Genomes and Genes
Summary: Biologically functional sequences of DNA chemically synthesized in vitro.
- Larsen L, Wassman C, Hatfield G, Lathrop R. Computationally Optimised DNA Assembly of synthetic genes. Int J Bioinform Res Appl. 2008;4:324-36 pubmed..The CODA algorithm and these biological methods enable fast, simple and reliable assemblies of sequence-correct full-length genes. ..
- Xiong A, Yao Q, Peng R, Duan H, Li X, Fan H, et al. PCR-based accurate synthesis of long DNA sequences. Nat Protoc. 2006;1:791-7 pubmed..5 to 12.0 kb, with high G+C content, repetitive sequences or complex secondary structures. The PAS protocol therefore provides a simple, rapid, reliable and relatively inexpensive method for synthesizing long, accurate DNA sequences. ..
- Nálezková M, de Groot A, Graf M, Gans P, Blanchard L. Overexpression and purification of Pyrococcus abyssi phosphopantetheine adenylyltransferase from an optimized synthetic gene for NMR studies. Protein Expr Purif. 2005;39:296-306 pubmed..Circular dichroism and 2D NMR experiments indicate the presence of a well-ordered structure for P. abyssi PPAT and also confirm the existence of this enzyme as a monomer in solution...
- Raymond A, Lovell S, Lorimer D, Walchli J, Mixon M, Wallace E, et al. Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer. BMC Biotechnol. 2009;9:37 pubmed publisher..These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research. ..
- Jo Y, Cheng H, Wang S, Moeckel G, Harris R. Puromycin induces reversible proteinuric injury in transgenic mice expressing cyclooxygenase-2 in podocytes. Nephron Exp Nephrol. 2007;107:e87-94 pubmed..In summary, in transgenic mice with podocyte COX-2 overexpression, PAN increased albuminuria and induced foot process fusion. Thus, increased COX-2 expression increased podocyte susceptibility to further injury. ..
- Gao X, Yo P, Keith A, Ragan T, Harris T. Thermodynamically balanced inside-out (TBIO) PCR-based gene synthesis: a novel method of primer design for high-fidelity assembly of longer gene sequences. Nucleic Acids Res. 2003;31:e143 pubmed..4-0.5 kb. By using the newly developed TBIO method of PCR-based gene synthesis, error-free synthetic genes for the human protein kinases PKB2, S6K1 and PDK1 were obtained with little or no corrective mutagenesis.
- Welch M, Govindarajan S, Ness J, Villalobos A, Gurney A, Minshull J, et al. Design parameters to control synthetic gene expression in Escherichia coli. PLoS ONE. 2009;4:e7002 pubmed publisher..b>Synthetic genes are increasingly used for protein production because sequence information is easier to obtain than the ..
- Young L, Dong Q. Two-step total gene synthesis method. Nucleic Acids Res. 2004;32:e59 pubmed..Additionally, the method is easily amenable to automation. ..
- Au L, Yang F, Yang W, Lo S, Kao C. Gene synthesis by a LCR-based approach: high-level production of leptin-L54 using synthetic gene in Escherichia coli. Biochem Biophys Res Commun. 1998;248:200-3 pubmedb>Synthetic genes are very useful in genetic and protein engineering. Here we propose a general method for construction of synthetic genes...
- Huang M, Ye H, Kuan Y, Li M, Ying J. Integrated two-step gene synthesis in a microfluidic device. Lab Chip. 2009;9:276-85 pubmed publisher..The resulting error rate determined by DNA sequencing was 1 per 250 bp. To our knowledge, this is the first microfluidic device demonstrating integrated two-step gene synthesis. ..
- Cormack B, Bertram G, Egerton M, Gow N, Falkow S, Brown A. Yeast-enhanced green fluorescent protein (yEGFP): a reporter of gene expression in Candida albicans. Microbiology. 1997;143 ( Pt 2):303-11 pubmed..yEGFP3 can be used as a versatile reporter of gene expression in C. albicans and Saccharomyces cerevisiae and the optimized GFP described here should have broad applications in these and other fungal species. ..
- Kim J, White K, Winfree E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol Syst Biol. 2006;2:68 pubmed..Construction of larger synthetic circuits provides a unique opportunity for evaluating model inference, prediction, and design of complex biochemical systems and could be used to control nanoscale devices and artificial cells. ..
