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.
Sunday, May 4, 2008
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)
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
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
Laboratory Manual for Biomedical Research
New Edition
Chapter 1. General Lab Techniques
Lab security and basic techniques
Advanced lab skills
Advanced lab skills (2)
Chapter 2. Molecular Biology -- Molecular Separation
Molecular Separation
DNA Agarose Gel Electrophoresis
RNA Agarose Gel Electrophoresis
SDS-Page - Polyacrylamide gel electrophoresis
2D Page-Two - Dimensional Polyacrylamide Gel Electrophoresis
Ion Exchange Chromatography
Gel Filtration Chromatography
Affinity chromatography
Chapter 3. Molecular Biology -- DNA and RNA
Nucleic acid methods (1)
Nucleic acid methods (2)
DNA isolation & related protocols
DNA Purification (glass milk vs electroelution)
DNA, RNA Sequencing
RNA Isolation and Purification
Isolation of DNA,RNA, and Protein simultaneously.
DNA mutation detection by SSCP
Preparation of DNA and RNA probes
Southern blot hybridization
Northern blot hybridization
Loss of Heterozygosity (LOH)
Gene knockout protocol
SiRNA gene knockout
Plasmid and its usefulness
DNA library construction
Microarray protocols.
Basic knowledge of microarray.
Introduction to Microarray.
MicroArray Procedure
Total RNA Isolation from cultured cells.
DNase Treatment of Total RNA
Making the single strand cDNA probe.
Automated Slide Processor (ASP) Version for hybridization.
Washing microarrays in ASP.
Processing of Array slide
Pre-hybridization of the processed slides (NON-Automated version).
Hybridization of Cy3 + Cy5 probe to glass array (NON-Automated version).
Preparation of Dendrimer Cy3 and Cy5.
Washing unbound probe from glass array (NON-Automated version).
Hybridization of Dendrimers (Cy3 and Cy5) to Array (NON-Automated version).
Washing unbound dendrimer from glass array(NON-Automated version).
Microarray Dababases
Troubleshooting
Other Microarray Protocols (1,2)
Gene transfection
Gene therapy for cancer
Molecular cloning
Conditional gene transfection(Tet on/off)
Chapter 4. Genetics
Epigenetics protocols
Mutagenesis protocols
Single nucleotide polymorphisms (SNPs)
Chapter 5. Molecular Biology --PCR Serials
PCR,RT-PCR,Real time PCR etc.
PCR (General Procedure)
Recommended Reagent Concentrations
Recommended Reaction Conditions
Initial Conditions
Temperature Cycling
"Hot Start" PCR
Asymmetric PCR for ssDNA Production
Detecting Products
Labelling PCR Products with Digoxigenin
Cleaning PCR Products
Sequencing PCR Products
Cloning PCR Products
AND ALWAYS REMEMBER
PCR Primer Design Tools
RT-PCR
Real time PCR
More PCR Protocols Online
Video and Animation of PCR
Mouse Genotyping by PCR
PCR Based Molecular Cloning
PCR Troubleshootings
Chapter 6. Molecular Biology – Protein
Protein methods
Protein labeling techniques
Protein sequencing
Subcellular fractionations
Western blot hybridization
Western Blot Hybridization Center
Western Blot Full Procedure (from Pierce)
Western Blotting Procedure with Video Show
Protocol 1: Western Blot
Sample protein preparation
Protein concentration assay
Electrophoresis and blotting
Blocking non-specific antigen
Incubation with primary antibody
Incubation with secondary antibody
Substrate (ECL) incubation
Restore a western blot using pierce stripping buffer
Western blot related solutions and buffers
Western blot handbook
Western blot troubleshooting
Protocol 2: Western Blot 2.
Protocol 3: Western Blot 3.
More online Western blot protocols (1) (2)
Protein chips
Kinase assay
Methods for detecting protein phosphorylation
Chapter 7. DNA Protein Interactions
EMSA
ChIP assay
Chapter 8. Immunohistochemistry/immunology
Immunology/Histology
Preparing silanized (+plus) slides
Microscopy Techniques
Confocal microscope technique
Electron microscopy
HE staining
DAPI & PI nucleic acid stain
Hybridization in situ
FISH
Special cell & cell fraction stains
Antibody purification
Antibody storage and handling
Conjugation of monoclonal antibodies
Antigen retrieval
Immunoperoxidase staining techniques
Immunofluorohistochemistry
Immunoprecipitation
Histotechnology--technical methods
FRQs for histochemistry
Laser Capture Microdissection
Elisa
Chapter 9. Cellular Biology
General cell culture protocols
Chromosome karyotype
Proliferation assays (MTT, BrdU, 3H-Thymidine incoporation)
Cell cycle assay
Migration assay
Stem cell & related protocols
Introduction
What are the unique properties of all stem cells?
