Bank of Bioprotocols

Web links of bioprotocols (1)

Web links of bioprotocols (2)

Web Source Protocols for Molecular Biology

1.General Lab Techniques
2. Lab security and basic techniques
3. Advanced lab skills-(1)
4. Advanced lab skills-(2)
5. Molecular Biology
6. DNA isolation & related protocols
7. DNA Purification (glass milk vs electroelution)
8. DNA and RNA sequencing
9. Nucleic acid methods (1)
10.Nucleic acid methods (2)
11.Isolation of DNA,RNA, and Protein simultaneously.
12.DNA mutation detection by SSCP
13.Mouse genotyping by PCR
14.PCR,RT-PCR,Real time PCR etc.
15.Southern blot hybridization
16. Loss of Heterozygosity (LOH)
17.Gene knockout protocol
18.RNA Isolation and Purification
19.Preparation of DNA and RNA probes
20.Northern blot hybridization
21.SiRNA gene knockout
22.Western blot hybridization
23.Molecular cloning
24.Conditional gene transfection(Tet on/off)
25.Protein sequencing
26.Protein labeling techniques
27.Subcellular fractionations
28.EMSA
29.Methylation interference
30.Southwestern blotting
31.Filter binding protocols
32.Footpring protocols
33.DNA (RNA) protein interactions
34.Plasmid and its usefulness
35.DNA library construction
36.Microarray protocols.
37. Protein chips
38.Detecting of protein phosphorylation
39.Protein methods
40.Molecular separation
41.Gene therapy for cancer
42.X-ray crystallography
43.Metabolism and chromatographies
44.GC/MS Background
45.Glucose metabolism and its related protocols
46.PAS staining
47.Polysaccharide sequencing
48.Deoxyribose procedure
49.Ribose metabolism analysis
50.Lactate cleanup and derivative
51.Amino acids
52.Fatty acids
53.Lipid protocols
54.Cholesterol
55.Bile acids
56.Urea procedure
57.Choline Incorporation Assay
58.Isotope Ratio Mass Spectrometer (IRMS)
59.Liquid chromatography / mass spectrometer (LC/MS)
60.Proteomics
61.NMR protocols and tutorials
62.HPLC protocols
63.TLC
64.Molecular labeling
65.Immunology/immunohistochemistry
66.Preparing silanized (+plus) slides
67.Histological fixation
68.Microwave histology
69.Microscopy Techniques
70. Electron microscopy
71.HE staining
72.Nucleic acid stain
73.Special cell & cell fraction stains
74.Antibody purification
75.Antibody storage and handling
76.Conjugation of monoclonal antibodies
77.Antigen retrieval
78.Elisa
79.FRQs for histochemistry
80.Immunoperoxidase staining techniques
81.Immunofluorohistochemistry
82.Confocal microscope technique
83.Laser Capture Microdissection
84.Immunoprecipitation
85.ChIP assay
86.Hybridization in situ
87.Histotechnology--technical methods
88. Flow cytometry (FCM)
89.Kinase assay
90.Cellular Biology
91.General cell culture protocols
92.Chromosome karyotype
93.Proliferation assays (MTT, BrdU, 3H-Thymidine incoporation)
94.Cell cycle assay
95.Migration assay
96.Stem cell & related protocols
97.Apoptosis and related protocols
98.Soft Agar Assay for Colony Formation
99.Aorta ring assay
100.GFP transfection
101.Gene transfection
102.Transformation protocols
103.Blood cell fractionation (white blood cell isolation)
104.Endothelial isolation and culture
105.Isolation and culture human brain microvessel endothelial cells
106.Animal Experiments
107.Blood sampling from animals
108.Basic skills for animal experiments
109.Cancer xenograft animal models
110.Transgenic animal procedures
111.Transgenic cancer models
112.Animal search
113.Animal models for depression-like and anxiety-like behavior
114.Genetics
115.Epigenetics protocols
116.SNPs
117.Genetic analysis
118.Mutagenesis
119.Model Organisms
120.C. Elegans
121.Yeast protocols and resource

