Using Raman spectroscopy to characterize biological materials.

Abstract:

:Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and polymer science fields. The application of Raman spectroscopy and microscopy within biology is rapidly increasing because it can provide chemical and compositional information, but it does not typically suffer from interference from water molecules. Analysis does not conventionally require extensive sample preparation; biochemical and structural information can usually be obtained without labeling. In this protocol, we aim to standardize and bring together multiple experimental approaches from key leaders in the field for obtaining Raman spectra using a microspectrometer. As examples of the range of biological samples that can be analyzed, we provide instructions for acquiring Raman spectra, maps and images for fresh plant tissue, formalin-fixed and fresh frozen mammalian tissue, fixed cells and biofluids. We explore a robust approach for sample preparation, instrumentation, acquisition parameters and data processing. By using this approach, we expect that a typical Raman experiment can be performed by a nonspecialist user to generate high-quality data for biological materials analysis.

journal_name

Nat Protoc

journal_title

Nature protocols

authors

Butler HJ,Ashton L,Bird B,Cinque G,Curtis K,Dorney J,Esmonde-White K,Fullwood NJ,Gardner B,Martin-Hirsch PL,Walsh MJ,McAinsh MR,Stone N,Martin FL

doi

10.1038/nprot.2016.036

subject

Has Abstract

pub_date

2016-04-01 00:00:00

pages

664-87

issue

4

eissn

1754-2189

issn

1750-2799

pii

nprot.2016.036

journal_volume

11

pub_type

杂志文章
  • The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins.

    abstract::The Strep-tag II is an eight-residue minimal peptide sequence (Trp-Ser-His-Pro-Gln-Phe-Glu-Lys) that exhibits intrinsic affinity toward streptavidin and can be fused to recombinant proteins in various fashions. We describe a protocol that enables quick and mild purification of corresponding Strep-tag II fusion protein...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.209

    authors: Schmidt TG,Skerra A

    更新日期:2007-01-01 00:00:00

  • Methods for isolation, purification and structural elucidation of bioactive secondary metabolites from marine invertebrates.

    abstract::In the past few decades, marine natural products bioprospecting has yielded a considerable number of drug candidates. Two marine natural products have recently been admitted as new drugs: Prialt (also known as ziconotide) as a potent analgesic for severe chronic pain and Yondelis (known also as trabectedin or E-743) a...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.182

    authors: Ebada SS,Edrada RA,Lin W,Proksch P

    更新日期:2008-01-01 00:00:00

  • Selective enrichment of sialic acid-containing glycopeptides using titanium dioxide chromatography with analysis by HILIC and mass spectrometry.

    abstract::The terminal monosaccharide of cell surface glycoconjugates is typically a sialic acid (SA), and aberrant sialylation is involved in several diseases. Several methodological approaches in sample preparation and subsequent analysis using mass spectrometry (MS) have enabled the identification of glycosylation sites and ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2010.167

    authors: Palmisano G,Lendal SE,Engholm-Keller K,Leth-Larsen R,Parker BL,Larsen MR

    更新日期:2010-12-01 00:00:00

  • Self-assembly and characterization of 2D plasmene nanosheets.

    abstract::Freestanding plasmonic nanoparticle (NP) superlattice sheets are novel 2D nanomaterials with tailorable properties that enable their use for broad applications in sensing, anticounterfeit measures, ionic gating, nanophotonics and flat lenses. We recently developed a robust, yet general, two-step drying-mediated approa...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0200-4

    authors: Dong D,Fu R,Shi Q,Cheng W

    更新日期:2019-09-01 00:00:00

  • Labeling of biotin antibodies with horseradish peroxidase using cyanuric chloride.

    abstract::In this report, we describe a two-step protocol for labeling of an affinity-purified antibody to biotin with horseradish peroxidase (HRP) using cyanuric chloride (CC) as a bridge. The enzyme was first modified with CC, and following chromatography on a PD-10 column, the activated HRP was incubated with the antibody to...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.6

    authors: Abuknesha RA,Jeganathan F,Wu J,Baalawy Z

    更新日期:2009-01-01 00:00:00

  • In vivo two-photon imaging of sensory-evoked dendritic calcium signals in cortical neurons.

    abstract::Neurons in cortical sensory regions receive modality-specific information through synapses that are located on their dendrites. Recently, the use of two-photon microscopy combined with whole-cell recordings has helped to identify visually evoked dendritic calcium signals in mouse visual cortical neurons in vivo. The c...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2010.169

    authors: Jia H,Rochefort NL,Chen X,Konnerth A

    更新日期:2011-01-01 00:00:00

  • Application of anisotropic NMR parameters to the confirmation of molecular structure.