What are embryonic stem cells?
What are adult stem cells?
What are the similarities and differences between embryonic and adult stem cells?
What are the potential uses of human stem cells and the obstacles that must be overcome before these potential uses will be realized?
Where can I get more information?
International Society for Stem Cell Research (ISSCR)
Culture of Human Embryonic Stem Cells (hESC)
Establishment and characterization of human embryonic stem cell line
Rat stem cell isolation and culture
Mouse stem cell isolation and culture
Induction of Stem Cell Differentiation
Cancer stem cells
Video Data on Stem Cell Research (click to show)
Apoptosis and related protocols
Soft Agar Assay for Colony Formation
Aorta ring assay
GFP transfection
Blood cell fractionation (white blood cell isolation)
Endothelial cell isolation and culture protocols
Flow cytometry (FCM)
Chapter 10. Metabolism, GC/MS, NMR and Proteomics
GC/MS Background
Glucose metabolism and its related protocols
PAS staining
Deoxyribose procedure
Ribose metabolism analysis
Polysaccharide sequencing
Lactate cleanup and derivative
Amino acids
Fatty acids
Lipid protocols
Cholesterol
Bile acids
Urea procedure
Choline Incorporation Assay
Isotope Ratio Mass Spectrometer (IRMS)
Liquid chromatography / mass spectrometer (LC/MS)
Proteomics
NMR protocols and tutorials
Chapter 11. Animal Experiments
Blood sampling from animals
Basic skills for animal experiments
Anatomy and physiology of animals
Cancer xenograft animal models
Transgenic animal procedures
Transgenic cancer models
Animal models for depression-like and anxiety-like behavior
Chapter 12. Worm: C. Elegans
C. Elegans Protocols
Chapter 13. HPLC and TLC
HPLC protocols
TLC
Chapter 14. Buffers and Solutions in Lab.
Commonly Used Buffer and solution (114 formats in alphabeta)
Compound solutions (Practical Molecular Biology)How to Make Simple Solutions and Dilutions (Department of Biology, Bates College)Reto's Buffers&Media Book (Private Page)Salt solutions(Practical Molecular Biology)Single Component Solutions (Practical Molecular Biology)Buffers (Gerard R. Lazo)
Antibiotics (Gerard R. Lazo)Buffer Listing (Salmon Lab.)
Cell Culture Media and Solutions (Donis-Keller lab)
Commonly used solutions (1)--- 1 ) 2 ) 3 ) 4 ) 5 ) 6 )
Commonly used solutions (2)--- 1 ) 2 ) 3 )
Solutions for molecular cloning---1 ) 2 ) 3 ) 4 ) 5 ) 6 ) 7 ) 8 ) 9 )
Chapter 15. Other Resources
Free eBooks at Library Online
Cinema Online, Free Movies --(1) (2) (3)
Progresses in Life Science
Progress in Cancer Apoptosis -- (1) (2) (3)
Progress in Gene Therapy --- (1) (2) (3)
Progress in Neuronal Regeneration -- (1) (2) (3)
Progress in AIDS Treatment -- (1) (2) (3)
Progress in Organ Transplantation -- (1) (2) (3)
Progress in Stem Cell Research -- (1) (2) (3)
Free eBooks in life science (1)
Free eBooks in life science (2,3)
Most Updated Biomedical Books
Pathway databases
Pathway Search
Biomedical Job Opportunities
Tools for Statistics
Free Software pDRAW32 to Draw DNA Analysis Charts
Biological Educational Resources
Genetics Education
Resources of Medical Biochemistry
Textbooks and Lab Manuals
New Edition
Chapter 1. General Lab Techniques
Lab security and basic techniques
Advanced lab skills
Advanced lab skills (2)
Chapter 2. Molecular Biology -- Molecular Separation
Molecular Separation
DNA Agarose Gel Electrophoresis
RNA Agarose Gel Electrophoresis
SDS-Page - Polyacrylamide gel electrophoresis
2D Page-Two - Dimensional Polyacrylamide Gel Electrophoresis
Ion Exchange Chromatography
Gel Filtration Chromatography
Affinity chromatography
Chapter 3. Molecular Biology -- DNA and RNA
Nucleic acid methods (1)
Nucleic acid methods (2)
DNA isolation & related protocols
DNA Purification (glass milk vs electroelution)
DNA, RNA Sequencing
RNA Isolation and Purification
Isolation of DNA,RNA, and Protein simultaneously.
