dna shuffling

Summary

Summary: The use of DNA recombination (RECOMBINATION, GENETIC) to prepare a large gene library of novel, chimeric genes from a population of randomly fragmented DNA from related gene sequences.

Top Publications

  1. Xiong A, Peng R, Liu J, Zhuang J, Qiao Y, Xu F, et al. High efficiency and throughput system in directed evolution in vitro of reporter gene. Appl Microbiol Biotechnol. 2007;74:160-8 pubmed
    In vitro directed evolution, especially with DNA shuffling, is a powerful means in biological studies of protein structure and function, and consequently for industrial applications...
  2. Ryu K, Hwang S, Kim K, Kang J, Lee E. Functionality improvement of fungal lignin peroxidase by DNA shuffling for 2,4-dichlorophenol degradability and H2O2 stability. J Biotechnol. 2008;133:110-5 pubmed
    ..We expect that these results coupled with recombining mutation can be successfully applied to the molecular evolution cycles for screening of LiPs and other oxidative enzymes with improved functionality and stability. ..
  3. Sen S, Venkata Dasu V, Mandal B. Developments in directed evolution for improving enzyme functions. Appl Biochem Biotechnol. 2007;143:212-23 pubmed
    ..In vitro recombination techniques such as DNA shuffling, staggered extension process (StEP), random chimeragenesis on transient templates (RACHITT), iterative ..
  4. Zhou L, Ni Y, Piñeyro P, Sanford B, Cossaboom C, Dryman B, et al. DNA shuffling of the GP3 genes of porcine reproductive and respiratory syndrome virus (PRRSV) produces a chimeric virus with an improved cross-neutralizing ability against a heterologous PRRSV strain. Virology. 2012;434:96-109 pubmed publisher
    Porcine reproductive and respiratory syndrome virus (PRRSV) is an important swine pathogen. Here we applied the DNA shuffling approaches to molecularly breed the PRRSV GP3 gene, a neutralizing antibodies inducer, in an attempt to improve ..
  5. Jézéquel L, Loeper J, Pompon D. Sequence-independent construction of ordered combinatorial libraries with predefined crossover points. Biotechniques. 2008;45:523-32 pubmed publisher
    ..Fragments are finally reassembled using a fusion PCR. The process is illustrated via the construction of a set of mosaic CYP2B enzymes using this highly modular approach. ..
  6. Bernal A, Pan Q, Pollack J, Rose L, Kozik A, Willits N, et al. Functional analysis of the plant disease resistance gene Pto using DNA shuffling. J Biol Chem. 2005;280:23073-83 pubmed
    ..tomato expressing the (a)virulence proteins AvrPto or AvrPtoB. DNA shuffling was used as a combinatorial in vitro genetic approach to dissect the functional regions of Pto...
  7. Wallner M, Stöcklinger A, Thalhamer T, Bohle B, Vogel L, Briza P, et al. Allergy multivaccines created by DNA shuffling of tree pollen allergens. J Allergy Clin Immunol. 2007;120:374-80 pubmed
    ..Fourteen genes of the Bet v 1 family were randomly recombined in vitro by means of DNA shuffling. This library of chimeric proteins was screened for molecules displaying low capacity to induce release of ..
  8. Kurtovic S, Modén O, Shokeer A, Mannervik B. Structural determinants of glutathione transferases with azathioprine activity identified by DNA shuffling of alpha class members. J Mol Biol. 2008;375:1365-79 pubmed
    ..A1-1, A2-2 and A3-3), bovine (A1-1) and rat (A2-2 and A3-3) cDNA sequences was constructed by the method of DNA shuffling. The GST variants were screened in bacterial lysates for activity with the immunosuppressive agent ..
  9. Moose S, Mumm R. Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol. 2008;147:969-77 pubmed publisher

More Information

Publications62

  1. Castle L, Siehl D, Gorton R, Patten P, Chen Y, Bertain S, et al. Discovery and directed evolution of a glyphosate tolerance gene. Science. 2004;304:1151-4 pubmed
    ..Eleven iterations of DNA shuffling improved enzyme efficiency by nearly four orders of magnitude from 0.87 mM-1 min-1 to 8320 mM-1 min-1...
  2. Ranjan R, Patro S, Pradhan B, Kumar A, Maiti I, Dey N. Development and functional analysis of novel genetic promoters using DNA shuffling, hybridization and a combination thereof. PLoS ONE. 2012;7:e31931 pubmed publisher
    ..Both shuffled and hybrid promoters developed in the present study can be used as molecular tools to study the regulation of ectopic gene expression in plants. ..