Protocols for Molecular Biology

Protocols for DNA
1 Methylene Blue DNA staining protocol
2 Plasmid Protocols--(31-37)
3 Plasmid Protocols--(21-30)
4 Plasmid Protocol--(1-10)
5 Microsatellites Protocols
6 In-Situ hybridization to Embryonic Tissue Section
7 DNA ligation Protocol
8 Colony Hybridization Protocols
9 Colony Hybridization
10 DNA Isolation, Purification and Troubleshooting
11 Deoxyribose Isolation from DNA Degrasion
12 Mitochondrial DNA Isolation
13 Genomic DNA Isolation from Specific Samples
14 Genome DNA Extraction
Protocols for RNA
1 IN VITRO TRANSCRIPTION OF RNA
2 SINGLE CELL mRNA AMPLIFICATION (REVERSE NORTHERN ANALYSIS)
3 Protocols for SiRNA
4 SELEX—in vitro selection
5 Nucleic Acids Research Methods (2)
6 RNA MicroArray Protocol
7 RNA Isolation
Protocols for PCR
1 PCR Based Molecular Cloning
2 Handbook for DNA isolation, RAPD-PCR and PCR-RFLP
3 Introduction to PCR
4 General PCR introduction
5 PCR Animations
6 PCR, RT PCR and Real Time PCR Tutorials
7 PCR Application Manual
8 PCR Elisa
9 PCR RFLP
10 PCR SSCP
11 Real Time PCR
12 RT-PCR Protocols
13 Variants of PCR (2)
14 Variants of PCR (1)
15 AFLP PCR
16 Alu-PCR
17 Asymmetric PCR
18 Colony PCR Protocols
19 Competitive and Quantitative RT-PCR
20 Degenerate PCR
21 Differential Display PCR
22 In Situ PCR
23 Inverse PCR
24 Ligation Mediated Suppression PCR
25 Long PCR Protocols
26 Methylation Specific PCR
27 Multiplex PCR
28 Nested PCR
29 RACE PCR
30 RAPD PCR
31 Rep-PCR
32 TAIL PCR
33 Touchdown PCR
34 Vectorette PCR

Other PCR Web Source (from Google directory)

A Rapid DNA Minipreparation Method Suitable for AFLP and Other PCR Applications - http://pubs.nrc-cnrc.gc.ca/ispmb/ispmb17/17053-1.pdf
Preparation of DNA from plant tissues suitable for PCR methods including AFLP, article by DH CHEN and PC RONALD Department of Plant Pathology, University of California, Davis.

Adjuvants in PCR Reactions - http://info.med.yale.edu/genetics/ward/tavi/p16.html
Brief discussion of additives to improve amplification efficiency and specificity of PCR, by Octavian Henegariu, Yale-New Haven Medical Center.

Amberg Laboratory Protocols: - http://www.upstate.edu/biochem/amberg/protocols.php
Laboratory protocols for PCR work used by the group of David Amberg at the Department of Biochemistry and Molecular Biology Upstate Medical University, Syracuse, New York.

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Anchor Probes for Comparative Mapping of Grass Species - http://greengenes.cit.cornell.edu/anchors/
Article in which probes from different libraries were used to hybridize seven cereals at the Department of Plant Breeding and Biometry, Cornell University, NY.

Attotron Biosensor Corporation - http://www.attotron.com
Research and development company for development of biosensors and related products for the research and educational markets.

BioRad, Amplification, PCR - http://www.bio-rad.com/B2B/BioRad/product/br_category.jsp?
Division of BioRad Laboratories that manufactures and sells instruments for PCR, in Hercules, California, USA.

Degenerate PCR - http://www.dartmouth.edu/~ambros/protocols/other/koelle/degenerate_PCR.html
The identification of novel members of gene families by PCR using degenerate primers is described and protocols given. Article by Michael Koelle 1996 on the web site of Dartmouth College.

Detection of Point Mutations by RFLP of PCR Amplified DNA Sequences - http://www.uni-graz.at/~binder/thesis/node64.html
Thesis abstract about restriction fragment length polymorphism (RFLP) by Alexander Binder 1997.

Detection of Single Nucleotide Mutations in Wheat Using Single Strand Conformation Polymorphism Gels - http://pubs.nrc-cnrc.gc.ca/ispmb/ispmb19/R01-013.pdf
P Martins-Lopez, H Zhang, R Koebner, Plant Mol. Biol. Reporter 19(2001): 159-162. From National Research Coouncil Canada.

DNALC: PCR Animation - http://www.dnalc.org/ddnalc/resources/shockwave/pcranwhole.html
An animation explaining how the Polymerase Chain Reaction (PCR) works, from the Dolan DNA learning center, Cold Spring Harbor Laboratory, USA.

