Research Topics
| Shuang yong XuSummaryAffiliation: New England Biolabs Country: USA Publications
Research Grants
| Collaborators
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Detail Information
Publications
Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonucleaseShuang yong Xu
New England Biolabs, Inc, Research Department, 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 41:378-90. 2013..In addition, the engineered ZF nickase is useful for evaluation of off-target sites in vitro before performing cell-based gene modification...- Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579Shuang yong Xu
New England Biolabs, Inc, Ipswich, Massachusetts, USA
J Bacteriol 194:49-60. 2012..A survey of type II and III restriction-modification (R-M) system genes is presented from sequenced B. cereus, Bacillus anthracis, and Bacillus thuringiensis strains... - A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300Shuang yong Xu
New England Biolabs, Inc 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 39:5597-610. 2011..aureus strain SA564, and in restricting phage λ infection when the endonuclease is expressed in E. coli... - Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsIShuang yong Xu
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 35:4608-18. 2007..Top-strand specific nicking variants, Nt.BsrDI and Nt.BtsI, were successfully engineered by combining the catalytic-deficient B subunit with wild-type A subunit... - Cloning of the BssHII restriction-modification system in Escherichia coli : BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifsS Xu
New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 25:3991-4. 1997..BssHII that may be responsible for the recognition of the guanine 5' of the target cytosine. The BssHII restriction endonuclease gene was expressed in E.coli via a T7 expression vector... 
Cloning and expression of the ApaLI, NspI, NspHI, SacI, ScaI, and SapI restriction-modification systems in Escherichia coliS Y Xu
New England Biolabs, Inc, Beverly, MA 01915, USA
Mol Gen Genet 260:226-31. 1998..N4mC modification of ScaI site blocks ScaI digetion. A DNA invertase homolog was found adjacent to the ApaLI restriction-modification system. A DNA transposase subunit homolog was found upstream of the SapI restriction endonuclease gene...- Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificitiesSiu Hong Chan
New England Biolabs, Inc 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 35:6238-48. 2007..The resulting endonucleases will be useful in vitro and in vivo to create ds breaks at specific sites and generate deletions... - Cofactor requirement of HpyAV restriction endonucleaseSiu Hong Chan
Research Department, New England Biolabs, Inc, Ipswich, Massachusetts, United States of America
PLoS ONE 5:e9071. 2010..Helicobacter pylori is the etiologic agent of common gastritis and a risk factor for gastric cancer. It is also one of the richest sources of Type II restriction-modification (R-M) systems in microorganisms... - Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangsPriscilla Hiu Mei Too
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 38:1294-303. 2010.... - Expression and purification of BmrI restriction endonuclease and its N-terminal cleavage domain variantsYongming Bao
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
Protein Expr Purif 58:42-52. 2008..The Cys-containing BmrI192 and BmrI200 nuclease variants may be useful for coupling to other DNA binding elements such as synthetic zinc fingers, thio-containing locked nucleic acids (LNA) or peptide nucleic acids (PNA)... - Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNAPenghua Zhang
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
Protein Expr Purif 69:226-34. 2010..Restriction mapping and run-off DNA sequencing of digested products from the partially purified enzyme indicated that it is an EarI isoschizomer with 6-bp recognition, which we named CatHI (CTCTTC N1/N4)... - Rational design of a chimeric endonuclease targeted to NotI recognition sitePenghua Zhang
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
Protein Eng Des Sel 20:497-504. 2007..The fusion of the BmrI cleavage domain to cleavage-deficient variants of Type II restriction enzymes to generate novel cleavage sites will provide useful tools for DNA manipulation... - Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variantsJames C Samuelson
New England Biolabs, Inc 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 34:796-805. 2006..2 x 10(4) U/mg, a 32-fold increase over variant E156K. A comprehensive analysis indicates that the cleavage specificity of M91V/E156K is relaxed to a small set of 8 bp substrates while retaining activity towards the NotI sequence... 
