Skip to main content
SpringerLink
Log in

DNA cleavage function of seryl-histidine dipeptide and its application

  • Review Article
  • Published:
Amino Acids Aims and scope Submit manuscript

Summary.

The double-stranded DNA or circular plasmid DNA can be cleaved by the Ser-His dipeptide by hydrolysis of the DNA-phospho-diester bond. The proper sequential order of the amino acids serine and histidine is apparently crucial in its unique cleavage activity as compared to the other di- or tri-peptides containing one of these amino acids. An inverted sequence of this dipeptide to a His-Ser linkage renders the peptide ineffective in the cleavage of DNA. In addition to the DNA cleavage function, Ser-His is also capable of cleaving other molecules, e.g., proteins, esters and RNAs. The cooperative actions of the hydroxyl group and the basic groups in the serine and histidine or related amino acids can be found in contemporary enzymes, such as DNase, serine proteases, lipases, esterases, chymotrypsin, trypsin, and elastase, etc. The Ser-His and related oligopeptides might have played important roles in the evolution of enzyme functions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • H Åström R Strömberg (2004) ArticleTitleSynthesis of New OBAN’s and further studied on positioning of the catalytic group Org Biomol Chem 2 1901–1907 Occurrence Handle15227543 Occurrence Handle10.1039/b403652b Occurrence Handle1:CAS:528:DC%2BD2cXlt1alt78%3D

    Article  PubMed  CAS  Google Scholar 

  • NG Beloglazova MM Fabani MA Zenkova EV Bichenkova NN Polushin VV Sil’nikov KT Douglas VV Vlassov (2004) ArticleTitleSequence-specific artificial ribonucleases. I. Bis-imidazole-containing oligonucleotide conjugates prepared using precursor-based strategy Nucleic Acids Res 13 3887–2897 Occurrence Handle10.1093/nar/gkh702

    Article  Google Scholar 

  • E Boseggia M Gatos L Lucatello F Mancin S Moro M Palumbo C Sissi P Tecilla U Tonellato G Zagotto (2004) ArticleTitleToward efficient Zn(II)-based artificial nucleases J Am Chem Soc 126 4543–4549 Occurrence Handle15070372 Occurrence Handle10.1021/ja039465q Occurrence Handle1:CAS:528:DC%2BD2cXitFyis7c%3D

    Article  PubMed  CAS  Google Scholar 

  • L Brady AM Brzozowski ZS Derewenda E Dodson G Dodson S Tolley JP Turkenburg L Christiansen B Huge-Jensen L Norskov L Thim U Menge (1990) ArticleTitleA serine protease triad forms the catalytic centre of a triacylglycerol lipase Nature 343 767–770 Occurrence Handle2304552 Occurrence Handle10.1038/343767a0 Occurrence Handle1:CAS:528:DyaK3cXhsFCgtr4%3D

    Article  PubMed  CAS  Google Scholar 

  • R Breslow (1991) ArticleTitleHow do imidazole groups catalyze the cleavage of RNA in enzyme models and in enzymes? Evidence from “negative catalysis” Acc Chem Res 24 317–324 Occurrence Handle10.1021/ar00011a001 Occurrence Handle1:CAS:528:DyaK3MXmslequro%3D

    Article  CAS  Google Scholar 

  • M Brzyska A Bacia D Elbaum (2001) ArticleTitleOxidative and hydrolytic properties of β-amyloid Eur J Biochem 268 3443–3454 Occurrence Handle11422374 Occurrence Handle10.1046/j.1432-1327.2001.02248.x Occurrence Handle1:CAS:528:DC%2BD3MXkslWrsro%3D

    Article  PubMed  CAS  Google Scholar 

  • P Carter JA Wells (1988) ArticleTitleDissecting the catalytic triad of a serine protease Nature 332 564–568 Occurrence Handle3282170 Occurrence Handle10.1038/332564a0 Occurrence Handle1:CAS:528:DyaL1cXktVaqtLo%3D

    Article  PubMed  CAS  Google Scholar 

  • MA Catry A Madder (2007) ArticleTitleSynthesis of functionalized nucleosides for incorporation into nucleic acid-based serine protease mimics Molecules 12 114–129 Occurrence Handle17693958 Occurrence Handle1:CAS:528:DC%2BD2sXhsVShu7g%3D

    PubMed  CAS  Google Scholar 

  • JA Contreras M Karlsson T Osterlund H Laurell A Svensson C Holm (1996) ArticleTitleHormone-sensitive lipase is structurally related to acetylcholinesterase, bile salt-stimulated lipase, and several fungal lipases – building of a three-dimensional model for the catalytic domain of hormone-sensitive lipase J Biol Chem 271 31426–31430 Occurrence Handle8940153 Occurrence Handle10.1074/jbc.271.49.31426 Occurrence Handle1:CAS:528:DyaK28Xns1aitbk%3D