DNA mutation detection by SSCP
Preparation of DNA and RNA probes
Southern blot hybridization
Northern blot hybridization
Loss of Heterozygosity (LOH)
Gene knockout protocol
SiRNA gene knockout
Plasmid and its usefulness
DNA library construction
Microarray protocols.
Basic knowledge of microarray.
Introduction to Microarray.
MicroArray Procedure
Total RNA Isolation from cultured cells.
DNase Treatment of Total RNA
Making the single strand cDNA probe.
Automated Slide Processor (ASP) Version for hybridization.
Washing microarrays in ASP.
Processing of Array slide
Pre-hybridization of the processed slides (NON-Automated version).
Hybridization of Cy3 + Cy5 probe to glass array (NON-Automated version).
Preparation of Dendrimer Cy3 and Cy5.
Washing unbound probe from glass array (NON-Automated version).
Hybridization of Dendrimers (Cy3 and Cy5) to Array (NON-Automated version).
Washing unbound dendrimer from glass array(NON-Automated version).
Microarray Dababases
Troubleshooting
Other Microarray Protocols (1,2)
Gene transfection
Gene therapy for cancer
Molecular cloning
Conditional gene transfection(Tet on/off)
Chapter 4. Genetics
Epigenetics protocols
Mutagenesis protocols
Single nucleotide polymorphisms (SNPs)
Chapter 5. Molecular Biology --PCR Serials
PCR,RT-PCR,Real time PCR etc.
PCR (General Procedure)
Recommended Reagent Concentrations
Recommended Reaction Conditions
Initial Conditions
Temperature Cycling
"Hot Start" PCR
Asymmetric PCR for ssDNA Production
Detecting Products
Labelling PCR Products with Digoxigenin
Cleaning PCR Products
Sequencing PCR Products
Cloning PCR Products
AND ALWAYS REMEMBER
PCR Primer Design Tools
RT-PCR
Real time PCR
More PCR Protocols Online
Video and Animation of PCR
Mouse Genotyping by PCR
PCR Based Molecular Cloning
PCR Troubleshootings
Chapter 6. Molecular Biology – Protein
Protein methods
Protein labeling techniques
Protein sequencing
Subcellular fractionations
Western blot hybridization
Western Blot Hybridization Center
Western Blot Full Procedure (from Pierce)
Western Blotting Procedure with Video Show
Protocol 1: Western Blot
Sample protein preparation
Protein concentration assay
Electrophoresis and blotting
Blocking non-specific antigen
Incubation with primary antibody
Incubation with secondary antibody
Substrate (ECL) incubation
Restore a western blot using pierce stripping buffer
Western blot related solutions and buffers
Western blot handbook
Western blot troubleshooting
Protocol 2: Western Blot 2.
Protocol 3: Western Blot 3.
More online Western blot protocols (1) (2)
Protein chips
Kinase assay
Methods for detecting protein phosphorylation
Chapter 7. DNA Protein Interactions
EMSA
ChIP assay
Chapter 8. Immunohistochemistry/immunology
Immunology/Histology
Preparing silanized (+plus) slides
Microscopy Techniques
Confocal microscope technique
Electron microscopy
HE staining
DAPI & PI nucleic acid stain
Hybridization in situ
FISH
Special cell & cell fraction stains
Antibody purification
Antibody storage and handling
Conjugation of monoclonal antibodies
Antigen retrieval
Immunoperoxidase staining techniques
Immunofluorohistochemistry
Immunoprecipitation
Histotechnology--technical methods
FRQs for histochemistry
Laser Capture Microdissection
Elisa
Chapter 9. Cellular Biology
General cell culture protocols
Chromosome karyotype
Proliferation assays (MTT, BrdU, 3H-Thymidine incoporation)
Cell cycle assay
Migration assay
Stem cell & related protocols
Introduction
What are the unique properties of all stem cells?
What are embryonic stem cells?
What are adult stem cells?
What are the similarities and differences between embryonic and adult stem cells?
What are the potential uses of human stem cells and the obstacles that must be overcome before these potential uses will be realized?
