In vitro 'sexual' evolution through the PCR-based staggered extension process (StEP).

Abstract:

:This protocol describes a directed evolution method for in vitro mutagenesis and recombination of polynucleotide sequences. The staggered extension process (StEP) is essentially a modified PCR that uses highly abbreviated annealing and extension steps to generate staggered DNA fragments and promote crossover events along the full length of the template sequence(s). The resulting library of chimeric polynucleotide sequence(s) is subjected to subsequent high-throughput functional analysis. The recombination efficiency of the StEP method is comparable to that of the most widely used in vitro DNA recombination method, DNA shuffling. However, the StEP method does not require DNA fragmentation and can be carried out in a single tube. This protocol can be completed in 4-6 h.

journal_name

Nat Protoc

journal_title

Nature protocols

authors

Zhao H,Zha W

doi

10.1038/nprot.2006.309

subject

Has Abstract

pub_date

2006-01-01 00:00:00

pages

1865-71

issue

4

eissn

1754-2189

issn

1750-2799

pii

nprot.2006.309

journal_volume

1

pub_type

杂志文章
  • Isolation and subsequent analysis of murine lamina propria mononuclear cells from colonic tissue.

    abstract::Studies on colonic cells in the lamina propria (LP) of mice are important for understanding the cellular and immune responses in the gut, especially in inflammatory bowel diseases (such as morbus crohn and colitis ulcerosa). This protocol details a method to isolate LP cells and characterize freshly isolated cells by ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.315

    authors: Weigmann B,Tubbe I,Seidel D,Nicolaev A,Becker C,Neurath MF

    更新日期:2007-01-01 00:00:00

  • Fluorescent Arabidopsis tetrads: a visual assay for quickly developing large crossover and crossover interference data sets.

    abstract::In most organisms, one crossover (CO) event inhibits the chances of another nearby event. The term used to describe this phenomenon is 'CO interference'. Here, we describe a protocol for quickly generating large data sets that are amenable to CO interference analysis in the flowering plant, Arabidopsis thaliana. We em...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.491

    authors: Berchowitz LE,Copenhaver GP

    更新日期:2008-01-01 00:00:00

  • A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor.

    abstract::The systematic mapping of protein interactions by bait-prey techniques, including affinity purification-mass spectrometry or the yeast two-hybrid system, contributes a unique and relevant perspective on the comprehensive picture of cellular machines. We describe here a protocol for statistical analysis of node-and-edg...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.26

    authors: Chiang T,Scholtens D

    更新日期:2009-01-01 00:00:00

  • Directed differentiation of human pluripotent cells to neural crest stem cells.

    abstract::Multipotent neural crest stem cells (NCSCs) have the potential to generate a wide range of cell types including melanocytes; peripheral neurons; and smooth muscle, bone, cartilage and fat cells. This protocol describes in detail how to perform a highly efficient, lineage-specific differentiation of human pluripotent c...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2012.156

    authors: Menendez L,Kulik MJ,Page AT,Park SS,Lauderdale JD,Cunningham ML,Dalton S

    更新日期:2013-01-01 00:00:00

  • Design of a functional cyclic HSV1-TK reporter and its application to PET imaging of apoptosis.

    abstract::Positron emission tomography (PET) is a sensitive and noninvasive imaging method that is widely used to explore molecular events in living subjects. PET can precisely and quantitatively evaluate cellular apoptosis, which has a crucial role in various physiological and pathological processes. In this protocol, we descr...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.048

    authors: Wang Z,Wang F,Hida N,Kiesewetter DO,Tian J,Niu G,Chen X

    更新日期:2015-05-01 00:00:00

  • Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences.

    abstract::This protocol explains how to discover functional signals in genomic sequences by detecting over- or under-represented oligonucleotides (words) or spaced pairs thereof (dyads) with the Regulatory Sequence Analysis Tools (http://rsat.ulb.ac.be/rsat/). Two typical applications are presented: (i) predicting transcription...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.98

    authors: Defrance M,Janky R,Sand O,van Helden J

    更新日期:2008-01-01 00:00:00

  • Design and implementation of in vivo imaging of neural injury responses in the adult Drosophila wing.

