Photocleavable linkage between genotype and phenotype for rapid and efficient recovery of nucleic acids encoding affinity-selected proteins.

Abstract:

:In vitro display technologies, such as mRNA display and DNA display are powerful tools to screen peptides and proteins with desired functions from combinatorial libraries in the fields of directed protein evolution and proteomics. When screening combinatorial libraries of polypeptides (phenotype), each of which is displayed on its gene (genotype), the problem remains, how best to recover the genotype moiety whose phenotype moiety has bound to the desired target. Here, we describe the use of a photocleavable 2-nitrobenzyl linker between genotype (DNA or mRNA) and phenotype (protein) in our DNA and mRNA display systems. This technique allows rapid and efficient recovery of selected nucleic acids by simple UV irradiation at 4 degrees C for 15 min. Further, we confirmed that the photocleavable DNA display and mRNA display systems are useful for in vitro selection of epitope peptides, recombinant antibodies, and drug-receptor interactions. Thus, these improved methods should be useful in therapeutics and diagnostics, e.g., for screening high-affinity binders, such as enzyme inhibitors and recombinant antibodies from random peptide and antibody libraries, as well as for screening drug-protein interactions from cDNA libraries.

journal_name

J Biotechnol

journal_title

Journal of biotechnology

authors

Doi N,Takashima H,Wada A,Oishi Y,Nagano T,Yanagawa H

doi

10.1016/j.jbiotec.2007.07.947

subject

Has Abstract

pub_date

2007-09-15 00:00:00

pages

231-9

issue

3

eissn

0168-1656

issn

1873-4863

pii

S0168-1656(07)01312-0

journal_volume

131

pub_type

杂志文章
  • Improvement of the thermostability and activity of halohydrin dehalogenase from Agrobacterium radiobacter AD1 by engineering C-terminal amino acids.

    abstract::In the current study, a three-tiered mutagenesis strategy was employed to simultaneously improve the thermostability and activity of halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) by engineering the last ten amino acids (Met245∼Glu254) of its C-terminal region. Initially, truncated mutagenesis resul...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.08.013

    authors: Wang X,Han S,Yang Z,Tang L

    更新日期:2015-10-20 00:00:00

  • Replacement of an amino acid residue of cyclodextrin glucanotransferase of Bacillus ohbensis doubles the production of gamma-cyclodextrin.

    abstract::Cyclodextrin glucanotransferase (CGTase; EC 2.4.1.19) produces cyclodextrin (CD) from starch through an intramolecular transglucosylation reaction. To obtain a better understanding of the amylolytic and cyclization mechanisms of CGTase, and furthermore to improve the production of gamma-CD, mutant CGTases were constru...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/0168-1656(94)90214-3

    authors: Sin KA,Nakamura A,Masaki H,Matsuura Y,Uozumi T

    更新日期:1994-02-28 00:00:00

  • Trehalose-6-phosphate synthase as an intrinsic selection marker for plant transformation.

    abstract::Insertion of foreign DNA into plant genomes occurs randomly and with low frequency. Hence, a selectable marker is generally required to identify transgenic plants. Until now, all selection systems have been based on the use of non-plant genes, derived from microorganisms and usually conferring antibiotic or herbicide ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.08.033

    authors: Leyman B,Avonce N,Ramon M,Van Dijck P,Iturriaga G,Thevelein JM

    更新日期:2006-02-10 00:00:00

  • The effects of ROS-mediating oxygen tension on human CD34(+)CD38(-) cells induced into mature dendritic cells.

    abstract::Oxygen tension regulates the biological characteristics of hematopoietic stem and progenitor cells (HSPCs) by modulating intracellular reactive oxygen species (ROS). To better understand oxygen tension mechanism on HSPCs culture, gene expression analysis of human CD34(+)CD38(-) HSPCs was performed using microarrays. T...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2012.01.017

    authors: Fan J,Cai H,Li Q,Du Z,Tan W

    更新日期:2012-04-15 00:00:00

  • Use of adapted Aspergillus niger in the bioleaching of spent refinery processing catalyst.

    abstract::Spent refinery processing catalyst is listed as a hazardous waste; the toxicity characteristic leaching procedure (TCLP) extracts of the catalyst are found to contain heavy metals at concentrations exceeding the regulated levels. In the present investigation, Aspergillus niger was adapted to single metal ions Ni, Mo o...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.07.002

    authors: Santhiya D,Ting YP

    更新日期:2006-01-02 00:00:00

  • Repeated-batch fermentations of xylose and glucose-xylose mixtures using a respiration-deficient Saccharomyces cerevisiae engineered for xylose metabolism.