Where can I get more information?
International Society for Stem Cell Research (ISSCR)
Culture of Human Embryonic Stem Cells (hESC)
Establishment and characterization of human embryonic stem cell line
Rat stem cell isolation and culture
Mouse stem cell isolation and culture
Induction of Stem Cell Differentiation
Cancer stem cells
Video Data on Stem Cell Research (click to show)
Apoptosis and related protocols
Soft Agar Assay for Colony Formation
Aorta ring assay
GFP transfection
Blood cell fractionation (white blood cell isolation)
Endothelial cell isolation and culture protocols
Flow cytometry (FCM)
Chapter 10. Metabolism, GC/MS, NMR and Proteomics
GC/MS Background
Glucose metabolism and its related protocols
PAS staining
Deoxyribose procedure
Ribose metabolism analysis
Polysaccharide sequencing
Lactate cleanup and derivative
Amino acids
Fatty acids
Lipid protocols
Cholesterol
Bile acids
Urea procedure
Choline Incorporation Assay
Isotope Ratio Mass Spectrometer (IRMS)
Liquid chromatography / mass spectrometer (LC/MS)
Proteomics
NMR protocols and tutorials
Chapter 11. Animal Experiments
Blood sampling from animals
Basic skills for animal experiments
Anatomy and physiology of animals
Cancer xenograft animal models
Transgenic animal procedures
Transgenic cancer models
Animal models for depression-like and anxiety-like behavior
Chapter 12. Worm: C. Elegans
C. Elegans Protocols
Chapter 13. HPLC and TLC
HPLC protocols
TLC
Chapter 14. Buffers and Solutions in Lab.
Commonly Used Buffer and solution (114 formats in alphabeta)
Compound solutions (Practical Molecular Biology)How to Make Simple Solutions and Dilutions (Department of Biology, Bates College)Reto's Buffers&Media Book (Private Page)Salt solutions(Practical Molecular Biology)Single Component Solutions (Practical Molecular Biology)Buffers (Gerard R. Lazo)
Antibiotics (Gerard R. Lazo)Buffer Listing (Salmon Lab.)
Cell Culture Media and Solutions (Donis-Keller lab)
Commonly used solutions (1)--- 1 ) 2 ) 3 ) 4 ) 5 ) 6 )
Commonly used solutions (2)--- 1 ) 2 ) 3 )
Solutions for molecular cloning---1 ) 2 ) 3 ) 4 ) 5 ) 6 ) 7 ) 8 ) 9 )
Chapter 15. Other Resources
Free eBooks at Library Online
Cinema Online, Free Movies --(1) (2) (3)
Progresses in Life Science
Progress in Cancer Apoptosis -- (1) (2) (3)
Progress in Gene Therapy --- (1) (2) (3)
Progress in Neuronal Regeneration -- (1) (2) (3)
Progress in AIDS Treatment -- (1) (2) (3)
Progress in Organ Transplantation -- (1) (2) (3)
Progress in Stem Cell Research -- (1) (2) (3)
Free eBooks in life science (1)
Free eBooks in life science (2,3)
Most Updated Biomedical Books
Pathway databases
Pathway Search
Biomedical Job Opportunities
Tools for Statistics
Free Software pDRAW32 to Draw DNA Analysis Charts
Biological Educational Resources
Genetics Education
Resources of Medical Biochemistry
Textbooks and Lab Manuals
DNase Footprinting
Solid phase DNase I footprinting: quick and versatile
Solid phase DNase I footprinting: quick and versatile. Raphael Sandaltzopoulos and Peter B.Becker*. European Molecular Biology Laboratory, Gene Expression ...
nar.oxfordjournals.org/cgi/reprint/22/8/1511.pdf
DNase I Footprinting DNase I Footprinting Title | Overview ...
DNase I Footprinting. Title | Overview | Procedure | Solutions | BioChemicals | Hints | Printable Version. Overview ...
www.koko.gov.my/CocoaBioTech/Protein%20DNA5.html
Springer Protocols: Abstract: DNase i footprinting using PCR ...