    abstract::Live-imaging technology has markedly advanced in the field of neural injury and axon degeneration; however, studies are still predominantly performed in in vitro settings such as cultured neuronal cells or in model organisms such as Caenorhabditis elegans in which axons lack glial wrappings. We recently developed a ne...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.042

    authors: Fang Y,Soares L,Bonini NM

    更新日期:2013-04-01 00:00:00

  • Protocol for the fast chromatin immunoprecipitation (ChIP) method.

    abstract::Chromatin and transcriptional processes are among the most intensively studied fields of biology today. The introduction of chromatin immunoprecipitations (ChIP) represents a major advancement in this area. This powerful method allows researchers to probe specific protein-DNA interactions in vivo and to estimate the d...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.27

    authors: Nelson JD,Denisenko O,Bomsztyk K

    更新日期:2006-01-01 00:00:00

  • Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing.

    abstract::This protocol and the accompanying software program called LEVER (lineage editing and validation) enable quantitative automated analysis of phase-contrast time-lapse images of cultured neural stem cells. Images are captured at 5-min intervals over a period of 5-15 d as the cells proliferate and differentiate. LEVER au...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2011.422

    authors: Winter M,Wait E,Roysam B,Goderie SK,Ali RA,Kokovay E,Temple S,Cohen AR

    更新日期:2011-11-17 00:00:00

  • Cytokinesis-block micronucleus cytome assay.

    abstract::The cytokinesis-block micronucleus cytome assay is a comprehensive system for measuring DNA damage, cytostasis and cytotoxicity. DNA damage events are scored specifically in once-divided binucleated (BN) cells and include (a) micronuclei (MNi), a biomarker of chromosome breakage and/or whole chromosome loss, (b) nucle...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.77

    authors: Fenech M

    更新日期:2007-01-01 00:00:00

  • Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments.

    abstract::Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2016.113

    authors: Jeffries CM,Graewert MA,Blanchet CE,Langley DB,Whitten AE,Svergun DI

    更新日期:2016-11-01 00:00:00

  • Analyzing bacterial extracellular vesicles in human body fluids by orthogonal biophysical separation and biochemical characterization.

    abstract::Gram-negative and Gram-positive bacteria release a variety of membrane vesicles through different formation routes. Knowledge of the structure, molecular cargo and function of bacterial extracellular vesicles (BEVs) is primarily obtained from bacteria cultured in laboratory conditions. BEVs in human body fluids have b...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0236-5

    authors: Tulkens J,De Wever O,Hendrix A

    更新日期:2020-01-01 00:00:00

  • Femtosecond optical transfection of individual mammalian cells.

    abstract::Laser-mediated gene transfection into mammalian cells has recently emerged as a powerful alternative to more traditional transfection techniques. In particular, the use of a femtosecond-pulsed laser operating in the near-infrared (NIR) region has been proven to provide single-cell selectivity, localized delivery, low ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.071

    authors: Antkowiak M,Torres-Mapa ML,Stevenson DJ,Dholakia K,Gunn-Moore FJ

    更新日期:2013-06-01 00:00:00

  • Derivation and characterization of mouse embryonic stem cells from permissive and nonpermissive strains.

    abstract::Mouse embryonic stem cells (mESCs) are key tools for genetic engineering, development of stem cell-based therapies and basic research on pluripotency and early lineage commitment. However, successful derivation of germline-competent embryonic stem cell lines has, until recently, been limited to a small number of inbre...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2014.030

    authors: Czechanski A,Byers C,Greenstein I,Schrode N,Donahue LR,Hadjantonakis AK,Reinholdt LG

    更新日期:2014-03-01 00:00:00

  • A protocol for efficiently retrieving and characterizing flanking sequence tags (FSTs) in Brachypodium distachyon T-DNA insertional mutants.