Targeting DNA 5mCpG sites with chimeric endonucleasesAlexey Fomenkov
New England Biolabs, Inc, 240 County Road Ipswich, MA 01938 2723, USA
Anal Biochem 381:135-41. 2008..Such (5)mCpG-specific endonucleases will be useful to study CpG island modification of the regulatory regions of tumor suppressor genes, and for the construction of cell-specific and tumor-specific modified CpG island databases...- Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificitySiu Hong Chan
New England Biolabs, Inc Ipswich, MA 01938, USA
Nucleic Acids Res 39:1-18. 2011..This review aims at providing an overview of the cleavage mechanisms of Types IIS and IIA REases and LAGLIDADG HEases, the engineering of their nicking variants, and the applications of NEases and nicking HEases... - Cloning of NruI and Sbo13I restriction and modification sstems in E. coli and amino acid sequence comparison of M.NruI and M.Sbo13I with other amino-methyltransferasesZhenyu Zhu
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
BMC Res Notes 3:139. 2010..coli. The NruI restriction endonuclease gene (nruIR) was cloned by PCR and inverse PCR using primers designed from the N-terminal amino acid sequence. The NruI methylase gene (nruIM) was derived by inverse PCR walking... - A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genesRichard J Roberts
New England Biolabs, Beverly, MA 01915, USA
Nucleic Acids Res 31:1805-12. 2003..It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes... - Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA bindingAbigail R Lambert
Graduate Program in Biomolecular Structure and Design, University of Washington, Seattle, WA 98195, USA
Structure 16:558-69. 2008..NotI may represent an evolutionary intermediate between mobile endonucleases (which recognize longer target sites) and canonical restriction endonucleases... - Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificityJames C Samuelson
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
J Mol Biol 319:673-83. 2002..Moreover, cleavage of the GGATCC sequence is no longer detected. This study provides further evidence that laboratory evolution strategies offer a powerful alternative to structure-guided protein design... - PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymesVera Pingoud
Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
J Mol Biol 329:913-29. 2003..These results are discussed in an evolutionary context... - Isolation of BsoBI restriction endonuclease variants with altered substrate specificityZhenyu Zhu
New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
J Mol Biol 330:359-72. 2003..This study demonstrates that endonuclease mutants with altered specificity and non-lethal activity can be evolved towards more active variants using a laboratory evolution strategy... - Engineering strand-specific DNA nicking enzymes from the type IIS restriction endonucleases BsaI, BsmBI, and BsmAIZhenyu Zhu
New England Biolabs, Inc. 32 Tozer Road, Beverly, MA 01915, USA
J Mol Biol 337:573-83. 2004..This work provides strong evidence that some type IIS restriction endonucleases carry two separate active sites. When one of the active sites is inactivated, the type IIS restriction endonuclease may nick only one strand... - Crystal structure of BstYI at 1.85A resolution: a thermophilic restriction endonuclease with overlapping specificities to BamHI and BglIISharon A Townson
Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
J Mol Biol 338:725-33. 2004..This arm substructure may underlie the thermostability of BstYI. We identify putative DNA recognition residues and speculate as to how this enzyme achieves a "relaxed" DNA specificity... - The isolation of strand-specific nicking endonucleases from a randomized SapI expression libraryJames C Samuelson
New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 32:3661-71. 2004..The nature of the amino acid substitutions found in the selected variants provides evidence that SapI may possess two active sites per monomer. This work presents a framework for establishing the mechanism of SapI DNA cleavage... - Cloning of CviPII nicking and modification system from chlorella virus NYs-1 and application of Nt.CviPII in random DNA amplificationSiu-Hong Chan
New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 32:6187-99. 2004..Nt.CviPII was used in combination with Bst DNA polymerase I large fragment to rapidly amplify anonymous DNA from genomic DNA or from a single bacterial colony... - Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequenceSharon A Townson
Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, New York 10029, USA
Structure 13:791-801. 2005..Taken together, the structure reveals a mechanism of degenerate DNA recognition and offers insights into the possibilities and limitations in altering specificities of closely related restriction enzymes... - Cloning of Nt.CviQII nicking endonuclease and its cognate methyltransferase: M.CviQII methylates AG sequencesSiu-Hong Chan
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
Protein Expr Purif 49:138-50. 2006..To our knowledge, M.CviQII is the first adenine methyltransferase that recognizes a dinucleotide. Therefore, M.CviQII may be a useful reagent for blocking endonuclease cleavage when restriction sites overlap with AG sequences... - BstYI bound to noncognate DNA reveals a "hemispecific" complex: implications for DNA scanningSharon A Townson
Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
Structure 15:449-59. 2007..Taken together, the structure provides a snapshot of an enzyme in a "paused" intermediate state that may be part of a more general mechanism of scanning DNA... - Crystal structure of the restriction-modification system control element C.Bcll and mapping of its binding siteMichael R Sawaya
UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, 205 Boyer Hall, Box 951570, Los Angeles, California 90095, USA
Structure 13:1837-47. 2005..The C.Bcll-DNA model proposed suggests that DNA bending might play an important role in gene regulation, and that Glu27 and Asp31 in C.Bcll might function critically in the regulation... - Efficient isolation of targeted Caenorhabditis elegans deletion strains using highly thermostable restriction endonucleases and PCRAguan Wei
Department of Anatomy and Neurobiology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, USA
Nucleic Acids Res 30:e110. 2002..The increased efficiency of this technique makes it more practical for small laboratories to undertake gene knock-out screens... - TspMI, a thermostable isoschizomer of XmaI (5'C/CCGGG3'): characterization and single molecule imaging with DNAVijay Parashar
Department of Microbiology, Panjab University, Chandigarh 160014, India
Appl Microbiol Biotechnol 72:917-23. 2006..5 M trehalose without any activity loss and, hence, is suitable for incorporation in restriction-endonuclease-mediated selective-PCR for various applications...
Research Grants
- Cloning and Engineering of Nicking enzymesShuang yong Xu; Fiscal Year: 2004..abstract_text> ..
- A universal DNA endonucleaseShuang yong Xu; Fiscal Year: 2005..For isothermal applications of the universal nuclease at 50oC-70oC, the nuclease domain will be derived from thermophilic endonucleases. ..
- A Genetic System Able to Screen for Active DNA DemethylationShuang yong Xu; Fiscal Year: 2006..In addition, knowledge of the mechanism of demethylation could be crucial in converting fully differentiated adult stem cells into totipotent stem cells. ..
- Engineering DNA nicking endonucleasesShuang yong Xu; Fiscal Year: 2006..Under Phase II funding, this isothermal amplification method (NEMDA) will be optimized and the sensitivity will be improved. Finally, we will investigate the potential of NEMDA for detections of pathogens and its use in bio-prospecting. ..