Dolan DNA Learning Centers Gene Almanac - http://www.dnalc.org/home.html
Educational site on topics in genetics and gene expression from Cold Spring Harbor Laboratory, USA.

Effect of PCR Buffer on Multiplex PCR - http://www.qiagen.com/literature/brochures/pcr/pdf/pcrcha03.pdf
Multiplex PCR employs different primer pairs in the same amplification reaction. This requires extensive optimization of annealing conditions. From Quiagen (company).

Fidelity of DNA Polymerases for PCR - http://www.lecb.ncifcrf.gov/~pnh/papers/TIBS/aug95.html
Article by PN Hengen from TIBS 1995

FISH Guide and Troubleshooting - http://info.med.yale.edu/genetics/ward/tavi/FISHguide.html
Links to pages describing influential parameters, with guides on PCR, RT-PCR and multiplex PCR reactions, Taq, FISH, CM-FISH, TM-FISH, microarrays, CCK, slide prep and labeling, maintained by Octavian Henegariu from Yale University, New Haven, CT.

Fluorescence in Situ Hybridisation - http://info.med.yale.edu/genetics/ward/tavi/FISH.html
Technical notes on Fluorescence in situ hybridisation from the Institute of Genetics of Yale School of Medicine, New Haven, Connecticut, USA.

GeneOhm Sciences - http://www.geneohm.com
Tests on group B Streptococcus and methicillin resistant Staphylococcus aureus by PCR / DNA sequencing.

GenHunter - http://www.genhunter.com
Manufacturer of material for differential display PCR in Nashville, Tenn USA.

HiFi DNA - http://www.hifidna.com/
HiFi DNA is a company selling a DNA polymerase for PCR at low temperature giving accurate replication of certain sequences where Taq fails.

Ingenetix GmbH - http://www.ingenetix.com/
Develops technology and products for DNA and mRNA research. Also provide DNA testing for the determination of parentage/paternity and custom DNA sequencing, oligonucleotide synthesis, genotyping services, pharmacogenetics and quantitative PCR, in Vienna, Austria.

Inverse PCR and Cycle Sequencing of P Element Insertions for STS Generation - http://www.fruitfly.org/about/methods/inverse.pcr.html
Step by step protocol, by EJ Rehm, Berkeley Drosophila Genome Project, USA.

Inverse PCR for PAC-end Sequencing - http://www.genetics.wustl.edu/fish_lab/frank/cgi-bin/fish/prot2.html
To generate PCR fragments that contain the ends of PAC inserts that can be sequenced. Protocol by B Barbazuk, Washington University Zebrafish Genome Resources Project, USA.

Inverse PCR for Use with Snyder mTn-lacZ/LEU2-based Mutagenesis - http://labs.fhcrc.org/gottschling/General%20Protocols/ipcr.html
Protocol by M McMurray, Fred Hutchinson Cancer Research Center, Seattle, Wa. USA.

Inverse PCR Protocol - http://www.mcdb.lsa.umich.edu/labs/maddock/protocols/PCR/inverse_pcr_protocol.html
Step by step protocol, from the web site of the Department of Biology, University of Michigan, USA.

Kary B. Mullis - Autobiography - http://nobelprize.org/chemistry/laureates/1993/mullis-autobio.html
The originator of PCR, from the Nobel e-museum web site.

Kary Mullis - http://www.invent.org/hall_of_fame/109.html
Inventor Profile of Kary Mullis, the originator of PCR, from the National Inventors Hall of Fame web site.

Long PCR Protocol - http://twod.med.harvard.edu/labgc/estep/longPCR_protocol.html
Protocol and guidelines for choice of conditions for PCR of long sequences (10 kb or larger). From Genetics Dept., Harvard Medical School, Boston, MA, USA

Nematode ITS1 Size Variation - http://nematode.unl.edu/its_id/EXAMPLES/index.htm
Examples of Restriction Fragment Length Polymorphism (RFLP)electrophoresis slabs for different nematodes, from University of Nebrasca.

Optimizing Multiplex and LA-PCR with Betaine - http://www-lecb.ncifcrf.gov/~pnh/papers/TIBS/jun97.html
LA-PCR = "long and accurate PCR". Article by PN Hengen in TIBS June 1997.

Optimizing PCR Protocols - http://www.jax.org/imr/optimize_pcr.html
Brief guidelines. From the Jackson Laboratory, University of Maine, USA.