- Orjuela K, Amador C, Patarroyo M. Synthetic genes: a tool for identifying human papillomavirus genotypes by hybridization and polymerase chain reaction-based assays. Diagn Microbiol Infect Dis. 2007;59:101-4 pubmed..Overlapping oligonucleotides were designed for HPV-18, HPV-31, HPV-45, and HPV-58 type-specific (TS) sequences. Synthetic HPV viral genes were constructed by 2-step assembly PCR for accurately diagnosing TS HPV infection. ..
- Nagaraj S, Davies S. Inverting amplifier genetic circuit performance. Conf Proc IEEE Eng Med Biol Soc. 2006;1:3142-5 pubmed..Models developed earlier are compared with the experimental results. The circuit does indeed perform as an inverting amplifier. ..
- Marchisio M, Stelling J. Computational design of synthetic gene circuits with composable parts. Bioinformatics. 2008;24:1903-10 pubmed publisher..Our simulations of well-known synthetic circuits agree well with published computational and experimental results. The code is available on request from the authors. ..
- Jayaraj S, Reid R, Santi D. GeMS: an advanced software package for designing synthetic genes. Nucleic Acids Res. 2005;33:3011-6 pubmed..The software has been extensively tested in the design and successful synthesis of over 400 kb of genes, many of which exceeded 5 kb in length. ..
- Zhou X, Cai S, Hong A, You Q, Yu P, Sheng N, et al. Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences. Nucleic Acids Res. 2004;32:5409-17 pubmed..The ability to mass produce these synthetic genes readily will have a significant impact on research in biology and medicine...
- Christ D, Chin J. Engineering Escherichia coli heat-resistance by synthetic gene amplification. Protein Eng Des Sel. 2008;21:121-5 pubmed publisher..While the detailed mechanisms of this resistance remained unclear, our results demonstrate the potential of copy number manipulation for the engineering of organisms. ..
- Fuhrmann M, Oertel W, Berthold P, Hegemann P. Removal of mismatched bases from synthetic genes by enzymatic mismatch cleavage. Nucleic Acids Res. 2005;33:e58 pubmed..coli endonucleases reduced the occurrence of mutations in cloned synthetic gene products. The EMC treatment was successful especially in the removal of deletions and insertions from the primary ligation products. ..
- Tian J, Ma K, Saaem I. Advancing high-throughput gene synthesis technology. Mol Biosyst. 2009;5:714-22 pubmed publisherThe emerging field of synthetic biology is generating insatiable demands for synthetic genes, which far exceed existing gene synthesis capabilities...
- Dymond J, Scheifele L, Richardson S, Lee P, Chandrasegaran S, Bader J, et al. Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course. Genetics. 2009;181:13-21 pubmed publisher..Regular "lab meeting" sessions help prepare them for future roles in laboratory science. ..
- Villalobos A, Ness J, Gustafsson C, Minshull J, Govindarajan S. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics. 2006;7:285 pubmed..Here we introduce a software tool that drastically facilitates the design of synthetic genes. Gene Designer is a stand-alone software for fast and easy design of synthetic DNA segments...
- Wu G, Zheng Y, Qureshi I, Zin H, Beck T, Bulka B, et al. SGDB: a database of synthetic genes re-designed for optimizing protein over-expression. Nucleic Acids Res. 2007;35:D76-9 pubmed..We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index...
- Lorimer D, Raymond A, Walchli J, Mixon M, Barrow A, Wallace E, et al. Gene composer: database software for protein construct design, codon engineering, and gene synthesis. BMC Biotechnol. 2009;9:36 pubmed publisher..In a sister manuscript we present data on how Gene Composer designed genes and protein constructs can result in improved protein production for structural studies. ..
- Kramer B, Fussenegger M. Hysteresis in a synthetic mammalian gene network. Proc Natl Acad Sci U S A. 2005;102:9517-22 pubmed..These findings are consistent with a mathematical model. Synthetic gene networks, which are able to emulate natural gene expression behavior, may foster progress in future gene therapy and tissue engineering initiatives. ..
- Bode M, Khor S, Ye H, Li M, Ying J. TmPrime: fast, flexible oligonucleotide design software for gene synthesis. Nucleic Acids Res. 2009;37:W214-21 pubmed publisher..This program is freely available at http://prime.ibn.a-star.edu.sg. ..