  3. Hou L. Improved production of ethanol by novel genome shuffling in Saccharomyces cerevisiae. Appl Biochem Biotechnol. 2010;160:1084-93 pubmed publisher
    ..96% compared with the control in very-high-gravity (VHG) fermentations. In total, S3-10 possesses optimized fermentation characteristics, which will be propitious to the development of bioethanol fermentation industry. ..
  4. Tominaga T, Hatakeyama Y. Development of innovative pediocin PA-1 by DNA shuffling among class IIa bacteriocins. Appl Environ Microbiol. 2007;73:5292-9 pubmed
    ..These new and improved DNA-shuffled bacteriocins could prove useful as food additives for inhibiting sour spoilage of dairy products. ..
  5. Ni J, Takehara M, Watanabe H. Heterologous overexpression of a mutant termite cellulase gene in Escherichia coli by DNA shuffling of four orthologous parental cDNAs. Biosci Biotechnol Biochem. 2005;69:1711-20 pubmed
    ..coli harboring the mutant genes was 20-30 fold higher than that of wild-type genes. The mutant enzyme showed high activity against CMC and properties similar to those of the native enzymes. ..
  6. Sun J, Katzenellenbogen J, Zhao H, Katzenellenbogen B. DNA shuffling method for generating estrogen receptor alpha and beta chimeras in yeast. Biotechniques. 2003;34:278-80, 282, 284 passim pubmed
    ..our study of the molecular basis for the estrogen receptor (ER) subtype selectivity of novel ligands, we used DNA shuffling to construct chimeric ERs having ligand binding domains derived from both ER alpha and ER beta...
  7. Maheshri N, Schaffer D. Computational and experimental analysis of DNA shuffling. Proc Natl Acad Sci U S A. 2003;100:3071-6 pubmed
    We describe a computational model of DNA shuffling based on the thermodynamics and kinetics of this process...
  8. Park Y, Ghim S. Enhancement of the activity and pH-performance of chitosanase from Bacillus cereus strains by DNA shuffling. Biotechnol Lett. 2009;31:1463-7 pubmed publisher
    b>DNA shuffling was carried out with two chitosanase genes belonging to glycoside hydrolase family eight from Bacillus cereus KNUC51 and B. cereus KNUC55...
  9. Engler C, Gruetzner R, Kandzia R, Marillonnet S. Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS ONE. 2009;4:e5553 pubmed publisher
  10. Locher C, Paidhungat M, Whalen R, Punnonen J. DNA shuffling and screening strategies for improving vaccine efficacy. DNA Cell Biol. 2005;24:256-63 pubmed
    ..We have used DNA shuffling and screening strategies to develop and improve vaccine candidates against several infectious pathogens ..
  11. Behrendorff J, Johnston W, Gillam E. DNA shuffling of cytochrome P450 enzymes. Methods Mol Biol. 2013;987:177-88 pubmed publisher
    ..This chapter provides a general method for creating libraries of shuffled P450s from two or more related sequences and incorporates several recent improvements to previously published methods. ..
  12. Gao X, Zhao H, Zhang G, He K, Jin Y. Genome shuffling of Clostridium acetobutylicum CICC 8012 for improved production of acetone-butanol-ethanol (ABE). Curr Microbiol. 2012;65:128-32 pubmed publisher
    ..These results demonstrated the potential use of genome shuffling to microbial breeding which were difficult to deal with traditional methods...
  13. Tang S, Le Q, Shim J, Yang S, Auh J, Park C, et al. Enhancing thermostability of maltogenic amylase from Bacillus thermoalkalophilus ET2 by DNA shuffling. FEBS J. 2006;273:3335-45 pubmed
    b>DNA shuffling was used to improve the thermostability of maltogenic amylase from Bacillus thermoalkalophilus ET2...
  14. Yang L, Jiang J, Drouin L, Agbandje McKenna M, Chen C, Qiao C, et al. A myocardium tropic adeno-associated virus (AAV) evolved by DNA shuffling and in vivo selection. Proc Natl Acad Sci U S A. 2009;106:3946-51 pubmed publisher
    ..Thus, direct in vivo panning of capsid libraries is a simple tool for the de-targeting and retargeting of viral vector tissue tropisms facilitated by acquisition of desirable sequences and properties. ..