    Article  PubMed  CAS  Google Scholar 

  • DR Corey WS Willett GS Coombs CS Craik (1995) ArticleTitleTrypsin specificity increased through substrate-assisted catalysis Biochemistry 34 11521–11527 Occurrence Handle7547882 Occurrence Handle10.1021/bi00036a027 Occurrence Handle1:CAS:528:DyaK2MXns1Cjtrc%3D

    Article  PubMed  CAS  Google Scholar 

  • JA Cowan (2001) ArticleTitleChemical nucleases Curr Opin Chem Biol 5 634–642 Occurrence Handle11738172 Occurrence Handle10.1016/S1367-5931(01)00259-9 Occurrence Handle1:CAS:528:DC%2BD3MXovVCnsbw%3D

    Article  PubMed  CAS  Google Scholar 

  • KR Fox MJ Waring (2001) ArticleTitleHigh resolution footprinting studies of drug-DNA complexes using chemical and enzymatic probes Methods Enzymol 340 412–430 Occurrence Handle11529207 Occurrence Handle10.1016/S0076-6879(01)40434-4 Occurrence Handle1:CAS:528:DC%2BD3MXmslWksLo%3D

    Article  PubMed  CAS  Google Scholar 

  • C Gnaccarini S Peter U Scheffer S Vonhoff S Klussmann MW Göbel (2006) ArticleTitleSite-specific cleavage of RNAby a metal-free artificial nuclease attached to antisense oligonucleotides J Am Chem Soc 128 8063–8067 Occurrence Handle16771522 Occurrence Handle10.1021/ja061036f Occurrence Handle1:CAS:528:DC%2BD28XkvVGgurw%3D

    Article  PubMed  CAS  Google Scholar 

  • GF Joyce (2007) ArticleTitleA glimpse of biology’s first enzyme Science 315 1507–1508 Occurrence Handle17363651 Occurrence Handle10.1126/science.1140736 Occurrence Handle1:CAS:528:DC%2BD2sXjsFOrurY%3D

    Article  PubMed  CAS  Google Scholar 

  • GF Joyce LE Orgel (1993) Prospects for understanding the origin of the RNA world RF Gesteland JF Atkins (Eds) The RNA world Cold Spring Harbor Laboratory Press New York 1–26

    Google Scholar 

  • PM Kane CT Yamashiro DF Wolczyk N Neff M Goebl TH Stevens (1990) ArticleTitleProtein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase Science 250 651–657 Occurrence Handle2146742 Occurrence Handle10.1126/science.2146742 Occurrence Handle1:CAS:528:DyaK3MXitVOrug%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • H Kuhn Y Hu MD Frank-Kamenetskii VV Demidov (2003) ArticleTitleArtifical site-specific DNA-nicking system based on common restriction enzymes assisted by PNA openers Biochemistry 42 4985–4992 Occurrence Handle12718541 Occurrence Handle10.1021/bi020669d

    Article  PubMed  Google Scholar 

  • XH Li Y Ma Y Chen YF Zhao (1997) ArticleTitleRNA cleavage by N-phosphoryl serine in histidine buffer Chin Chem Lett 8 53–56 Occurrence Handle1:CAS:528:DyaK2sXhsV2lt7k%3D

    CAS  Google Scholar 

  • Y Li YF Zhao S Hatfield R Wan Q Zhu X Li M McMills Y Ma J Li KL Brown C He F Liu XZ Chen (2000) ArticleTitleDipeptide seryl-histidine and related oligopeptides cleave DNA, protein, and a carboxyl ester Bioorg Med Chem 8 2675–2680 Occurrence Handle11131157 Occurrence Handle10.1016/S0968-0896(00)00208-X Occurrence Handle1:CAS:528:DC%2BD3cXot12mtL4%3D

    Article  PubMed  CAS  Google Scholar 

  • Y Li S Hatfield J Li M McMills Y Zhao X Chen (2002) ArticleTitleSeryl-histidine as an alternative DNA nicking agent in nick translation yields superior DNA probes and hybridization Bioorg Med Chem 10 667–673 Occurrence Handle11814854 Occurrence Handle10.1016/S0968-0896(01)00339-X Occurrence Handle1:CAS:528:DC%2BD38XovFSmtA%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • WN Lipscomb N Strater (1996) ArticleTitleRecent advances in zinc enzymology Chem Rev 96 2375–2433 Occurrence Handle11848831 Occurrence Handle10.1021/cr950042j Occurrence Handle1:CAS:528:DyaK28Xmt1GisLc%3D