    abstract::Brachypodium distachyon is emerging as a new model system for bridging research into temperate cereal crops, such as wheat and barley, and for promoting research in novel biomass grasses. Here, we provide an adapter ligation PCR protocol that allows the large-scale characterization of T-DNA insertions into the genome ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.32

    authors: Thole V,Alves SC,Worland B,Bevan MW,Vain P

    更新日期:2009-01-01 00:00:00

  • Pulsed-field gel electrophoresis.

    abstract::This protocol describes pulsed-field gel electrophoresis (PFGE), a method developed for separation of large DNA molecules. Whereas standard DNA gel electrophoresis commonly resolves fragments up to approximately 50 kb in size, PFGE fractionates DNA molecules up to 10 Mb. The mechanism driving these separations exploit...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.94

    authors: Herschleb J,Ananiev G,Schwartz DC

    更新日期:2007-01-01 00:00:00

  • Genetic transformation of tobacco NT1 cells with Agrobacterium tumefaciens.

    abstract::This protocol is used to produce stably transformed tobacco (Nicotiana tabacum) NT1 cell lines, using Agrobacterium tumefaciens-mediated DNA delivery of a binary vector containing a gene encoding hepatitis B surface antigen and a gene encoding the kanamycin selection marker. The NT1 cultures, at the appropriate stage ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.176

    authors: Mayo KJ,Gonzales BJ,Mason HS

    更新日期:2006-01-01 00:00:00

  • Characterization of bacterial spore germination using phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers.

    abstract::This protocol describes a method combining phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers to characterize the germination of single bacterial spores. The characterization consists of the following steps: (i) loading heat-activated dormant spores into a temperature-controlled micros...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2011.307

    authors: Kong L,Zhang P,Wang G,Yu J,Setlow P,Li YQ

    更新日期:2011-05-01 00:00:00

  • Using hyperLOPIT to perform high-resolution mapping of the spatial proteome.

    abstract::The organization of eukaryotic cells into distinct subcompartments is vital for all functional processes, and aberrant protein localization is a hallmark of many diseases. Microscopy methods, although powerful, are usually low-throughput and dependent on the availability of fluorescent fusion proteins or highly specif...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2017.026

    authors: Mulvey CM,Breckels LM,Geladaki A,Britovšek NK,Nightingale DJH,Christoforou A,Elzek M,Deery MJ,Gatto L,Lilley KS

    更新日期:2017-06-01 00:00:00

  • Metabolic labeling of glycans with azido sugars and subsequent glycan-profiling and visualization via Staudinger ligation.

    abstract::Metabolic labeling of glycans with a bioorthogonal chemical reporter such as the azide enables their visualization in cells and organisms as well as the enrichment of specific glycoprotein types for proteomic analysis. This process involves two steps. Azido sugars are fed to cells or organisms and integrated by the gl...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.422

    authors: Laughlin ST,Bertozzi CR

    更新日期:2007-01-01 00:00:00

  • A strategy for co-translational folding studies of ribosome-bound nascent chain complexes using NMR spectroscopy.

    abstract::During biosynthesis on the ribosome, an elongating nascent polypeptide chain can begin to fold, in a process that is central to all living systems. Detailed structural studies of co-translational protein folding are now beginning to emerge; such studies were previously limited, at least in part, by the inherently dyna...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2016.101

    authors: Cassaignau AM,Launay HM,Karyadi ME,Wang X,Waudby CA,Deckert A,Robertson AL,Christodoulou J,Cabrita LD

    更新日期:2016-08-01 00:00:00

  • Expander: from expression microarrays to networks and functions.

    abstract::A major challenge in the analysis of gene expression microarray data is to extract meaningful biological knowledge out of the huge volume of raw data. Expander (EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use. It...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.230

    authors: Ulitsky I,Maron-Katz A,Shavit S,Sagir D,Linhart C,Elkon R,Tanay A,Sharan R,Shiloh Y,Shamir R