PCR Amplification of cDNA Segments by 2 Stage Nested PCR - http://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?type=method&method_id=555
Protocol from the method database of NIH, USA.

PCR and Multiplex PCR Guide - http://www.info.med.yale.edu/genetics/ward/tavi/Guide.html
Discussions of the parameters influencing the PCR reaction and some PCR and multiplex PCR applications, by Octavian Henegariu on the web site of the Yale - New Haven Medical center.

PCR Animated - http://users.ugent.be/~avierstr/principles/pcrani.html
Animation illustrating the principle of PCR, from the University of Ghent, Belgium.

PCR Gateway - http://www.horizonpress.com/pcr/
A directory of PCR techniques, PCR protocols, PCR troubleshooting, PCR websites and online resources from the publisher Horizon Press.

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PCR Guru - http://www.pcrguru.com/
A downloadable textbook on PCR setup and optimization, not free.

PCR Method Protocols - http://hg.wustl.edu/hdk_lab_manual/pcr/pcrcontents.html
Protocols for PCR posted by the Helen Donis-Keller Laboratory.

PCR Primer Design and Reaction Optimisation - http://web.uct.ac.za/microbiology/pcroptim.htm
Article by Ed Rybicki, Department of Molecular and Cell Biology, University of Cape Town in: Molecular Biology Techniques Manual, on the web site of the University of Cape Town.

PCR Project - http://sunsite.berkeley.edu/biotech/pcr/
Presentations from the University of California at Berkley on PCR, both current research reports and reviews.

PCR Protocol - http://www.mcdb.lsa.umich.edu/labs/maddock/protocols/PCR/general_pcr_protocol.html
Detailed PCR protocol from the web site of the Department of Biology, University of Michigan, USA.

PCR Protocols - http://www.cas.psu.edu/docs/CASDEPT/VET/jackvh/jvhpcr.html
Protocols and technical hints, particularly for reverse transcription PCR, somewhat outdated, compiled by Dr Jack Vanden Heuvel, Department of Veterinary Science and Molecular Toxicology Program, Penn State University

PCR Technology - http://www.accessexcellence.org/LC/SS/PS/PCR/PCR_technology.html
An introduction by Connie Veilleux from the US National Health Museum website.

PCR Troubleshooting - http://info.med.yale.edu/genetics/ward/tavi/Trblesht.html
Limited to conventional straight forward PCR. Page designed and maintained by Octavian Henegariu on the web site of the Yale - New Haven Medical Center.

PCR World - http://pcrworld.blogspot.com
Collection of unreferenced texts on various aspects of PCR.

PCR-ELISA and Related - http://www.btc-bti.com/pcrelisa.htm
P Zhang, CJ Gebhart, D Burden, GE Duhamel: A low technology alternative to real time PCR, technical article on the site of BT&C, Inc Bridgewater, NJ, USA.

Polymerase Chain Reaction - http://www.accessexcellence.com/RC/CT/polymerase_chain_reaction.html
Popular survey article by Mark V. Bloom, DNA Learning Center, Cold Spring Harbor Laboratory, from the web site of the US National Health Museum.

Polymerase Chain Reaction (PCR) - http://www.accessexcellence.org/AB/GG/polymerase.html
A graphic description of the principle of PCR from the US National Health Museum web site.

PrimerDigital - http://primerdigital.com/index.php
International biotechnology company specialized in a design service for PCR primers and probes, PCR-based technology development, projects for development of polymorphism and software development.

Primerfox - http://www.primerfox.com
Free online tool for generation of PCR primers.

Principle of PCR - http://users.ugent.be/~avierstr/principles/pcr.html
Applications in work on aging of Caenorhabditis elegans and phylogeny of nematodes, by Andy Vierstraete, Department of Biology, University of Ghent, Belgium.

Protocols Online: PCR Protocols - http://www.protocol-online.org/prot/Molecular_Biology/PCR/
Extensive collection of PCR protocols and methods from Protocol On Line.

Quantitative PCR Protocol - http://www.jax.org/cyto/quanpcr.html
From the Jackson Laboratory, University of Maine, USA.

RAPD PCR - http://avery.rutgers.edu/WSSP/StudentScholars/project/archives/onions/rapd.html
RAPD stands for Random Amplification of Polymorphic DNA, where the target sequence(s) (to be amplified) is unknown.Brief description, from Rutgers University, USA.

