Shuang yong Xu

Summary

Affiliation: New England Biolabs
Country: USA

Publications

  1. pmc Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities
    Siu Hong Chan
    New England Biolabs, Inc 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 35:6238-48. 2007
  2. pmc Cofactor requirement of HpyAV restriction endonuclease
    Siu Hong Chan
    Research Department, New England Biolabs, Inc, Ipswich, Massachusetts, United States of America
    PLoS ONE 5:e9071. 2010
  3. pmc Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs
    Priscilla Hiu Mei Too
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 38:1294-303. 2010
  4. pmc Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI
    John R Horton
    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
    Sci Rep 4:4246. 2014
  5. pmc Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonuclease
    Shuang yong Xu
    New England Biolabs, Inc, Research Department, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 41:378-90. 2013
  6. pmc Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579
    Shuang yong Xu
    New England Biolabs, Inc, Ipswich, Massachusetts, USA
    J Bacteriol 194:49-60. 2012
  7. pmc A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300
    Shuang yong Xu
    New England Biolabs, Inc 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 39:5597-610. 2011
  8. pmc Cloning of the BssHII restriction-modification system in Escherichia coli : BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifs
    S Xu
    New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 25:3991-4. 1997
  9. pmc Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI
    Shuang yong Xu
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 35:4608-18. 2007
  10. ncbi request reprint Cloning and expression of the ApaLI, NspI, NspHI, SacI, ScaI, and SapI restriction-modification systems in Escherichia coli
    S Y Xu
    New England Biolabs, Inc, Beverly, MA 01915, USA
    Mol Gen Genet 260:226-31. 1998

Research Grants

  1. Cloning and Engineering of Nicking enzymes
    Shuang yong Xu; Fiscal Year: 2004
  2. A universal DNA endonuclease
    Shuang yong Xu; Fiscal Year: 2005
  3. A Genetic System Able to Screen for Active DNA Demethylation
    Shuang yong Xu; Fiscal Year: 2006
  4. Engineering DNA nicking endonucleases
    Shuang yong Xu; Fiscal Year: 2006

