MN 55455, USA.
| |
Collapse
|
31
|
Hiller DA, Rodriguez AM, Perona JJ. Non-cognate Enzyme–DNA Complex: Structural and Kinetic Analysis of EcoRV Endonuclease Bound to the EcoRI Recognition Site GAATTC. J Mol Biol 2005; 354:121-36. [PMID: 16236314 DOI: 10.1016/j.jmb.2005.09.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 09/14/2005] [Accepted: 09/15/2005] [Indexed: 11/25/2022]
Abstract
The crystal structure of EcoRV endonuclease bound to non-cognate DNA at 2.0 angstroms resolution shows that very small structural adaptations are sufficient to ensure the extreme sequence specificity characteristic of restriction enzymes. EcoRV bends its specific GATATC site sharply by 50 degrees into the major groove at the center TA step, generating unusual base-base interactions along each individual DNA strand. In the symmetric non-cognate complex bound to GAATTC, the center step bend is relaxed to avoid steric hindrance caused by the different placement of the exocyclic thymine methyl groups. The decreased base-pair unstacking in turn leads to small conformational rearrangements in the sugar-phosphate backbone, sufficient to destabilize binding of crucial divalent metal ions in the active site. A second crystal structure of EcoRV bound to the base-analog GAAUTC site shows that the 50 degrees center-step bend of the DNA is restored. However, while divalent metals bind at high occupancy in this structure, one metal ion shifts away from binding at the scissile DNA phosphate to a position near the 3'-adjacent phosphate group. This may explain why the 10(4)-fold attenuated cleavage efficiency toward GAATTC is reconstituted by less than tenfold toward GAAUTC. Examination of DNA binding and bending by equilibrium and stopped-flow florescence quenching and fluorescence resonance energy transfer (FRET) methods demonstrates that the capacity of EcoRV to bend the GAATTC non-cognate site is severely limited, but that full bending of GAAUTC is achieved at only a threefold reduced rate compared with the cognate complex. Together, the structural and biochemical data demonstrate the existence of distinct mechanisms for ensuring specificity at the bending and catalytic steps, respectively. The limited conformational rearrangements observed in the EcoRV non-cognate complex provide a sharp contrast to the extensive structural changes found in a non-cognate BamHI-DNA crystal structure, thus demonstrating a diversity of mechanisms by which restriction enzymes are able to achieve specificity.
Collapse
Affiliation(s)
- David A Hiller
- Department of Chemistry and Biochemistry, and Interdepartmental Program in Biomolecular Science and Engineering, University of California at Santa Barbara, Santa Barbara, CA 93106-9510, USA
| | | | | |
Collapse
|
32
|
Density functional theory analysis of dimethylphosphate hydrolysis: effect of solvation and nucleophile variation. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2004.10.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
33
|
|
34
|
Abstract
DNA nucleases (DNases) perform a wide variety of important cellular functions and are also very useful for research and in biotechnological applications. Due to the biological and technological importance of DNases and their use in a wide range of applications, DNase activity assays are essential. Traditional DNase assays employ radiolabeled DNA substrates and require separation of the products of the reaction from the unreacted substrate before quantification of enzyme activity. As a consequence, these methods are discontinuous. In this report, we describe a continuous DNase assay based on the differential fluorescence output of a DNA dye ligand called PicoGreen. The assay was developed to characterize a processive dsDNA exonuclease, lambda exonuclease. The assay appears to have general utility as it is also suitable for measuring the DNA digestion activities of a processive helicase/nuclease, RecBCD, a distributive exonuclease, T7 gene 6 exonuclease, and an endonuclease, DNaseI. The benefits of, and limitations to, the method are discussed.
Collapse
Affiliation(s)
- Gökhan Tolun
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, PO Box 016129, Miami, FL 33101-6129, USA
| | | |
Collapse
|