  15. Xu K, Zhang H, Blumwald E, Xia T. A novel plant vacuolar Na+/H+ antiporter gene evolved by DNA shuffling confers improved salt tolerance in yeast. J Biol Chem. 2010;285:22999-3006 pubmed publisher
    ..In this study, we applied DNA shuffling methodology to generate and recombine the mutations of Arabidopsis thaliana vacuolar Na(+)/H(+) antiporter ..
  16. Rosic N, Huang W, Johnston W, DeVoss J, Gillam E. Extending the diversity of cytochrome P450 enzymes by DNA family shuffling. Gene. 2007;395:40-8 pubmed
    ..The modifications made to the traditional DNA shuffling protocols involved non-random digestion via the use of different combinations of restriction enzymes (REs) ..
  17. Shi D, Wang C, Wang K. Genome shuffling to improve thermotolerance, ethanol tolerance and ethanol productivity of Saccharomyces cerevisiae. J Ind Microbiol Biotechnol. 2009;36:139-47 pubmed publisher
    ..It was found capable of completely utilizing 20% (w/v) glucose at 45-48 degrees C, producing 9.95% (w/v) ethanol, and tolerating 25% (v/v) ethanol stress. ..
  18. Moore G, Maranas C. Predicting out-of-sequence reassembly in DNA shuffling. J Theor Biol. 2002;219:9-17 pubmed
    We present an analysis for calculating the frequency of out-of-sequence reassembly in DNA shuffling experiments...
  19. Ness J, Kim S, Gottman A, Pak R, Krebber A, Borchert T, et al. Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently. Nat Biotechnol. 2002;20:1251-5 pubmed
    ..We performed synthetic shuffling of 15 subtilisin genes and obtained active and highly chimeric enzymes with desirable combinations of properties that we did not obtain by other directed-evolution methods. ..
  20. Müller K, Stebel S, Knall S, Zipf G, Bernauer H, Arndt K. Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution. Nucleic Acids Res. 2005;33:e117 pubmed
    b>DNA shuffling is widely used for optimizing complex properties contained within DNA and proteins...
  21. Fox R. Directed molecular evolution by machine learning and the influence of nonlinear interactions. J Theor Biol. 2005;234:187-99 pubmed
    ..Simulated molecular evolution on a synthetic protein landscape shows the use of machine learning techniques to guide library design can be a powerful addition to library generation methods such as DNA shuffling.
  22. Remans T, Grof C, Ebert P, Schenk P. Functional promoter analysis using an approach based on an in vitro evolution strategy. Biotechniques. 2005;38:209-10, 212, 214-6 pubmed
    ..analysis by applying an in vitro evolution scheme consisting of rounds of error-prone PCR, followed by DNA shuffling and selection of mutant promoter activities...
  23. Craveiro K, Gomes Júnior J, Silva M, Macedo L, Lucena W, Silva M, et al. Variant Cry1Ia toxins generated by DNA shuffling are active against sugarcane giant borer. J Biotechnol. 2010;145:215-21 pubmed publisher
    ..Therefore, we have four genes encoding Cry1Ia12synth variants active against T. l. licus promising for future development of resistant transgenic sugarcane lines. ..
  24. Fox R, Roy A, Govindarajan S, Minshull J, Gustafsson C, Jones J, et al. Optimizing the search algorithm for protein engineering by directed evolution. Protein Eng. 2003;16:589-97 pubmed
    ..A simple genetic algorithm (GA) was used to model the performance of a standard DNA shuffling protocol...
  25. Hu H, Qian J, Chu J, Wang Y, Zhuang Y, Zhang S. DNA shuffling of methionine adenosyltransferase gene leads to improved S-adenosyl-L-methionine production in Pichia pastoris. J Biotechnol. 2009;141:97-103 pubmed publisher
    ..MAT genes from Escherichia coli, Saccharmyces cerevisiae, and Streptomyces spectabilis were recombined by DNA shuffling. The shuffled genes were transformed into P...
  26. Locher C, Heinrichs V, Apt D, Whalen R. Overcoming antigenic diversity and improving vaccines using DNA shuffling and screening technologies. Expert Opin Biol Ther. 2004;4:589-97 pubmed
    ..b>DNA shuffling and screening technologies, also known as MolecularBreeding (Maxygen, Inc...
  27. Fermer C, Andersson I, Nilsson K, Nilsson O. Specificity rescue and affinity maturation of a low-affinity IgM antibody against pro-gastrin-releasing peptide using phage display and DNA shuffling. Tumour Biol. 2004;25:7-13 pubmed
    ..of the present study were to use phage display to rescue the specificity of an IgM antibody and by the use of DNA shuffling to construct a sublibrary from which mutants with higher affinity could be selected...