Springer Protocols is the largest subscription-based electronic database of reproducible laboratory protocols in the Life and Biomedical Sciences.
www.springerprotocols.com/Abstract/doi/10.1385/0-89603-288-4:379
Springer Protocols: Abstract: DNase I Footprinting
Low C. M. L., Olsen R. K., and Waring M. J. (1984) Sequence preferences in the binding to DNA of triosim A and TANDEM as reported by DNase I footprinting. ...
www.springerprotocols.com/Abstract/doi/10.1385/0-89603-447-X:1
Solid-phase DNase I Footprinting
4 [ 1 9 9 5 ]. 25. CONTENTS. Introduction. Solid-phase techniques have diversified. the repertoire of tools in molecular biology ...
www.roche-applied-science.com/PROD_INF/BIOCHEMI/No.4_95/p25-27.pdf
Footprinting in the 21st century Chromatin preparation and DNase I ...
Footprinting in the 21st century. Chromatin preparation and DNase I treatment. Summary. Cells are spun down, the supernatant removed, the pellet resuspended ...
science.cancerresearchuk.org/sci/chromrep/pdf/footprint.pdf?version=1
Chapter 16: Protease Footprinting (PDF)
INTRODUCTION, 285. Advantages and limitations, 287. Types of proteolysis, 288. Alternative methods, 289. OUTLINE OF PROCEDURE, 290. End labeling, 290 ...
www.proteinsandproteomics.org/content/free/protocols_2/285-312-PI-Ch16.pdf
Biochemistry 611 Nucleic Acids 8-28-07
Biochemistry 611 Nucleic Acids 8-28-07.
www.mc.uky.edu/biochemistry/courses/bch611/2007/wilkerson/Bioch611_8_28_2007.ppt
DNase I-Primer Extension Footprinting Of Chromatin Assembled On Template DNA
Mapping DNase-I-Hypersensitive Sites (Subscription Required)
Mapping Protein-Binding Sites On DNA By DNase I Footprinting - Subscription Required
Preparation Of End-Labeled DNA Probes By Conventional Kinase For DNA Footprinting Analysis
DNase Footprinting (1)
Core Footprinting System Technical Bulletin TB137
T e ch ni cal Bu llet in. Core Footprinting System. INSTRUCTIONS FOR USE OF PRODUCT E3730. PRINTED IN
www.promega.com/tbs/tb137/tb137.pdf
Catharineís Footprint Protocol
Catharineís Footprint Protocol. August, 1999. This protocol assumes that the user has already performed gel-shift experiments with their fragment and ...
www.stanford.edu/~ceastman/footprint.html
DNase I footprinting. P.J. Shaw pjs14 at le.ac.uk Sat Jul 26 04:12:40 EST 1997. Previous message: DNase I footprinting; Next message: QIAQuick and QIAPrep
www.bio.net/bionet/mm/methods/1997-July/059706.html
staff.aist.go.jp/m.machida/technicalnote.htm
Mapping Protein-binding Sites on DNA by DNase I Footprinting ...
Search CSH Protocols. Advanced Search · Find Protocols · Find a Kit · Access Personal Page · Submit Protocols · Help · Subscribe · About CSH Protocols ...
www.cshprotocols.org/cgi/content/full/2006/2/pdb.prot3947
1. DNase I Footprinting. Keith R. Fox. 1. Introduction. Footprinting provides a simple, quick, and reasonably inexpensive method ...
www.springerlink.com/index/tv748uh685874403.pdf
Analysis of Protein-DNA Interactions
The characterization of the protein-DNA interactions usually requires three levels of analysis:. GENETIC. determination of the nucleotide sequence of the ...
www.mun.ca/biochem/courses/4103/topics/protein_DNA.html
DNA Footprinting with an automated DNA Analyzer: does the shoe fit?
DNA Footprinting with an. automated DNA Analyzer:. does the shoe fit? Michael Zianni. Manager, Plant-Microbe Genomics Facility ...
www.abrf.org/ResearchGroups/DNASequencing/Activities/DNAFootprinting.pdf
Core Footprinting System Technical Bulletin TB137
T e ch ni cal Bu llet in. Core Footprinting System. INSTRUCTIONS FOR USE OF PRODUCT E3730. PRINTED IN
www.promega.com/tbs/tb137/tb137.pdf
DNase I footprinting. P.J. Shaw pjs14 at le.ac.uk Sat Jul 26 04:12:40 EST 1997. Previous message: DNase I footprinting; Next message: QIAQuick and QIAPrep
www.bio.net/bionet/mm/methods/1997-July/059706.html
Protocol F.2. DNaseI Footprintint. Solutions. 10X Binding Buffer. 200 mM Tris 8.0 200 ml 1M Tris pH 8.0. 500 mM NaCl 100 ml 5M NaCl ...
genetics.med.harvard.edu/~cepko/protocol/mike/F2.html
staff.aist.go.jp/m.machida/technicalnote.htm
1. DNase I Footprinting. Keith R. Fox. 1. Introduction. Footprinting provides a simple, quick, and reasonably inexpensive method ...
www.springerlink.com/index/tv748uh685874403.pdf
Analysis of Protein-DNA Interactions DNA Footprinting with an automated DNA Analyzer: does the shoe fit?