    Article  PubMed  CAS  Google Scholar 

  • X Liu C Cheng C Zhu Y Zhao (2005) ArticleTitleTheoretical study on the binding of L/D Ser/histamine amide with 5′-TpTpdC-3′ J Mol Struct 723 101–104 Occurrence Handle1:CAS:528:DC%2BD2MXktFWiu7k%3D

    CAS  Google Scholar 

  • XQ Liu (2000) ArticleTitleProtein-splicing intein: genetic mobility, origin, and evolution Annu Rev Genet 34 61–76 Occurrence Handle11092822 Occurrence Handle10.1146/annurev.genet.34.1.61 Occurrence Handle1:CAS:528:DC%2BD3MXlvFKruw%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • Ma Y (1996) Ph.D. Dissertation, Department of Chemistry, Tsinghua University

  • A Madder L Li HD Muynck N Farcy D Van Haver F Fant G Vanhoenacker P Sandra AP Davis PJ De Clercq (2002) J Comb Chem 4 552–562 Occurrence Handle12425599 Occurrence Handle10.1021/cc020016g Occurrence Handle1:CAS:528:DC%2BD38XntlOrur0%3D

    Article  PubMed  CAS  Google Scholar 

  • A Nomura Y Sugiura (2004) ArticleTitleSequence-selective and hydrolytic cleavage of DNA by zinc finger mutants J Am Chem Soc 126 15374–15375 Occurrence Handle15563152 Occurrence Handle10.1021/ja045663l Occurrence Handle1:CAS:528:DC%2BD2cXpt1Sktb4%3D

    Article  PubMed  CAS  Google Scholar 

  • FB Perler FQ Davis GE Dean FS Gimble WE Jack N Neff CJ Noren J Thorner M Belfort (1994) Nucleic Acids Res 22 1125–1127 Occurrence Handle8165123 Occurrence Handle10.1093/nar/22.7.1125 Occurrence Handle1:CAS:528:DyaK2cXktVamt7c%3D

    Article  PubMed  CAS  Google Scholar 

  • PR Reddy KS Rao SK Mohan (2004) ArticleTitleCopper(II) complexes containing N,N-donor ligands and dipeptides act as hydrolytic DNA-cleavage agents Chem Biodiv 1 839–851 Occurrence Handle10.1002/cbdv.200490066 Occurrence Handle1:CAS:528:DC%2BD2cXlslehtro%3D

    Article  CAS  Google Scholar 

  • A Roth RR Breaker (1998) ArticleTitleAn amino acid as a cofactor for a catalytic polynucleotide Proc Natl Acad Sci USA 95 6027–6031 Occurrence Handle9600911 Occurrence Handle10.1073/pnas.95.11.6027 Occurrence Handle1:CAS:528:DyaK1cXjtlKhu7Y%3D

    Article  PubMed  CAS  Google Scholar 

  • SW Santoro GF Joyce K Sakthivel S Gramatikova CF Barbas SuffixIII (2000) ArticleTitleRNA cleavage by a DNA enzyme with extended chemical functionality J Am Chem Soc 122 2433–2439 Occurrence Handle11543272 Occurrence Handle10.1021/ja993688s Occurrence Handle1:CAS:528:DC%2BD3cXhsVGhs7w%3D

    Article  PubMed  CAS  Google Scholar 

  • JD Schrag Y Li S Wu M Cygler (1991) ArticleTitleSer-His-Glu triad forms the catalytic site of the lipase from Geotrichum candidum Nature 351 761–764 Occurrence Handle2062369 Occurrence Handle10.1038/351761a0 Occurrence Handle1:CAS:528:DyaK3MXmslCnt7s%3D

    Article  PubMed  CAS  Google Scholar 

  • DS Sigman CHB Chen (1990) ArticleTitleChemical nucleases: new reagents in molecular biology Annu Rev Biochem 59 207–236 Occurrence Handle1695832 Occurrence Handle10.1146/annurev.bi.59.070190.001231 Occurrence Handle1:CAS:528:DyaK3cXlvVOgtbk%3D

    Article  PubMed  CAS  Google Scholar 

  • TA Steitz RG Shulman (1982) ArticleTitleCrystallographic and NMR studies of the serine proteases Annu Rev Biophys Bioeng 11 419–444 Occurrence Handle7049067 Occurrence Handle10.1146/annurev.bb.11.060182.002223 Occurrence Handle1:CAS:528:DyaL38Xks1yhsb8%3D