    abstract::Xylose-fermenting Saccharomyces strains are needed for commercialization of ethanol production from lignocellulosic biomass. Engineered Saccharomyces cerevisiae strains expressing XYL1, XYL2 and XYL3 from Pichia stipitis, however, utilize xylose in an oxidative manner, which results in significantly lower ethanol yiel...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2010.09.962

    authors: Kim SR,Lee KS,Choi JH,Ha SJ,Kweon DH,Seo JH,Jin YS

    更新日期:2010-11-01 00:00:00

  • Generation of protective immune response against anthrax by oral immunization with protective antigen plant-based vaccine.

    abstract::In concern with frequent recurrence of anthrax in endemic areas and inadvertent use of its spores as biological weapon, the development of an effective anthrax vaccine suitable for both human and veterinary needs is highly desirable. A simple oral delivery through expression in plant system could offer promising alter...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2014.01.033

    authors: Gorantala J,Grover S,Rahi A,Chaudhary P,Rajwanshi R,Sarin NB,Bhatnagar R

    更新日期:2014-04-20 00:00:00

  • Production of single chain fragment variable (scFv) antibodies in Escherichia coli using the LEX™ bioreactor.

    abstract::For proteome research, antibodies against a growing number of antigens must be generated and characterized. The high throughput generation of antibody fragments, using in vitro selection, requires bacterial expression of antibody fragments. This created a need to establish an expression method to improve the parallel ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2012.07.011

    authors: Miethe S,Meyer T,Wöhl-Bruhn S,Frenzel A,Schirrmann T,Dübel S,Hust M

    更新日期:2013-01-20 00:00:00

  • Effects of purified endo-beta-1,4-xylanases of family 10 and 11 and acetyl xylan esterases on eucalypt sulfite dissolving pulp.

    abstract::Sulfite dissolving pulp from Eucalyptus grandis contained approximately 3.8% O-acetyl-4-O-methylglucuronoxylan with a molar ratio of xylose:4-O-methylglucuronic acid:acetyl group close to 13.6:1:6.2. The effects produced by purified endo-xylanases from two different glycosyl hydrolase families (family 10 and 11) as we...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(00)00324-2

    authors: Christov L,Biely P,Kalogeris E,Christakopoulos P,Prior BA,Bhat MK

    更新日期:2000-10-13 00:00:00

  • Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes.

    abstract::Lentinula edodes, the popular shiitake mushroom, is one of the most important cultivated edible mushrooms. It is used as a food and for medicinal purposes. Here, we present the 46.1 Mb draft genome of L. edodes, comprising 13,028 predicted gene models. The genome assembly consists of 31 scaffolds. Gene annotation prov...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2016.02.032

    authors: Shim D,Park SG,Kim K,Bae W,Lee GW,Ha BS,Ro HS,Kim M,Ryoo R,Rhee SK,Nou IS,Koo CD,Hong CP,Ryu H

    更新日期:2016-04-10 00:00:00

  • An improved fluorescence polarization assay in 5'-nuclease reaction for gene promoter methylation detection.

    abstract::The detection of gene promoter methylation plays increasing roles in personalized medicine. In this study, an improved gene promoter methylation assay based on fluorescence polarization in 5'-nuclease reaction was developed. The novel assay offered a homogeneous annealing and cleavage reaction fully integrated with PC...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.07.003

    authors: Su H,Wu Z,Wang Y,Jiang Y,Qiang S,Cheng H,Liu W,Zhang J

    更新日期:2015-10-10 00:00:00

  • Stability and stabilization of globular proteins in solution.

    abstract::Proteins are multifunctional: their amino acid sequences simultaneously determine folding, function and turnover. Correspondingly, evolution selected for compromises between rigidity (stability) and flexibility (folding/function/degradation), to the result that generally the free energy of stabilization of globular pr...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0168-1656(00)00236-4

    authors: Jaenicke R

    更新日期:2000-05-26 00:00:00

  • Markerless genome editing in Clostridium beijerinckii using the CRISPR-Cpf1 system.

    abstract::CRISPR-Cpf1 is a type V CRISPR system that has recently been exploited for genome engineering purposes. Compared to the well-known Streptococcus pyogenes CRISPR-Cas9 system, the effector protein Cpf1 recognizes T-rich protospacer-adjacent motif (PAM) instead of G-rich PAM (used by CRISPR-Cas9), which could offer a sub...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2018.07.040

    authors: Zhang J,Hong W,Zong W,Wang P,Wang Y

    更新日期:2018-10-20 00:00:00

  • Construction of cellobiose-growing and fermenting Saccharomyces cerevisiae strains.

