Comparison of Southern,Northern, and Western analysesof Gene X
Southern hybridization First described by E. M. Southern in 1975. Applications of Southern hybridization   RFLP’s, VNTR...
Southern hybridization    Transfer buffer
Detection of an RFLP bySouthern blotting
Detection of the sickle-cellglobin gene by Southernblotting
Checking of the gene knockoutmice
Flow chart of Southernhybridization     Preparing the samples and running the gel                   Southern transfer     ...
Preparing the samples andrunning the gel   Digest 10 pg to 10 µg of desired DNA samples    to completion.   Prepare an a...
Critical parameters (I) Note the complexity of DNA   Genomic DNA     A single-copy of mammalian gene, 3 Kb      average...
Gel treatment Acid treatment   0.2 N HCl solution Denaturation   NaOH solution Neutralization   Tris-Cl buffer (pH8.0)
Southern transfer            Measure gel and set up transfer             assembly:                Wick in tray with 20x ...
After Southern transfer            Dissemble transfer             pyramid and rinse             nitrocellulose in 2x SSC ...
Preparation of probes  Synthesis of uniformly labeled   double-stranded DNA probes  Preparation of single-stranded probe...
Synthesis of double-stranded DNAprobes - Nick translation of DNA - Labeled DNA probes using random  oligonucleotide primers
Nick translation
Preparation of single-strandedprobes  Synthesis of single-stranded DNA probes   using bacteriophage M13 vectors.  Synthe...
In vitrotranscription
Labeling the 5′ and 3′ termini of DNA   Labeling the 3′ termini of double-stranded DNA    using the Klenow fragment of E....
T4 polynucleotide kinaseactivity
Non-isotope labeling Digoxigenin-11-dUTP (DIG-dUTP) labeling  - DNA labeling  - Oligonucleotide labeling  - RNA labeling
PCR Labeling, Random PrimedLabeling, and RNA Labeling
Prehybridization Add prehybridization solution and  prehybridize at hybridization temperature for  2-4 hr
Hybridization            Remove prehybridization             solution and add             hybridization solution         ...
Post-hybridization washing Wash twice, 15 min each, in 1x SSC, 0.1% SDS at  room temperature. Wash twice, 15 min each, i...
Critical parameters (II)  Homology between the probe and the sequences   being detected    Tm = 81 +16.6 (log Ci) + 0.4 ...
Comparison of nitrocelluloseand nylon membranes    NC                   Nylon    Hydrophobic binding Covalent binding    F...
Signals detection Autoradioragraphy Non-isotope detection system  - Chemiluminescent detection  - Colorimetric detection...
Autoradiography              Exposure to x-ray film
Northern blotting or Northernhybridization  Technique for detecting specific RNAs   separated by electrophoresis by hybri...
The flow chart of Northernhybridization samples and run RNA gel        Prepare RNA                  Northern transfer     ...
Preparation ofagarose/formaldehyde gel  E.g. Prepare a 350 ml 1.2%   agarose/formaldehyde gel    4.2 g agarose in 304.5 ...
Preparation of RNA samples Prepare a premix:    5 µl of 10x MOPS running buffer    8.75 µl of 37% formaldehyde    25 µ...
Running the RNA gel Add 10 µl formaldehyde loading buffer to  each sample and load gel. Run gel at 100 to  120 V for ~3hr...
An example of Northern blottingNorthern blot  RNA gel                 28 S                          18 S
Western blotting, orimmunoblottingTechnique for detecting specific proteinsseparated by electrophoresis by use oflabeled a...
Flow chart of Western blotting                   Electrophoresing the protein sample                 Assembling the Wester...
SDS polyacrylamide-gelelectrophoresis (SDS-PAGE)
Analysis of protein samples by SDSpolyacrylamide-gel electrophoresis andWestern blotting                                  ...
Comparison of Southern, Northern,and Western blotting techniques                  Southern blotting   Northern blotting   ...