    Article  PubMed  CAS  Google Scholar 

  • M Sun CJ Zhu B Tan Y Jin YF Zhao (2003) ArticleTitleMolecular modeling of diastereoisomeric aggregates of L/D ser/histamine amide with 5′-TpTpdC-3′ J Mol Modeling 9 84–87 Occurrence Handle1:CAS:528:DC%2BD3sXjvFSmt7w%3D Occurrence Handle10.1007/s00894-002-0114-9

    Article  CAS  Google Scholar 

  • M Sun Y Ma SH Ji H Liu YF Zhao (2004) ArticleTitleMolecular modeling on DNA cleavage activity of seryl-histidine and related dipeptide Bioorg Med Chem Lett 14 3711–3714 Occurrence Handle15203148 Occurrence Handle10.1016/j.bmcl.2004.05.008 Occurrence Handle1:CAS:528:DC%2BD2cXkvFymtb4%3D

    Article  PubMed  CAS  Google Scholar 

  • JL Sussman M Harel F Frolow C Oefner A Goldman L Toker I Silman (1991) ArticleTitleAtomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein Science 253 872–879 Occurrence Handle1678899 Occurrence Handle10.1126/science.1678899 Occurrence Handle1:CAS:528:DyaK3MXlslyitrc%3D

    Article  PubMed  CAS  Google Scholar 

  • Wan R (2000a) Ph.D. Dissertation, Department of Chemistry, Tsinghua University

  • R Wan N Wang G Zhao YF Zhao (2000b) ArticleTitleSeryl-histidine dipeptide side chains effects on its DNA cleavage reaction Chem J Chin Univ 21 1864–1866 Occurrence Handle1:CAS:528:DC%2BD3MXhtleis70%3D

    CAS  Google Scholar 

  • MQ Xu CE Thomas SuffixJr (2005) ArticleTitleRecent advances in protein splicing: manipulating proteins in vitro and in vivo Curr Opin Biotech 16 440–446 Occurrence Handle16026977 Occurrence Handle10.1016/j.copbio.2005.06.012 Occurrence Handle1:CAS:528:DC%2BD2MXntVCqtbo%3D

    Article  PubMed  CAS  Google Scholar 

  • P Yang R Ren M Guo A Song X Meng C Yuan X Zhou H Chen Z Xiong X Gao (2004) ArticleTitleDouble-strand hydrolysis of DNA by a magnesium(II) complex with diethylenetriamine J Biol Inorg Chem 9 495–506 Occurrence Handle15112075 Occurrence Handle10.1007/s00775-004-0548-x Occurrence Handle1:CAS:528:DC%2BD2cXksVSnsbk%3D

    Article  PubMed  CAS  Google Scholar 

  • Z Zhao JG Peacock DA Gubler MA Peterson (2005) ArticleTitlePhotoinduced Bergman cycloaromatization of imidazole-fused enediyne Tetrahedron Lett 46 1373–1375 Occurrence Handle10.1016/j.tetlet.2004.12.136 Occurrence Handle1:CAS:528:DC%2BD2MXos1Sjsw%3D%3D

    Article  CAS  Google Scholar 

  • RG Zhong LJ Zhao YF Zhao (2004) ArticleTitleA QM-MM study on DNA cleavage by seryl-histidine dipeptide Acta Chim Sinica 62 2444–2446 Occurrence Handle1:CAS:528:DC%2BD2MXitlSlsw%3D%3D

    CAS  Google Scholar 

  • CJ Zhu Y Lu HL Du YY Jiang YF Zhao (2004) ArticleTitleA pair of new enantiomeric amides with DNA cleaving function Chem J Chin Univ 25 1065–1068

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. The Key Laboratory of Bioorganic Phosphorus and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, China

    Y. Ma, M. Sun, R. Wan, C. Zhu, Y. Li & Y. Zhao

  2. Departments of Chemistry and Biochemistry and Biomedical Science, Ohio University, Athens, OH, U.S.A.

    X. Chen

  3. The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemistry, Xiamen University, Xiamen, China

    Y. Zhao

Authors
  1. Y. Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. X. Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. R. Wan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. C. Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Y. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Y. Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

Authors’ address: Dr. Yuan Ma, Department of Chemistry, Tsinghua University, Beijing 100084, China

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ma, Y., Chen, X., Sun, M. et al. DNA cleavage function of seryl-histidine dipeptide and its application. Amino Acids 35, 251–256 (2008). https://doi.org/10.1007/s00726-007-0597-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00726-007-0597-x

Search

Navigation