Collaborators

Detail Information

Publications37

  1. pmc Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities
    Siu 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...
  2. pmc Cofactor requirement of HpyAV restriction endonuclease
    Siu 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...
  3. pmc Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs
    Priscilla Hiu Mei Too
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 38:1294-303. 2010
    ....
  4. pmc Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI
    John R Horton
    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
    Sci Rep 4:4246. 2014
    ..Substitution of Ser41 with alanine (S41A) and cysteine (S41C) resulted in mutants with altered cleavage activity. All 19 Arg42 variants resulted in loss of endonuclease activity. ..
  5. pmc Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonuclease
    Shuang 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...
  6. pmc Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579
    Shuang 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...
  7. pmc A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300
    Shuang 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...
  8. pmc Cloning of the BssHII restriction-modification system in Escherichia coli : BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifs
    S 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...
  9. pmc Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI
    Shuang 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...
  10. ncbi request reprint Cloning and expression of the ApaLI, NspI, NspHI, SacI, ScaI, and SapI restriction-modification systems in Escherichia coli
    S 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...
  11. pmc Expression and purification of BmrI restriction endonuclease and its N-terminal cleavage domain variants
    Yongming 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)...
  12. pmc Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA
    Penghua 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)...
  13. ncbi request reprint Isolation of BsoBI restriction endonuclease variants with altered substrate specificity
    Zhenyu 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...
  14. ncbi request reprint Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity
    James 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...
  15. pmc The isolation of strand-specific nicking endonucleases from a randomized SapI expression library
    James 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...
  16. ncbi request reprint Cloning of Nt.CviQII nicking endonuclease and its cognate methyltransferase: M.CviQII methylates AG sequences
    Siu 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...
  17. ncbi request reprint Targeting DNA 5mCpG sites with chimeric endonucleases
    Alexey 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...
  18. pmc Rational design of a chimeric endonuclease targeted to NotI recognition site
    Penghua 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...
  19. pmc Cloning of CviPII nicking and modification system from chlorella virus NYs-1 and application of Nt.CviPII in random DNA amplification
    Siu 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...
  20. pmc Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants
    James 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...
  21. ncbi request reprint Engineering strand-specific DNA nicking enzymes from the type IIS restriction endonucleases BsaI, BsmBI, and BsmAI
    Zhenyu 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...
  22. pmc Increasing cleavage specificity and activity of restriction endonuclease KpnI
    Kommireddy Vasu
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India, Department of Chemistry, New York University, NY, USA, Department of Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany, New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA and Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
    Nucleic Acids Res 41:9812-24. 2013
    ..Our results show that active site plasticity in coordinating different metal ions is related to KpnI promiscuous activity, and tinkering the metal ion coordination is a plausible way to reduce promiscuous activity of metalloenzymes. ..
  23. pmc Structure determination and biochemical characterization of a putative HNH endonuclease from Geobacter metallireducens GS-15
    Shuang yong Xu
    New England Biolabs, Inc Research Department, Ipswich, Massachusetts, United States of America
    PLoS ONE 8:e72114. 2013
    ..The preferred substrate appears to be acid and heat-treated DNA with AP sites, suggesting Gmet_0936 may be a DNA repair enzyme...
  24. pmc The role of the methyltransferase domain of bifunctional restriction enzyme RM.BpuSI in cleavage activity
    Arthur Sarrade-Loucheur
    New England Biolabs, Inc, Ipswich, Massachusetts, United States of America
    PLoS ONE 8:e80967. 2013
    ..The present study underscores the role of the MTase domain as facilitator of efficient cleavage activity for RM.BpuSI. ..
  25. pmc Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity
    Siu 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...
  26. pmc A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
    Richard 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...
  27. pmc 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-methyltransferases
    Zhenyu 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...
  28. pmc Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNA
    Alice Gutjahr
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 42:e77. 2014
    ..Gamma was confirmed by mutagenesis. We found that the wild-type enzyme N.ϕGamma prefers to nick 5mCG-modified DNA in Ni2+ buffer even though the nicking activity is sub-optimal compared to the activity in Mg2+ buffer...
  29. pmc Characterization of cleavage intermediate and star sites of RM.Tth111II
    Zhenyu Zhu
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Sci Rep 4:3838. 2014
    ..We cloned and sequenced a number of Tth111II star sites which are 1-bp different from the cognate sites. A biochemical pathway is proposed for the restriction and methylation activities of Tth111II. ..
  30. ncbi request reprint BstYI bound to noncognate DNA reveals a "hemispecific" complex: implications for DNA scanning
    Sharon 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...
  31. ncbi request reprint Crystal structure of BstYI at 1.85A resolution: a thermophilic restriction endonuclease with overlapping specificities to BamHI and BglII
    Sharon 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...
  32. pmc Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding
    Abigail 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...
  33. ncbi request reprint Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence
    Sharon 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...
  34. ncbi request reprint 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 enzymes
    Vera 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...
  35. ncbi request reprint Crystal structure of the restriction-modification system control element C.Bcll and mapping of its binding site
    Michael 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...
  36. pmc Efficient isolation of targeted Caenorhabditis elegans deletion strains using highly thermostable restriction endonucleases and PCR
    Aguan 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...
  37. ncbi request reprint TspMI, a thermostable isoschizomer of XmaI (5'C/CCGGG3'): characterization and single molecule imaging with DNA
    Vijay 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 Grants4

  1. Cloning and Engineering of Nicking enzymes
    Shuang yong Xu; Fiscal Year: 2004
    ..abstract_text> ..
  2. A universal DNA endonuclease
    Shuang yong Xu; Fiscal Year: 2005
    ..For isothermal applications of the universal nuclease at 50oC-70oC, the nuclease domain will be derived from thermophilic endonucleases. ..
  3. A Genetic System Able to Screen for Active DNA Demethylation
    Shuang 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. ..
  4. Engineering DNA nicking endonucleases
    Shuang 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. ..