- Wu G, Dress L, Freeland S. Optimal encoding rules for synthetic genes: the need for a community effort. Mol Syst Biol. 2007;3:134 pubmed
- Czar M, Cai Y, Peccoud J. Writing DNA with GenoCAD. Nucleic Acids Res. 2009;37:W40-7 pubmed publisher..Users who elect to create a personal account on the system can customize their workspace by creating their own parts libraries, adding new parts to the libraries, or reusing designs to quickly generate sets of related constructs. ..
- Lin Y, Cheng G, Wang X, Clark T. The use of synthetic genes for the expression of ciliate proteins in heterologous systems. Gene. 2002;288:85-94 pubmed..Construction of synthetic alleles should have practical utility in the development of vaccines against Ichthyophthirius, and at the same time, provide a general method for the expression of ciliate genes in heterologous systems. ..
- Smith H, Hutchison C, Pfannkoch C, Venter J. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A. 2003;100:15440-5 pubmed..One such isolate had exactly the intended sequence. We propose to assemble larger genomes by joining separately assembled 5- to 6-kb segments; approximately 60 such segments would be required for a minimal cellular genome. ..
- Stricker J, Cookson S, Bennett M, Mather W, Tsimring L, Hasty J. A fast, robust and tunable synthetic gene oscillator. Nature. 2008;456:516-9 pubmed publisher..Examination of our refined model suggested the existence of a simplified oscillator design without positive feedback, and we construct an oscillator strain confirming this computational prediction. ..
- Binkowski B, Richmond K, Kaysen J, Sussman M, Belshaw P. Correcting errors in synthetic DNA through consensus shuffling. Nucleic Acids Res. 2005;33:e55 pubmed..Consensus shuffling should facilitate the rapid and accurate synthesis of long DNA sequences. ..
- Rydzanicz R, Zhao X, Johnson P. Assembly PCR oligo maker: a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production. Nucleic Acids Res. 2005;33:W521-5 pubmed..The validity of the program was verified experimentally by synthesizing a 191-nt long DNA molecule using the DNA sequences suggested by the program. ..
- Kudla G, Murray A, Tollervey D, Plotkin J. Coding-sequence determinants of gene expression in Escherichia coli. Science. 2009;324:255-8 pubmed publisher..In our analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness. ..
- Cao Y, Sun P, Fu Y, Bai X, Tian F, Liu X, et al. Formation of virus-like particles from O-type foot-and-mouth disease virus in insect cells using codon-optimized synthetic genes. Biotechnol Lett. 2010;32:1223-9 pubmed publisher..This information should prove useful for the development of more efficient VLP assembly using shorter genes. ..
- Burgess Brown N, Sharma S, Sobott F, Loenarz C, Oppermann U, Gileadi O. Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study. Protein Expr Purif. 2008;59:94-102 pubmed publisher..Recently, improvements in technology have enabled cost-effective production of synthetic genes, making this a feasible alternative. To explore this option, the expression patterns in E...
- Binnie C, Jenish D, Cossar D, Szabo A, Trudeau D, Krygsman P, et al. Expression and characterization of soluble human erythropoietin receptor made in Streptomyces lividans 66. Protein Expr Purif. 1997;11:271-8 pubmed..Specific binding of S. lividans-expressed EPO-R to recombinant human glycosylated EPO was demonstrated using BIAcore (surface plasmon resonance) analysis and native gel shift assays. ..
- Seyrantepe V, Hinek A, Peng J, Fedjaev M, Ernest S, Kadota Y, et al. Enzymatic activity of lysosomal carboxypeptidase (cathepsin) A is required for proper elastic fiber formation and inactivation of endothelin-1. Circulation. 2008;117:1973-81 pubmed publisher..Our results provide the first evidence that CathA acts in vivo as an endothelin-1-inactivating enzyme and strongly confirm a crucial role of this enzyme in effective elastic fiber formation. ..
- Shin J, Yi J, Lee Y, Kim A, Park M, Kim S, et al. Development of artificial chimerical gene regulatory elements specific for cancer gene therapy. Oncol Rep. 2003;10:2063-9 pubmed
- Garbe D, Doto J, Sundaram M. Caenorhabditis elegans lin-35/Rb, efl-1/E2F and other synthetic multivulva genes negatively regulate the anaphase-promoting complex gene mat-3/APC8. Genetics. 2004;167:663-72 pubmed..Loss-of-function alleles of lin-35/Rb and other SynMuv B genes suppress mat-3(ku233) defects by restoring mat-3 mRNA to wild-type levels. Therefore, Rb/E2F complexes appear to repress mat-3 expression. ..