Rational Primer Design Greatly Improves Differential Display-PCR (DD-PCR) - http://nar.oxfordjournals.org/cgi/content/full/25/11/2239
Article: D Graf, AG Fisher, M Merkenschlager: Nucl. Acids Res. 25:11 2239-2240.

Reference in PCR - http://www.gene-quantification.org
Technical aspects of quantitative real-time PCR and RT-PCR. Instruments, kits, dyes, chemistries, and services presented by their manufacturers.

Rep-PCR Genomic Fingerprinting - http://www.msu.edu/user/debruijn/
Bacteria are characterized by Rep-PCR fingerprinting using primers corresponding to naturally occurring repetitive sequences in the interspersed regions.

RFLP Definition - http://vm.cfsan.fda.gov/~frf/rflp.html
RFLP = Restriction Fragment Length Polymorphism, from FDA

Roe Laboratory Protocols - http://www.genome.ou.edu/proto.html
Molecular biological protocols, mostly PCR related used by Bruce A. Roe at the Dept. of Chemistry and Biochemistry, OU, Norman, OK.

Single Tube Confirmation PCR Protocol - http://www-sequence.stanford.edu/group/yeast_deletion_project/single_tube_protocol.html
For characterization colonies of transformed clones of Saccharaomyces, from the web site of the Stanford Genome Technology Center, Palo Alto, CA, USA.

Standard PCR Protocols - http://web.uct.ac.za/microbiology/pcrcond.htm
From Molecular Biology Techniques Manual, from the web site of the University of Cape Town, South Africa.

T-DNA Generated Enhancer Traps in Arabidopsis - http://www.dartmouth.edu/~tjack/
Application of inverse PCR, partial genomic libraries and TAIL-PCR in cloning flanking, at the Department of Biological Sciences, Dartmouth College, Hanover, NH.

Tavi's PCR Protocols - http://info.med.yale.edu/genetics/ward/tavi/PCR.html
A page describing the main parameters and trouble-shooting in PCR. The page is somewhat dated (updated 1997) but still useful.

The PCR Encyclopedia - http://www.pcr-encyclopedia.com/
Describes plans for a free encyclopedia dedicated to the polymerase chain reaction (PCR).

The Web Guide of PCR - http://www.pcrlinks.com/
List of links and forum on the subject and related methodology. Set up and maintained by SJ Krivokapich, National University of Misiones, Argentina.

Thermostable DNA Polymerases - http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/enzymes/hotpolys.html
Discussion of their origin and briefly their properties. From the web site of Colorado State University.

Wayward PCR Primers - http://www-lecb.ncifcrf.gov/~pnh/papers/TIBS/jan95.html
Article by PN Hengen from TIBS 1995 on the loss of activity of PCR primers with time.

What the Heck is PCR? - http://people.ku.edu/~jbrown/pcr.html
Popular description of the PCR technique by John C Brown, University of Kansas 1995.

Which DNA Marker for Which Purpose? - http://webdoc.sub.gwdg.de/ebook/y/1999/whichmarker
Compendia of the Research Project "Development, optimisation and validation of molecular tools for assessment of biodiversity in forest trees", European Union DGXII Biotechnology FW IV Research Programme. From the web site of the University Library, Göttingen.

Protocols for Protein
1 Enzyme Assay（43-47）
2 Enzyme Assay（36-42）
3 Enzyme Assay（22-28）
4 Protocols for In Vitro Translation
5 Dot Blot Protocols
6 Selected Protocols of Protein Purification
7 Western Blotting Protocols (1)
Protocols for Cells
1 FACS for Bone marrow macrophages
2 Bone Marrow Macrophages
3 Metabolic Labeling of Cells with 35S
4 Protocols from the science advisory board
5 Introduction to Animal Cell Culture
6 Cell Transfection Protocols
7 Laser Capture Microdissection Protocols
8 Stem Cell Research Techniques and Protocols
9 XTT Cell Viability Assay Protocol
10 Apoptosis Assay Protocols
Protocols for Genetics
1 Genetic Analyses for DNA Protein Interactions
2 Comet Assay
3 Epigenetics Protocols
Protocols for Immunology and IHC
1 Grocott's Methenamine Silver (GMS) stain and troubleshooting
2 Elegans Immunohistochemistry
3 Cytokine Assay Protocols
4 Fluorescence in situ hybridization (FISH)
5 Radioimmunoassay--RIA Protocols
6 Competitive ELISA Protocols
7 Immunohistochemistry Stain for Frozen tissue
Protocols for Chromatography
1 Polysaccharide sequencing
2 Application Guides and Protocols (Nest Group)
3 HPLC Troubleshooting
4 Introduction to HPLC
Protocols for Model Organisms
1 Yeast Protocols
Protocols for Animal Experiment
1 Murine Models of Human Breast Cancer (B)
2 Chorioallantoic Membrane Vascular Assay
3 Guidelines for Techniques with Rodents (Duke University)
4 Tail Vein Injection Techniques
5 Animal Search Engines
Protocols for Basic Techniques
1 H & E Stain Troubleshooting
2 H and E Stain Protocols
3 Electrophoresis Protocols (11-26)
4 Lab. Safety in Life Science