    更新日期:2010-02-01 00:00:00

  • Comprehensive structural glycomic characterization of the glycocalyxes of cells and tissues.

    abstract::The glycocalyx comprises glycosylated proteins and lipids and fcorms the outermost layer of cells. It is involved in fundamental inter- and intracellular processes, including non-self-cell and self-cell recognition, cell signaling, cellular structure maintenance, and immune protection. Characterization of the glycocal...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-020-0350-4

    authors: Li Q,Xie Y,Wong M,Barboza M,Lebrilla CB

    更新日期:2020-08-01 00:00:00

  • Monitoring lymphocyte proliferation in vitro and in vivo with the intracellular fluorescent dye carboxyfluorescein diacetate succinimidyl ester.

    abstract::This protocol outlines the carboxyfluorescein diacetate succinimidyl ester (CFSE) method for following the proliferation of human lymphocytes in vitro and mouse lymphocytes both in vitro and in vivo. The method relies on the ability of CFSE to covalently label long-lived intracellular molecules with the highly fluores...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.296

    authors: Quah BJ,Warren HS,Parish CR

    更新日期:2007-01-01 00:00:00

  • Microfluidic assay for simultaneous culture of multiple cell types on surfaces or within hydrogels.

    abstract::This protocol describes a simple but robust microfluidic assay combining three-dimensional (3D) and two-dimensional (2D) cell culture. The microfluidic platform comprises hydrogel-incorporating chambers between surface-accessible microchannels. By using this platform, well-defined biochemical and biophysical stimuli c...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2012.051

    authors: Shin Y,Han S,Jeon JS,Yamamoto K,Zervantonakis IK,Sudo R,Kamm RD,Chung S

    更新日期:2012-06-07 00:00:00

  • Single nucleotide polymorphism detection by polymerase chain reaction-restriction fragment length polymorphism.

    abstract::Accurate analysis of DNA sequence variation in not only humans and animals but also other organisms has played a significant role in expanding our knowledge about genetic variety and diversity in a number of different biological areas. The search for an understanding of the causes of genetic variants and mutations has...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.407

    authors: Ota M,Fukushima H,Kulski JK,Inoko H

    更新日期:2007-01-01 00:00:00

  • Langmuir-Blodgett nanotemplates for protein crystallography.

    abstract::The new generation of synchrotrons and microfocused beamlines has enabled great progress in X-ray protein crystallography, resulting in new 3D atomic structures for proteins of high interest to the pharmaceutical industry and life sciences. It is, however, often still challenging to produce protein crystals of suffici...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2017.108

    authors: Pechkova E,Nicolini C

    更新日期:2017-12-01 00:00:00

  • Measuring bone blood supply in mice using fluorescent microspheres.

    abstract::Fluorescent microspheres are commonly used to assess bone blood supply in large animals, but the technique is not widely used in smaller mammals, as traditional methods such as reference blood sampling, ventilation and catheterization are not easily applied. This protocol describes a viable alternative for measuring b...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.190

    authors: Serrat MA

    更新日期:2009-01-01 00:00:00

  • Cell-type-specific metabolic labeling, detection and identification of nascent proteomes in vivo.

    abstract::A big challenge in proteomics is the identification of cell-type-specific proteomes in vivo. This protocol describes how to label, purify and identify cell-type-specific proteomes in living mice. To make this possible, we created a Cre-recombinase-inducible mouse line expressing a mutant methionyl-tRNA synthetase (L27...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-018-0106-6

    authors: Alvarez-Castelao B,Schanzenbächer CT,Langer JD,Schuman EM

    更新日期:2019-02-01 00:00:00

  • 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.

    abstract::Cap-analysis gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. CAGE allows mapping of all the initiation sites of both capped coding and noncoding RNAs. In addition, transcriptional start sites within promoters are characterized at single-nucleotide resolution. The latter allows t...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2012.005

    authors: Takahashi H,Lassmann T,Murata M,Carninci P

    更新日期:2012-02-23 00:00:00