- Pellestor F, Andréo B, Taneja K, Williams B. PNA on human sperm: a new approach for in situ aneuploidy estimation. Eur J Hum Genet. 2003;11:337-41 pubmed..The fast kinetics, stability and high specificity of PNA probes make PNA-based methodologies very valuable for in situ cytogenetic investigations. ..
- Dorsky R, Sheldahl L, Moon R. A transgenic Lef1/beta-catenin-dependent reporter is expressed in spatially restricted domains throughout zebrafish development. Dev Biol. 2002;241:229-37 pubmed..We conclude that our TOP-dGFP reporter line faithfully illustrates domains of beta-catenin activity and enables the identification of responsive cell populations. ..
- Geusz M, Blakely K, Hiler D, Jamasbi R. Elevated mPer1 gene expression in tumor stroma imaged through bioluminescence. Int J Cancer. 2010;126:620-30 pubmed publisher..These results suggest that mPer1 activity may play a localized role in the interactions between cancer and stromal cells. The effects might be exploited clinically by targeting the circadian clock genes of stromal cells. ..
- Li H, Zhuo M, Wang D, Wang A, Cai H, Sun L, et al. Targeted cardiac overexpression of A20 improves left ventricular performance and reduces compensatory hypertrophy after myocardial infarction. Circulation. 2007;115:1885-94 pubmed..Cardiac-specific overexpression of A20 improves cardiac function and inhibits cardiac remodeling, apoptosis, inflammation, and fibrosis after acute myocardial infarction. ..
- Azevedo R, Lohaus R, Srinivasan S, Dang K, Burch C. Sexual reproduction selects for robustness and negative epistasis in artificial gene networks. Nature. 2006;440:87-90 pubmed..Our results suggest that sexual reproduction selects for conditions that favour its own maintenance, a case of evolution forging its own path. ..
- Service R. Biosecurity. Synthetic biologists debate policing themselves. Science. 2006;312:1116 pubmed
- Li L, Pang D, Chen L, Wang T, Nie D, Yan S, et al. Establishment of a transgenic pig fetal fibroblast reporter cell line for monitoring Cre recombinase activity. DNA Cell Biol. 2009;28:303-8 pubmed publisher..The EGFP gene is expressed only after Cre-mediated excision of LoxP-flanked stop sequences. These fetal fibroblast cell lines will be of great value for constructing reporter transgenic pigs. ..
- Marshall E. Genetics. Venter gets down to life's basics. Science. 2002;298:1701 pubmed
- Stanojevic D, Young R. A highly potent artificial transcription factor. Biochemistry. 2002;41:7209-16 pubmed..The specific molecular design employed in the synthesis of ATFs may lead to the development of novel gene-targeting pharmaceuticals for treatment of fatal and chronic diseases. ..
- Signori E, Bagni C, Papa S, Primerano B, Rinaldi M, Amaldi F, et al. A somatic mutation in the 5'UTR of BRCA1 gene in sporadic breast cancer causes down-modulation of translation efficiency. Oncogene. 2001;20:4596-600 pubmed..Thus, characterization of BRCA1 5'UTR and translation efficiency seems to provide new insight into BRCA1 role in breast and ovarian cancer pathogenesis. ..
- Cano C. The multi-epitope polypeptide approach in HIV-1 vaccine development. Genet Anal. 1999;15:149-53 pubmed..A new formulation of TAB9 is currently in pre-clinical studies and is expected to enter clinical trials in 1999. ..
- Jan P, Huang H, Chen H. Expression of a synthesized gene encoding cationic peptide cecropin B in transgenic tomato plants protects against bacterial diseases. Appl Environ Microbiol. 2010;76:769-75 pubmed publisher..05 microg in 50 mg of leaves) were far lower than the S(50) determined in vitro. CB transgenic tomatoes could therefore be a new mode of bioprotection against these two plant diseases with significant agricultural applications. ..
- Miyagawa S, Yamada M, Matsunami K, Koresawa Y, Ikawa M, Okabe M, et al. A synthetic dDAF (CD55) gene based on optimal codon usage for transgenic animals. J Biochem. 2001;129:795-801 pubmed..The sDAF showed a high level of expression in SEC and transgenic mice, suggesting that it will be useful in the development of transgenic pigs with high levels of expression. ..