  28. Koerber J, Jang J, Schaffer D. DNA shuffling of adeno-associated virus yields functionally diverse viral progeny. Mol Ther. 2008;16:1703-9 pubmed publisher
    ..Thus, directed evolution can potentially yield unlimited numbers of new AAV variants with novel gene-delivery properties, and subsequent analysis of these variants can further extend basic knowledge of AAV biology. ..
  29. Rozak D, Bryan P. Offset recombinant PCR: a simple but effective method for shuffling compact heterologous domains. Nucleic Acids Res. 2005;33:e82 pubmed
    b>DNA shuffling and other in vitro recombination strategies have proven highly effective at generating complex libraries for mutagenesis studies...
  30. Keenan R, Siehl D, Gorton R, Castle L. DNA shuffling as a tool for protein crystallization. Proc Natl Acad Sci U S A. 2005;102:8887-92 pubmed
    ..Here, we present a strategy that addresses each of these three parameters simultaneously. Using DNA shuffling to introduce functional sequence variability into a protein of interest, we screened crude lysate supernatants ..
  31. Hou L. Novel methods of genome shuffling in Saccharomyces cerevisiae. Biotechnol Lett. 2009;31:671-7 pubmed publisher
    ..The selected strain obtained after three round genome shuffling not only distinctly improved the resistance to ethanol, but also, increased ethanol yield by up to 13% compared with the control. ..
  32. Parikh M, Matsumura I. Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of beta-fucosidase from beta-galactosidase. J Mol Biol. 2005;352:621-8 pubmed
    ..This sub-discipline was galvanized by the invention of DNA shuffling, a procedure that randomly recombines point mutations in vitro...
  33. Schürmann N, Trabuco L, Bender C, Russell R, Grimm D. Molecular dissection of human Argonaute proteins by DNA shuffling. Nat Struct Mol Biol. 2013;20:818-26 pubmed publisher
    ..We also present a Gateway library of codon-optimized chimeras of human Ago1-Ago4 and molecular evolution analysis software as resources for future investigations into RNA interference sequence-structure-function relationships. ..
  34. Fujii R, Kitaoka M, Hayashi K. RAISE: a simple and novel method of generating random insertion and deletion mutations. Nucleic Acids Res. 2006;34:e30 pubmed
    ..Our findings indicate that the RAISE method can yield unique mutants and may be a powerful technique of protein engineering. ..
  35. Yu L, Pei X, Lei T, Wang Y, Feng Y. Genome shuffling enhanced L-lactic acid production by improving glucose tolerance of Lactobacillus rhamnosus. J Biotechnol. 2008;134:154-9 pubmed publisher
    ..Furthermore, the higher lactic acid concentrations were obtained when the initial glucose concentrations increased to 160 and 200 g/l in batch fermentation. ..
  36. Ferrer M, Martínez Abarca F, Golyshin P. Mining genomes and 'metagenomes' for novel catalysts. Curr Opin Biotechnol. 2005;16:588-93 pubmed
    ..It will enable us to identify which organisms are present, what they do, and how their genetic information can be beneficial to mankind. ..
  37. Sandmann G. Novel carotenoids genetically engineered in a heterologous host. Chem Biol. 2003;10:478-9 pubmed
    ..Diverse carotenoids have been identified, but availability has impeded evaluation of their pharmaceutical potential. Molecular techniques have been developed to produce specific and novel carotenoids with improved biological activities. ..
  38. Zhou Z, Zhang A, Wang J, Chen M, Li R, Yang S, et al. Improving the specific synthetic activity of a penicillin g acylase using DNA family shuffling. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 2003;35:573-9 pubmed
    ..Results showed a recombinant PGA with higher synthetic activity was acquired by the method of DNA shuffling.
  39. Paul S, Ali N, Gayen D, Datta S, Datta K. Molecular breeding of Osfer 2 gene to increase iron nutrition in rice grain. GM Crops Food. 2012;3:310-6 pubmed publisher
    ..Our study suggested that overexpression of rice endogenous ferritin gene is a step ahead toward cisgenic approach and can act as an effective tool for iron biofortification. ..
  40. Qiu L, Xing L, Guo Y, Wang J, Jackson S, Chang R. A platform for soybean molecular breeding: the utilization of core collections for food security. Plant Mol Biol. 2013;83:41-50 pubmed publisher
    ..The efficient utilization of this platform in the future is relying on accurate phenotyping methods, abundant functional markers, high-throughput genotyping platforms, and effective breeding programs. ..