    abstract::The use of anisotropic NMR data, such as residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs), has emerged as a powerful technique for structural characterization of organic small molecules. RDCs typically report the relative orientations of different 1H-13C bonds; RCSAs report the relati...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-018-0091-9

    authors: Liu Y,Navarro-Vázquez A,Gil RR,Griesinger C,Martin GE,Williamson RT

    更新日期:2019-01-01 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

  • High-throughput assay for determining enantiomeric excess of chiral diols, amino alcohols, and amines and for direct asymmetric reaction screening.

    abstract::Determining enantiomeric excess (e.e.) in chiral compounds is key to development of chiral catalyst auxiliaries and chiral drugs. Here we describe a sensitive and robust fluorescence-based assay for determining e.e. in mixtures of enantiomers of 1,2- and 1,3-diols, chiral amines, amino alcohols, and amino-acid esters....

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-020-0329-1

    authors: Shcherbakova EG,James TD,Anzenbacher P Jr

    更新日期:2020-07-01 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

  • Simultaneous analysis of reactive oxygen species and reduced glutathione content in living cells by polychromatic flow cytometry.

    abstract::Reactive oxygen species (ROS) are continuously produced in the cell as a consequence of aerobic metabolism, and are controlled by several antioxidant mechanisms. An accurate measurement of ROS is essential to evaluate the redox status of the cell, or the effects of molecules with the pro-oxidant or antioxidant activit...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.189

    authors: Cossarizza A,Ferraresi R,Troiano L,Roat E,Gibellini L,Bertoncelli L,Nasi M,Pinti M

    更新日期:2009-01-01 00:00:00

  • Micropatterning of living cells by laser-guided direct writing: application to fabrication of hepatic-endothelial sinusoid-like structures.

    abstract::Here, we describe a simple protocol for the design and construction of a laser-guided direct writing (LGDW) system able to micropattern the self-assembly of liver sinusoid-like structures with micrometer resolution in vitro. To the best of our knowledge, LGDW is the only technique able to pattern cells "on the fly" wi...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.386

    authors: Nahmias Y,Odde DJ

    更新日期:2006-01-01 00:00:00

  • Direct ester condensation catalyzed by bulky diarylammonium pentafluorobenzenesulfonates.

    abstract::A protocol for ester condensation between equimolar amounts of carboxylic acids and alcohols catalyzed by bulky diarylammonium pentafluorobenzenesulfonate is described. We also present procedures for the synthesis of N-(2,6-diisopropylphenyl)-N-mesitylammonium pentafluorobenzenesulfonate. The present ester condensatio...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.254

    authors: Sakakura A,Nakagawa S,Ishihara K

    更新日期:2007-01-01 00:00:00

  • Genome editing comes of age.

    abstract::Genome editing harnesses programmable nucleases to cut and paste genetic information in a targeted manner in living cells and organisms. Here, I review the development of programmable nucleases, including zinc finger nucleases (ZFNs), TAL (transcription-activator-like) effector nucleases (TALENs) and CRISPR (cluster o...

    journal_title:Nature protocols

    pub_type: 杂志文章,评审

    doi:10.1038/nprot.2016.104

    authors: Kim JS

    更新日期:2016-09-01 00:00:00

  • Quantitative proteomic approach to study subcellular localization of membrane proteins.

    abstract::As proteins within cells are spatially organized according to their role, knowledge about protein localization gives insight into protein function. Here, we describe the LOPIT technique (localization of organelle proteins by isotope tagging) developed for the simultaneous and confident determination of the steady-stat...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.254

    authors: Sadowski PG,Dunkley TP,Shadforth IP,Dupree P,Bessant C,Griffin JL,Lilley KS

    更新日期:2006-01-01 00:00:00

  • A lectin microarray approach for the rapid analysis of bacterial glycans.

    abstract::Rapid evaluation of microbial cell-surface carbohydrates is essential to understanding the mechanisms by which bacteria use glycans to establish pathogenic or symbiotic relationships. Microbial glycan analysis is complicated both by the vast diversity of possible carbohydrate structures and by their dynamic nature. Ba...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.76

    authors: Hsu KL,Mahal LK

    更新日期:2006-01-01 00:00:00

  • Production of a site- and phosphorylation state-specific antibody.