    abstract::Beta-glucosidase genes of fungal origins were isolated and heterologously expressed in Saccharomyces cerevisiae to enable growth on the disaccharide, cellobiose. To promote secretion of the beta-glucosidases, the genes were fused to the secretion signal of the Trichoderma reesei xyn2 gene and constitutively expressed ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.06.013

    authors: van Rooyen R,Hahn-Hägerdal B,La Grange DC,van Zyl WH

    更新日期:2005-11-21 00:00:00

  • Abiotic stress and ABA-inducible Group 4 LEA from Brassica napus plays a key role in salt and drought tolerance.

    abstract::Late-embryogenesis abundant (LEA) proteins are a family of hydrophilic proteins that form an integral part of desiccation tolerance of seeds. LEA proteins have been also postulated to play a protective role under different abiotic stresses. Their role in abiotic stress tolerance has been well documented for Group 1, 2...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2008.09.014

    authors: Dalal M,Tayal D,Chinnusamy V,Bansal KC

    更新日期:2009-01-15 00:00:00

  • Effective delivery of anti-miRNA DNA oligonucleotides by functionalized gold nanoparticles.

    abstract::MicroRNAs (miRNAs) are gaining recognition as essential regulators involved in many biological processes, and they are emerging as therapeutic targets for treating disease. Here, we introduce a method for effective delivery of anti-miRNA oligonucleotides (AMOs) using functionalized gold nanoparticles (AuNPs). To demon...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2011.07.014

    authors: Kim JH,Yeom JH,Ko JJ,Han MS,Lee K,Na SY,Bae J

    更新日期:2011-09-20 00:00:00

  • New strategy for rapid isolation of stable cell lines from DNA-transformed insect cells using fluorescence activated cell-sorting.

    abstract::A stably transformed insect cell expression system is superior to a baculovirus expression system, since the expression system is sustained and there is no cell lysis, but the isolation of cell lines producing recombinant proteins is time-consuming and laborious. In this study, we developed a technique for the rapid i...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2010.03.011

    authors: Kato T,Yoshizuka K,Park EY

    更新日期:2010-05-17 00:00:00

  • Assessing gene expression variation in normal human tissues using GeneTag, a novel, global, sensitive profiling method.

    abstract::GeneTag is a novel expression profiling method that allows the visualization, quantification and identification of expressed genes-whether known or novel-in any species, tissue or cell type, independent of knowledge of the underlying sequence. Here we describe the application of this method to determine variation of g...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(02)00301-2

    authors: Wong LY,Hafeman A,Boyd VL,Bodeau J,Lazaruk KD,Liew SN,Casey P,Belonogoff V,Bit S,Sumner C,Bredo A,Ho N,Chu E,Olson S,Rabkin S,Maltchenko S,Spier G,Gilbert D,Baumhueter S

    更新日期:2003-03-20 00:00:00

  • A simple analysis system for the estimation of recombination efficiency using fluorescence-activated cell sorting.

    abstract::A simple and accurate analysis system for the estimation of recombination efficiency in vivo using fluorescence-activated cell sorting (FACS) was designed and was subsequently used to compare the efficiency of recombination related to different spacer mutants. F(3) and F(5) mutant sequences were used for Flpe-mediated...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2006.07.027

    authors: Kim MS,Kim WH,Lee GM

    更新日期:2007-01-10 00:00:00

  • Efficient production and recovery of diterpenoid tanshinones in Salvia miltiorrhiza hairy root cultures with in situ adsorption, elicitation and semi-continuous operation.

    abstract::In Salvia miltiorrhiza hairy root cultures, the desired secondary metabolites diterpenoid tanshinones are normally produced at low yields and stored within the roots. To enhance tanshinone production and the secondary product recovery, we employed three means, elicitation with a yeast elicitor (YE), in situ adsorption...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.04.020

    authors: Yan Q,Hu Z,Tan RX,Wu J

    更新日期:2005-10-10 00:00:00

  • Detection and characterization of single biomolecules at surfaces.

    abstract::The investigation of bio-molecules has entered a new age since the development of methodologies capable of studies at the level of single molecules. In biology, most molecules show a complex dynamical behavior, with individual motions and transitions between different states, occurring as highly correlated in space an...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s1389-0352(01)00030-7

    authors: Hinterdorfer P,Schütz G,Kienberger F,Schindler H

    更新日期:2001-11-01 00:00:00

  • Templates in protein de novo design.