Southern northern and western blotting
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Southern northern and western blotting

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Southern northern and western blotting

  1. 1. Comparison of Southern,Northern, and Western analysesof Gene X
  2. 2. Southern hybridization First described by E. M. Southern in 1975. Applications of Southern hybridization  RFLP’s, VNTR’s and DNA fingerprinting  Checking of the gene knockout mice The flow chart of Southern hybridization
  3. 3. Southern hybridization Transfer buffer
  4. 4. Detection of an RFLP bySouthern blotting
  5. 5. Detection of the sickle-cellglobin gene by Southernblotting
  6. 6. Checking of the gene knockoutmice
  7. 7. Flow chart of Southernhybridization Preparing the samples and running the gel Southern transfer Probe preparation Isotope Non-isotope Prehybridization Hybridization Post-hybridization washing Signal detection
  8. 8. Preparing the samples andrunning the gel  Digest 10 pg to 10 µg of desired DNA samples to completion.  Prepare an agarose gel, load samples (remember marker), and electrophorese.  Stain gel ethidium bromide solution (0.5 µg/ml).  Photograph gel (with ruler).
  9. 9. Critical parameters (I) Note the complexity of DNA  Genomic DNA  A single-copy of mammalian gene, 3 Kb average in length 10 µg x 3 Kb/3 x 106 Kb = 10 µg x 1/106 = 10 pg  Plasmid DNA or PCR products 0.1 µg of a 3 Kb plasmid DNA ≅100 ng
  10. 10. Gel treatment Acid treatment  0.2 N HCl solution Denaturation  NaOH solution Neutralization  Tris-Cl buffer (pH8.0)
  11. 11. Southern transfer  Measure gel and set up transfer assembly:  Wick in tray with 20x SSC  Gel  Nitrocellulose or Nylon filters (soaked in H2O and 20x SSC)  3MM Whatman filter paper  Paper towels  Weight
  12. 12. After Southern transfer  Dissemble transfer pyramid and rinse nitrocellulose in 2x SSC  Bake nitrocellulose at 80°C for 2 hr or UV-crosslink Nylon membrane for seconds
  13. 13. Preparation of probes  Synthesis of uniformly labeled double-stranded DNA probes  Preparation of single-stranded probes  Labeling the 5′ and 3′ termini of DNA
  14. 14. Synthesis of double-stranded DNAprobes - Nick translation of DNA - Labeled DNA probes using random oligonucleotide primers
  15. 15. Nick translation
  16. 16. Preparation of single-strandedprobes  Synthesis of single-stranded DNA probes using bacteriophage M13 vectors.  Synthesis of RNA probes by in vitro transcription by bacteriophage DNA- dependent RNA polymerase.
  17. 17. In vitrotranscription
  18. 18. Labeling the 5′ and 3′ termini of DNA  Labeling the 3′ termini of double-stranded DNA using the Klenow fragment of E. coli DNA polymerase I. (lack of 5’  3’ exonuclease activity)  Labeling the 3′ termini of double-stranded DNA using bacteriophage T4 DNA polymerase.  Labeling the 5′ termini of DNA with bacteriophage T4 polynucleotide kinase.
  19. 19. T4 polynucleotide kinaseactivity
  20. 20. Non-isotope labeling Digoxigenin-11-dUTP (DIG-dUTP) labeling - DNA labeling - Oligonucleotide labeling - RNA labeling
  21. 21. PCR Labeling, Random PrimedLabeling, and RNA Labeling
  22. 22. Prehybridization Add prehybridization solution and prehybridize at hybridization temperature for 2-4 hr
  23. 23. Hybridization  Remove prehybridization solution and add hybridization solution  Add 500,000 cpm of the probe/ml hybridization solution.  Hybridize overnight at appropriate temperature.