DNA Footprinting with an. automated DNA Analyzer:. does the shoe fit? Michael Zianni. Manager, Plant-Microbe Genomics Facility ...
www.abrf.org/ResearchGroups/DNASequencing/Activities/DNAFootprinting.pdf
Tsukiyama Lab/protocols/DNase_I_Footprinting. 1. DNase I footprinting. I. Labeling of probe. •. 5 pmoles of primer #1. •. 1.5 µl of 10 X T4 PNK buffer ...
www.fhcrc.org/science/labs/tsukiyama/protocols/dnase_i_footprinting.pdf
A 96-well DNase I footprinting screen for drug–DNA interactions
Supplementary Material. PDF (6.1M) · Contents · Archive. Related material:. PubMed record, PubMed related arts, PubMed LinkOut, Substance, Taxonomy ...
www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1919508
A modified protocol for in vivo footprinting by ligation-mediated ...
Selected References. Page Browse · PDF (545K) · Contents · Archive. Related material:. PubMed record, PubMed related arts, PubMed LinkOut, Substance ...
www.pubmedcentral.nih.gov/articlerender.fcgi?artid=523615
Using a comparative in vivo DNase I footprinting technique to ...
J BIOCHEM MOLECULAR TOXICOLOGY. Volume 21, Number 5, 2007. Using a Comparative In Vivo DNase I Footprinting. Technique to Analyze Changes in Protein–DNA ...
doi.wiley.com/10.1002/jbt.20192
DMS Footprinting Protocols
DMS Footprinting Protocols
- Overview – Slide Shows for Footprinting
Chromatin Immunoprecipitation (2)
Other ChIP Online Resources
Chromatin Immunoprecipitation (ChIP) Online Resources
Chromatin immunoprecipitation - Wikipedia, the free encyclopedia
Chromatin Immunoprecipitation (ChIP) Assay
Chromatin Immunoprecipitation (ChIPs) Articles
Chromatin Immunoprecipitation and Microarray-Based Analysis of Protein Location
Chromatin Immunoprecipitation (ChIPs) Protocol (Farnham Lab)
Chromatin Immunoprecipitation (ChIPs) Protocol for Tissues
Chromatin immunoprecipitation on native chromatin from cells and tissues
Chromatin Immunoprecipitation Protocol for Histone Modification & Chromatin Associated Proteins
Chromatin Immunoprecipitation Protocol to Analyze Histone Modifications in Arabidopsis thaliana
chIP on chip.org Hosted by Bing Ren's lab at UCSD.
Chromatin Immunoprecipitation Protocol
Chromatin Immunoprecipitation Supplies
Comparison of Sample Preparation Methods for ChIP-chip Assays
NATIVE CHROMATIN IMMUNOPRECIPITATION (N-ChIP) PROTOCOL
High Throughput Screening of Chromatin Immunoprecipitates Using CpG-Island Microarrays
Use of Chromatin Immunoprecipitation to Clone Novel E2F Target Promoters
WGA Publication Supplemental Information
Whole Genome Amplification Protocol
Protocol for the fast chromatin immunoprecipitation (ChIP) method.
Workshop Chromatin Immunoprecipitation Protocol
Q ChIP - quick and quantitative chromatin immunoprecipitation
Immunoprecipitation (IP)/Chromatin Immunoprecipitation (ChIP Assay ...
Chromatin IP Chromatin Immunoprecipitation ChIP-IT
CSH Protocols -- Collected Resources : Immunoprecipitation
Application Note, ChIP-on-chip Gene Regulation
MPromDb: an integrated resource for annotation and visualization ...
Assessment of sera for chromatin-immunoprecipitation | Archive ...
Application of the Chromatin Immunoprecipitation Method to ...
ChIP (Chromatin Immunoprecipitation): Frequently Asked Questions
GEArray Analysis—ChIP-qPCR
Cavalli lab - Inserm workshop on ChIP and Immuno-FISH, June 2001-bis
ChIP ASSAY GUIDELINES AND CHECKPOINTS--Affymetrix
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