    abstract::The de novo design of polypeptide sequences with a three-dimensional structure necessary for many biological functions is limited by the complex folding process, or 'protein folding problem'. This problem can be bypassed through constructing protein-like molecules with a 'built-in' device for intramolecular folding, t...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/0168-1656(95)00010-n

    authors: Tuchscherer G,Mutter M

    更新日期:1995-07-31 00:00:00

  • Improvement of heavy and light chain assembly by modification of heavy chain constant region 1 (CH1): Application for the construction of an anti-paclitaxel fragment antigen-binding (Fab) antibody.

    abstract::Formation of disulfide bonds between heavy and light chains is challenge for production of recombinant immunoglobulin G (IgG) and fragment antigen-binding (Fab). Insufficient formation of the bond influences productive yield and quality of recombinant IgG and Fab. To investigate how amino acid sequences of the first h...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2018.10.009

    authors: Yusakul G,Sakamoto S,Tanaka H,Morimoto S

    更新日期:2018-12-20 00:00:00

  • Two-stage cultures for the production of astaxanthin from Haematococcus pluvialis.

    abstract::A two-stage culture system was established for the production of astaxanthin from Haematococcus pluvialis. In a first stage green vegetative cells were produced in semicontinuous cultures maintained with daily renewal rates between 10 and 40%. The steady-state cell density decreased with increasing renewal rates. High...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(01)00289-9

    authors: Fábregas J,Otero A,Maseda A,Domínguez A

    更新日期:2001-07-26 00:00:00

  • Innovative use of Mucuna monosperma (Wight) callus cultures for continuous production of melanin by using statistically optimized biotransformation medium.

    abstract::Melanins are predominantly indolic polymers which are having extensive applications in cosmetics, agriculture and medicine. In the present study, optimization of nutritional parameters influencing melanin production by Mucuna monosperma callus cultures was attempted using the response surface methodology (RSM). Standa...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.11.012

    authors: Inamdar S,Joshi S,Bapat V,Jadhav J

    更新日期:2014-01-20 00:00:00

  • Investigation of relationship between lipid and Monascus pigment accumulation by extractive fermentation.

    abstract::Fermented Monascus pigments have been utilized as traditional Chinese medicine and food colorant for thousands of years. Under the limited nitrogen concentration and/or low initial pH 2.5 conditions, it was observed that production of intracellular pigments and accumulation of microbial lipids (high content reaching t...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.08.019

    authors: Wang B,Zhang X,Wu Z,Wang Z

    更新日期:2015-10-20 00:00:00

  • Elicitation studies in cell suspension cultures of Cannabis sativa L.

    abstract::Cannabis sativa L. plants produce a diverse array of secondary metabolites. Cannabis cell cultures were treated with biotic and abiotic elicitors to evaluate their effect on secondary metabolism. Metabolic profiles analysed by (1)H NMR spectroscopy and principal component analysis (PCA) showed variations in some of th...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2009.05.006

    authors: Flores-Sanchez IJ,Pec J,Fei J,Choi YH,Dusek J,Verpoorte R

    更新日期:2009-08-20 00:00:00

  • Analysis of polymer molecular weight distributions in aqueous two-phase systems.

    abstract::The partitioning of proteins and other biomaterials between two aqueous phases containing polyethyleneglycol and dextran is a strong function of the molecular weight of the two polymers. Although both polymers are polydispersed (especially Dx) most theoretical treatments refer only to the average molecular weight (num...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/0168-1656(91)90224-j

    authors: Forciniti D,Hall CK,Kula MR

    更新日期:1991-09-01 00:00:00

  • Mutants of listeriolysin O for enhanced liposomal delivery of macromolecules.

    abstract::Delivery of macromolecules into the cytosolic space of eukaryotic cells is a pressing challenge in biopharmaceutics. Macromolecules are often encapsulated into liposomes for protection and improved distribution, but the their size often induces endocytosis of the vehicle at the target site, leading to degradation of t...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.01.029

    authors: Walls ZF,Goodell S,Andrews CD,Mathis J,Lee KD

    更新日期:2013-04-15 00:00:00

  • Action of three GH51 and one GH54 α-arabinofuranosidases on internally and terminally located arabinofuranosyl branches.

    abstract::The action of three glycoside hydrolase family GH51 and one GH54 α-arabinofuranosidases (ABFs) was studied on polymeric arabinoxylan and arabinoxylooligosaccharides. The substrates covered all possible arabinofuranosyl (Araf) substituents, i.e., terminal and internal α(1→2) and α(1→3)-linked Araf monosubstitutions and...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2016.04.050

    authors: Koutaniemi S,Tenkanen M

    更新日期:2016-07-10 00:00:00