Mapping DNA/protein interactions by cross linking

Dissecting Fission Yeast Centromeres via SilencingRobin Allshire.

Localizing Replication Sites and Nuclear ProteinsAngela Taddei, Danièle Roche, Jean-Baptiste Sibarita, Sébastien Huart, Christèle Maison, Delphine Bailly, and Geneviève Almouzni.

Finding Downstream Target DNAs for Chromatin Proteins by X-CHIP in DrosophilaNicolas Nègre and Giacomo Cavalli.

Emerging Techniques: UV Laser Footprinting and Protein--DNA CrosslinkingStefan Dimitrov.

Nuclear Organization and Gene Expression: Visualization of Transcription and Higher Order Chromatin StructureRoel van Driel and Pernette J. Verschure.

Examining the Distribution of Telomeric and DNA Repair Proteins by ChrIP and Real-Time PCRKarine Dubrana.

Nuclear Organisation and Gene Silencing in LymphocytesAmanda Fisher and Matthias Merkenschlager.

Direct Visualization of Transcription Factor Binding to Regulatory Elements in Living CellsGordon L. Hager.

Part I. Chromatin Protein Complexes: Dynamic Assemblies in the NucleusDonna Jovin.

Isolation of Homeodomain Engrailed Target Genes by UV Cross-Linking and Chromatin IPFlorence Maschat.

Analysis of Chromatin Assembly, Chromatin Domains, and DNA Replication Using Xenopus SystemsJean-Marc Lemaitre, Yegor Vassetzky, and Marcel Méchali.

Binding Sights in Chromatin by X-ChIPAchim Breiling and Valerio Orlando.

Chromatin Immunoprecipitation in Budding YeastTomoyuki Tanaka.

ChIP with Native Chromatin: Advantages and Problems Relative to Methods Using Cross-Linked MaterialBryan Turner.

Highly Sensitive FISH in Combination with the Visualization of the Mammalian Genome: ArchitectureDaniele Zink.

Part II. Fly-FISHing: A Protocol to Localize Single Copy Genes inside the Nucleus in Whole Mount EmbryosMark J. Gemkow.
Part 2. Detailed Method for Immunoprecipitation of Unfixed Chromatin from Mammalian CellsLaura O'Neill and Bryan Turner.

x-ray crystallography for DNA protein interaction investigation

Background (by Bernhard Rupp)

What is X-ray Crystallography ?

X-ray crystallography is an experimental technique that exploits the fact that X-rays are diffracted by crystals. It is not an imaging technique. X-rays have the proper wavelength (in the Ångström range, ~10-8 cm) to be scattered by the electron cloud of an atom of comparable size. Based on the diffraction pattern obtained from X-ray scattering off the periodic assembly of molecules or atoms in the crystal, the electron density can be reconstructed. Additional phase information must be extracted either from the diffraction data or from supplementing diffraction experiments to complete the reconstruction (the phase problem in crystallography). A model is then progressively built into the experimental electron density, refined against the data and the result is a quite accurate molecular structure.

Why Crystallography ?

The knowledge of accurate molecular structures is a prerequisite for rational drug design and for structure based functional studies to aid the development of effective therapeutic agents and drugs. Crystallography can reliably provide the answer to many structure related questions, from global folds to atomic details of bonding. In contrast to NMR, which is an indirect spectroscopic method, no size limitation exists for the molecule or complex to be studied. The price for the high accuracy of crystallographic structures is that a good crystal must be found, and that limited information about the molecule's dynamic behavior in solution is available from one single diffraction experiment. In the core regions of the molecules, X-ray and NMR structures agree very well, and enzymes maintain their activity even in crystals, which often requires the design of non-reactive substrates to study enzyme mechanisms.