  41. Kramp B, Megens R, Sarabi A, Winkler S, Projahn D, Weber C, et al. Exchange of extracellular domains of CCR1 and CCR5 reveals confined functions in CCL5-mediated cell recruitment. Thromb Haemost. 2013;110:795-806 pubmed publisher
    ..Our data identify confined targetable regions of CCR1 specialised to facilitate CCL5-induced arrest and enhanced responsiveness to the CXCL4-CCL5 heteromer. ..
  42. Yang L, Xiao X. Creation of a cardiotropic adeno-associated virus: the story of viral directed evolution. Virol J. 2013;10:50 pubmed publisher
    ..We further attempted to evolve the AAV using DNA shuffling and in vivo biopanning in a mouse model...
  43. Shao Z, Zhang Y, Feng X, Wang B, Chen J. Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency. PLoS ONE. 2012;7:e33547 pubmed publisher
    ..The findings in this study also provide important clues to better understand the complex dynamics of translational process. ..
  44. Werkman J, Pattanaik S, Yuan L. Directed evolution through DNA shuffling for the improvement and understanding of genes and promoters. Methods Mol Biol. 2011;754:325-42 pubmed publisher
    ..By working within a subspace of homologous sequences, DNA shuffling recombines that subspace...
  45. Cao X, Meng M, Wang Y, Wang C, Hou L. Identification of salt-tolerant gene HOG1 in Torulopsis versatilis. Biotechnol Lett. 2011;33:1449-56 pubmed publisher
    ..versatilis and the mutant T. versatilis, respectively, play an important role for the osmo-adaption mechanism of the T. versatilis used in soy-sauce fermentation. ..
  46. Chaparro Riggers J, Loo B, Polizzi K, Gibbs P, Tang X, Nelson M, et al. Revealing biases inherent in recombination protocols. BMC Biotechnol. 2007;7:77 pubmed
    The recombination of homologous genes is an effective protein engineering tool to evolve proteins. DNA shuffling by gene fragmentation and reassembly has dominated the literature since its first publication, but this fragmentation-based ..
  47. Tian Y, Xu J, Xiong A, Zhao W, Fu X, Peng R, et al. Improvement of glyphosate resistance through concurrent mutations in three amino acids of the Ochrobactrum 5-enopyruvylshikimate-3-phosphate synthase. Appl Environ Microbiol. 2011;77:8409-14 pubmed publisher
    ..of 5-enopyruvylshikimate-3-phosphate synthase from Ochrobactrum anthropi was identified after four rounds of DNA shuffling and screening...
  48. Zhang Y, Liu J, Huang J, Mao Z. Genome shuffling of Propionibacterium shermanii for improving vitamin B12 production and comparative proteome analysis. J Biotechnol. 2010;148:139-43 pubmed publisher
    ..They may be the key enzymes of vitamin B12 biosynthesis. ..
  49. Jones A, Lamsa M, Frandsen T, Spendler T, Harris P, Sloma A, et al. Directed evolution of a maltogenic alpha-amylase from Bacillus sp. TS-25. J Biotechnol. 2008;134:325-33 pubmed publisher
    ..Variants exhibiting improved performance were iteratively recombined using DNA shuffling to create two generations of libraries...
  50. Lin J, Shi B, Shi Q, He Y, Wang M. [Rapid improvement of lipase production in Penicillium expansum by genome shuffling]. Sheng Wu Gong Cheng Xue Bao. 2007;23:672-6 pubmed
  51. Kanayama N, Todo K, Takahashi S, Magari M, Ohmori H. Genetic manipulation of an exogenous non-immunoglobulin protein by gene conversion machinery in a chicken B cell line. Nucleic Acids Res. 2006;34:e10 pubmed
    ..Thus, the gene conversion machinery in DT40 cells will be a useful means to engineer non-Ig proteins by a type of DNA shuffling.
  52. Silverman J, Liu Q, Lu Q, Bakker A, To W, Duguay A, et al. Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nat Biotechnol. 2005;23:1556-61 pubmed
    ..Avimers with sub-nM affinities were obtained against five targets. An avimer that inhibits interleukin 6 with 0.8 pM IC50 in cell-based assays is biologically active in two animal models. ..
  53. Lassner M, McElroy D. Directed molecular evolution: bridging the gap between genomics leads and commercial products. OMICS. 2002;6:153-62 pubmed