    abstract::Protein phosphorylation plays important roles in various aspects of cellular events. Visualization of site-specific phosphorylation in cells is of great importance not only to analyze spatial and temporal distribution but also to investigate biological function. Now, site- and phosphorylation state-specific antibodies...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.374

    authors: Goto H,Inagaki M

    更新日期:2007-01-01 00:00:00

  • Production and characterization of adeno-associated viral vectors.

    abstract::The adeno-associated virus (AAV) is one of the most promising viral vectors for human gene therapy. As with any potential therapeutic system, a thorough understanding of it at the in vitro and in vivo levels is required. Over the years, numerous methods have been developed to better characterize AAV vectors. These met...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.207

    authors: Grieger JC,Choi VW,Samulski RJ

    更新日期:2006-01-01 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

  • In vivo rapid gene delivery into postmitotic neocortical neurons using iontoporation.

    abstract::This protocol describes a method for directing the expression of genes of interest into postmitotic neocortical neurons in vivo. Microinjection of a DNA plasmid-amphiphilic molecule mix into the neocortex followed by delivery of an ad hoc electric pulse protocol during the first few days of life in mice allows rapid, ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.001

    authors: De la Rossa A,Jabaudon D

    更新日期:2015-01-01 00:00:00

  • Development of a highly reproducible three-dimensional organotypic model of the oral mucosa.

    abstract::In this report we describe the development of a standardized three-dimensional (3D) system of the human oral mucosa based on an immortalized human oral keratinocyte cell line (OKF6/TERT-2). The procedure takes approximately 2-3 weeks to complete and includes three main stages: preparation of collagen-embedded fibrobla...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.323

    authors: Dongari-Bagtzoglou A,Kashleva H

    更新日期:2006-01-01 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

  • Synthesis of complex head-to-side-chain cyclodepsipeptides.

    abstract::Cyclodepsipeptides are cyclic peptides in which at least one amide link on the backbone is replaced with an ester link. These natural products present a high structural diversity that corresponds to a broad range of biological activities. Therefore, they are very promising pharmaceutical candidates. Most of the cyclod...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2016.116

    authors: Pelay-Gimeno M,Albericio F,Tulla-Puche J

    更新日期:2016-10-01 00:00:00

  • Directed differentiation of forebrain GABA interneurons from human pluripotent stem cells.

    abstract::Forebrain γ-aminobutyric acid (GABA) interneurons have crucial roles in high-order brain function via modulating network activities and plasticity, and they are implicated in many psychiatric disorders. Availability of enriched functional human forebrain GABA interneurons, especially those from people affected by GABA...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.106

    authors: Liu Y,Liu H,Sauvey C,Yao L,Zarnowska ED,Zhang SC

    更新日期:2013-09-01 00:00:00

  • Visualization of protein interactions in living Caenorhabditis elegans using bimolecular fluorescence complementation analysis.

    abstract::The bimolecular fluorescence complementation (BiFC) assay is a powerful tool for visualizing and identifying protein interactions in living cells. This assay is based on the principle of protein-fragment complementation, using two nonfluorescent fragments derived from fluorescent proteins. When two fragments are broug...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.16

    authors: Shyu YJ,Hiatt SM,Duren HM,Ellis RE,Kerppola TK,Hu CD

    更新日期:2008-01-01 00:00:00

  • Probing 2-dimensional protein-protein interactions on model membranes.

    abstract::This protocol describes an in vitro approach for measuring the kinetics and affinities of interactions between membrane-anchored proteins. This method is particularly established for dissecting the interaction dynamics of cytokines with their receptor subunits. For this purpose, the receptor subunits are tethered in a...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.270

    authors: Gavutis M,Lata S,Piehler J

    更新日期:2006-01-01 00:00:00

  • In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples.

    abstract::High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.333

    authors: Hejátko J,Blilou I,Brewer PB,Friml J,Scheres B,Benková E

    更新日期:2006-01-01 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

  • 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

  • Assaying stem cell mechanobiology on microfabricated elastomeric substrates with geometrically modulated rigidity.

    abstract::We describe the use of a microfabricated cell culture substrate, consisting of a uniform array of closely spaced, vertical, elastomeric microposts, to study the effects of substrate rigidity on cell function. Elastomeric micropost substrates are micromolded from silicon masters comprised of microposts of different hei...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2010.189

    authors: Yang MT,Fu J,Wang YK,Desai RA,Chen CS

    更新日期:2011-02-01 00:00:00