5. Methods (From Wikipedia, the free encyclopedia)


5.1 Crystallization
5.2 Data collection
5.2.1 Mounting the crystal
5.2.2 X-ray sources
5.2.3 Recording the reflections
5.3 Data analysis
5.3.1 Crystal symmetry, unit cell, and image scaling
5.3.2 Initial phasing
5.3.3 Model building and phase refinement
5.4 Deposition of the structure

Protein crystallography
Tutorials
Primary databases
Derivative databases


Springer Protocols: Abstract: Preparation of DNA-Protein Complexes ...
Although a plethora of techniques is now available to study DNA-protein interaction, none provides detailed structural information at the molecular level ...
Protein:DNA Interaction Group
extensive surface for mediating protein-protein interactions. .... microscopy and X-ray crystallography. In the last year we have been able to purify the ...www.embl-grenoble.fr/groups/dna/rr03_94.pdf
Identification of DNA Recognition Sequences and Protein ...
meric and heteromeric protein-protein interaction and DNA-. protein interaction. ..... demonstrated by EMSA and X-ray crystallography of single- ...mcb.asm.org/cgi/reprint/18/11/6447.pdf
Structure determination techniques - X-ray and NMR
Protein secondary structure, DNA double helix and RNA stem and loop ... X-ray crystallography requires the growth of protein crystals up to 1 mm in size ...www.whatislife.com/reader/techniques/techniques.html
X-Ray Crystallography
The atoms in crystals interact with X-ray waves in such a way as to produce interference. The interaction can be thought of as if the atoms in a crystal ...www.tulane.edu/~sanelson/eens211/x-ray.htm
X-Ray Crystallography Subject Guide - Chemistry Library - UW-Madison
X-Ray Crystallography. Introduction; Repositories/Databases; Online Learning; Organizations; Books & Reference Works; Selected Journals; Journal Databases ...chemistry.library.wisc.edu/subject-guides/x-ray-crystallography.html
SCSB X-ray Crystallography
X-Ray Crystallography Homepage, X-ray Crystallography at the Sealy Center for Structural Biology ... PIPE (GO) Protein-protein & Protein-DNA interactions ...www.xray.utmb.edu/xray_software.html
The Structure of the DNA Molecule
After all, DNA is composed of a mere 4 subunits while protein is composed of 20, and DNA ... Together, Watson and Crick used X-ray crystallography data, ...www.accessexcellence.org/AE/AEC/CC/DNA_structure.html
DNA Structure and Function
Isolated T2, like other viruses, is just a crystal of DNA and protein, ... Someone else showed them Franklin’s photographs of DNA x-ray crystallography, ...biology.clc.uc.edu/courses/bio104/dna.htm
Overview of macromolecular crystallography
This series will cover the theory and practice of X-ray crystallography, .... or you know the structure of a closely-related protein) you can place a model ...www-structmed.cimr.cam.ac.uk/Course/Overview/Overview.html
Damaged DNA and Its Repair, Biomolecular X-Ray Crystallography Center
Without surprise, it has been uncovered that mutations in DNA repair genes ... for Calcium Regulation and Its Interaction with a Membrane Protein, Junctin, ...kang7.chem.wsu.edu/~kang/research.html
X-Ray Crystallography Gives Scientists New Understanding Of ...
X-Ray Crystallography Gives Scientists New Understanding Of Molecular Motor .... Scientists Map Structure Of DNA-doctoring Protein Complex (Dec. ...www.sciencedaily.com/releases/1999/10/991019075233.htm
Ethylation interference and X-ray crystallography identify similar ...
Our results strongly support the idea that the interactions between protein and the DNA phosphate backbone in the crystallized complex1 are the same as ...www.nature.com/nature/journal/v316/n6029/abs/316651a0.html
X-Ray Crystallography Reveals Helicase that Unwinds DNA
Peering at a Machine that Pries Apart DNA X-Ray Crystallography Gives ... In T7, the helicase is a double-decker protein with two enzyme activities. ...www.hms.harvard.edu/news/releases/1099helicase.html
Research projects X-ray crystallography Nederlands Kanker Instituut
Using X-ray crystallography we can obtain a pictorial view of the .... The protein-DNA recognition takes place through base and backbone contacts, ...xtal.nki.nl/Titia_group/proj_files/projects2.html
Identification of DNA Recognition Sequences and Protein ...
Biochemical characterization of the Roaz protein-protein interaction. .... by EMSA and X-ray crystallography of single-finger or two-finger peptides (28). ...www.pubmedcentral.nih.gov/articlerender.fcgi?artid=109231
Functional Characterization of DNA-binding Domains of the Subunits ...
timately, x-ray crystallography should definitively reveal the. structure of the DNA-protein interaction between the. AHR ARNT dimer and the XRE, ...www.jbc.org/cgi/reprint/271/15/8843.pdf
BioMed Central Full text Energetics of the protein-DNA-water ...
Even x-ray crystallography at high resolution likely underestimates the number of solvent ... Matthews, in his pioneering work on protein-DNA interaction, ...www.biomedcentral.com/1472-6807/7/4
NMR, synchrotrons & X-ray crystallography for pharmaceutical ...
NOE Nuclear Overhauser Effect: The interaction between the dipole moments ... Is there any kind of protein crystallography that isn't x-ray crystallography? ...www.genomicglossaries.com/content/nmr_email.asp