  24. 24. Post-hybridization washing Wash twice, 15 min each, in 1x SSC, 0.1% SDS at room temperature. Wash twice, 15 min each, in 0.25x SSC, 0.1%SDS at hybridization temp
  25. 25. Critical parameters (II)  Homology between the probe and the sequences being detected  Tm = 81 +16.6 (log Ci) + 0.4 [% (G+C)] - 0.6 (% formamide)- 600/n - 1.5 (% mismatch)  Factors can be changed:  Hybridization temp.  Washing temp.  Salt concentration during washing High temp., low salt: high stringency Low temp., high salt: low stringency  If 50 % formamide is used  42 oC for 95 ~ 100 % homology  37 oC for 90 ~ 95 % homology  32 oC for 85 ~ 90 % homology
  26. 26. Comparison of nitrocelluloseand nylon membranes NC Nylon Hydrophobic binding Covalent binding Fragile Durable Probe length > 200 ~ < 200 ~ 300 bp is 300 bp O.K. Lower background Higher background Cannot be exposed Can be exposed to to basic solution basic solution Not easily Can be reprobed reprobed several times
  27. 27. Signals detection Autoradioragraphy Non-isotope detection system - Chemiluminescent detection - Colorimetric detection - Multicolor detection
  28. 28. Autoradiography  Exposure to x-ray film
  29. 29. Northern blotting or Northernhybridization  Technique for detecting specific RNAs separated by electrophoresis by hybridization to a labeled DNA probe.
  30. 30. The flow chart of Northernhybridization samples and run RNA gel Prepare RNA Northern transfer Probe preparation Isotope Prehybridization Non-isotope Hybridization Post-hybridization washing Signal detection
  31. 31. Preparation ofagarose/formaldehyde gel  E.g. Prepare a 350 ml 1.2% agarose/formaldehyde gel  4.2 g agarose in 304.5 g water. Microwave, then cool to 60°C. Add 35 ml 10x MOPS running buffer and 10.5 ml 37% formaldehyde
  32. 32. Preparation of RNA samples Prepare a premix:  5 µl of 10x MOPS running buffer  8.75 µl of 37% formaldehyde  25 µl of formamide. Prepare RNA samples:  38.75 µl of premix  RNA (0.5 to 10 µg)*  water to 50 µl *If the mRNA species of interest makes up a relatively high percentage of the mRNA in the cell (>0.05% of the message), total cellular RNA can be used. If the mRNA species of interest is relatively rare, however, it is advisable to use poly(A)+ RNA. Incubate 15 min at 55°C
  33. 33. Running the RNA gel Add 10 µl formaldehyde loading buffer to each sample and load gel. Run gel at 100 to 120 V for ~3hr. Remove gel from the running tank and rinse several times in water. Place gel in 10x SSC for 45 min. Do not need post-transferring gel treatment
  34. 34. An example of Northern blottingNorthern blot RNA gel 28 S 18 S
  35. 35. Western blotting, orimmunoblottingTechnique for detecting specific proteinsseparated by electrophoresis by use oflabeled antibodies.
  36. 36. Flow chart of Western blotting Electrophoresing the protein sample Assembling the Western blot sandwich Transferring proteins from gel to nitrocellulose paper Staining of transferred proteins Blocking nonspecific antibody sites on the nitrocellulose paper Probing electroblotted proteins with primary antibody Washing away nonspecifically bound primary antibodyDetecting bound antibody by horseradish peroxidase-anti-Ig conjugate and formation of a diaminobenzidine (DAB) precipitate Photographing the immunoblot
  37. 37. SDS polyacrylamide-gelelectrophoresis (SDS-PAGE)
  38. 38. Analysis of protein samples by SDSpolyacrylamide-gel electrophoresis andWestern blotting Protein bands detected by specific antibody SDS-PAGE Western blot
  39. 39. Comparison of Southern, Northern,and Western blotting techniques Southern blotting Northern blotting Western blotting Molecule DNA (ds) mRNA (ss) Protein detected Gel Agarose gel Formaldehyde Polyacrylamide gelelectrophoresis agarose gel Gel Depurination, - - pretreatment denaturation, and neutralizationBlotting method Capillary transfer Capillary transfer Electric transfer Probes DNA cDNA, cRNA primary antibody Radioactive or Radioactive or nonradioactive nonradioactive Detection Autoradiography Autoradiography Chemiluminescent system Chemiluminescent Chemiluminescent Colorimetric Colorimetric Colorimetric
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