High Throughput Methods in Proteomics (very good slide shows)

Methylation Interference protocols

Methylation Interference Assay -- Carey and Smale 2007 (24): pdb ...
Methylation interference (and methylation protection) is the major technique for .... DNA-binding protein, 1.00 µL. 32P-end-labeled methylated DNA probe (50 ...www.cshprotocols.org/cgi/content/full/2007/24/pdb.prot4812
Methylation Interference
--Dry down and resuspend in 8 ul Q. Add 1 ul of cold complementary oligo and 1 ul 10X Annealing Buffer. Heat to 65C and allow to slow cool on ice in 50 ml of 65° water
http://www.e-biotek.com/ebiotek_283.htm
Analysis of Protein-DNA Interactions
The characterization of the protein-DNA interactions usually requires three .... approach is more general than methylation interference because hydroxyl ...www.mun.ca/biochem/courses/4103/topics/protein_DNA.html
Identification of a second inducible DNA-protein interaction in ...
previously defined sites of DNA-protein interaction, were constructed as ... Figure 2 A DNA probes used in mobility shift, methylation interference and ...nar.oxfordjournals.org/cgi/reprint/18/4/1037.pdf
Methylation & Uracil Interference Assays
These two analytical methods are presented in parallel, because they assay for similar information based on similar reactions. In both cases, the DNA is analyzed for nucleotides which are important for protein binding. The approach taken is to end label the DNA probe, so that cleavage of the DNA will yield labeled fragments whose size indicates the cleavage position, as in DNase I footprint analysis above.
http://www.e-biotek.com/ebiotek_283.htm
"DNA‐Protein Interactions". In: Current Protocols in ...
the techniques currently used to characterize DNA-protein interactions and ... bound DNA. While methylation interference tends to be more informative than ...doi.wiley.com/10.1002/0471142727.mb1200s56
Springer Protocols: Abstract: Identification of Protein-DNA ...
Identification of Protein-DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference. By: Peter E. Shaw2, A. Francis Stewart3 ...www.springerprotocols.com/Abstract/doi/10.1385/1-59259-208-2:221
In vitro analysis of DNA–protein interactions by proximity ligation
Activation of genes by DNA–protein interactions is a fundamental regulatory ..... as DNase I footprinting, methylation protection, ethylation interference, ...www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1805562
"Methylation and Uracil Interference Assays for Analysis of ...
protein-DNA interactions. BASIC. PROTOCOL. METHYLATION INTERFERENCE ASSAY. Methylation interference identifies guanines and adenines in the DNA binding site ...doi.wiley.com/10.1002/0471142727.mb1203s36
Interference Mapping of Nuclear Protein Binding to the Acute Phase ...
the DNA:protein interactions between C/EBP and. DNA by binding interference, ... amined by methylation interference using DNA modified at specific ...linkinghub.elsevier.com/retrieve/pii/S0006291X99902401
DNA Methylation And Transcriptional Repression
Imgenex Corp. develops novel reagents, including antibodies, gene and protein expression systems, and arrays of various cells and tissues for use in studies ...www.imgenex.com/tech_dna_meth.php