MCB 730: Southern Blot Lab

1. MCB 730: Southern Blot Lab Southern, Northern & Western blotting Background Overview Detailed Protocol

2. Who is this guy?

3. Sir Edwin Mellor Southern of course (1938- ) • Inventor of the Southern blot • http://en.wikipedia.org/wiki/Edwin_Southern

4. Characterization: Southern blot hybridization -transfer of DNA from a gel to a membrane (e.g., nitrocellulose, nylon) -developed by Edwin Southern

5. Characterization: Northern blot hybridization X RNA X x salt X RNA -transfer of RNA from a gel to a membrane (e.g., nitrocellulose, nylon) -reveals mRNA size (and approximate protein size), tissue- and organ- specific expression, and kinetic patterns of expression

6. Characterization: Western blotting X Protein Enzyme reaction or X React with Antibody X x Buffer; requires electric current X -transfer of protein from a gel to a membrane (e.g., nitrocellulose, nylon) -requires the use of an electric current to facilitate transfer

7. DNA Microarrays: An Introduction

8. Microarray Result: Much analysis to follow

9. Southern blot hybridization -transfer of DNA from a gel to a membrane (e.g., nitrocellulose, nylon) -developed by Edwin Southern

10. Southern blotting of genomic DNA Steps 1. Extraction of genomic DNA 2. Electrophoresis of genomic DNA (or more commonly restriction enzyme-digested genomic DNA)

11. 3. Before blotting, treat the gel with 0.2N HCl, denaturation and neutralization solution 4. Blotting- Transfer gel to the nitrocellulose membrane by capillary action A) Sponge method

12. B) Wick method

13. 5. After the transfer, cross-link the DNA to the nitrocellulose membrane A. UV- cross linking B. Bake at 120°C for 30 min C. Bake at 80°C for 2 hrs

14. 6. Making the probe Label the probe to be hybridized using radioactive or non-radioactive methods Non-radioactive methods A) Colorimetric B) Chemiluminescent * Roche DIG- DNA labeling (Non-radioactive) kits are used for detection

15. DIG or Digoxigenin is used for labeling the probe. DIG steroid found exclusively in the flowers and leaves of the plants Digitalis purpurea, Digitalis orientalis and Digitalis lanata (foxgloves). (see http://en.wikipedia.org/wiki/Digoxigenin) DIG-11-dUTP replaces dTTP in the random primed DNA labeling reaction. DIG-DNA Labeling: DNA is random primed labeled with Digoxigenin-11-dUTP using DIG-High Prime, a 5x concentrated labeling mixture of random hexamers, dNTP mix containing alkali-labile Digoxigenin-11-dUTP, labeling grade Klenow enzyme and an optimized reaction buffer.

16. Structure of digoxigenin- and biotin-modified nucleotides Note that the digoxigenin and biotin groups in these examples are linked to the 5′ carbon atom of the uridine of dUTP by spacer groups consisting respectively of a total of 11 carbon atoms (digoxigenin-11-UTP) or 16 carbon atoms (biotin-16-dUTP). The digoxigenin and biotin groups are reporter groups: after incorporation into a nucleic acid they are bound by specific ligands containing an attached marker such as a fluorophore.

17. Arabidopsis T-DNA mutant LB T-DNA RB Gene LB RB T-DNA 1000bp probe Disruptedgene

18. 7. Prehybridization and hybridization of probe to the membrane at the hybridization temperature. 8. Washes and immunological detection Detection after stringency washes using anti-digoxigenin antibody conjugated to AP (Alkaline phosphatase)

19. Colorimetric detection using NBT/ BCIP BCIP is colorless and is dephosphorylated by AP Dephosphorylated BCIP is oxidized by NBT Oxidized BCIP will turn into a dark blue indigo dye NBT is reduced to a dark blue dye

20. BCIP and NBT: additional information • 5-Bromo-4-chloro-3-indolyl phosphate (BCIP) is a chemical compound used in immunoblotting, in situ hybridization, and immunohistochemistry, with nitro blue tetrazolium chloride (NBT), for sensitive colorimetric detection of alkaline phosphatase.NBT serves as the oxidant (and gives also dark blue dye) and BCIP is the alkaline phosphatase substrate. Alkaline phosphatase is commonly conjugated to secondary antibodies. • BCIP (colorless)oxidation→ blue precipitate. BCIP-NBT naturally forms this bluish purple precipitate over time; however, alkaline phosphatase speeds up the process 1000 fold. BCIP binds very tightly in the alkaline phosphatase active site, but when NBT reacts with BCIP, it is released from the enzyme and the colored precipitate forms. • Nitro blue tetrazolium is a chemical compound composed of two tetrazolemoieties. It is used in immunology for sensitive detection of alkaline phosphatase (with BCIP). NBT serves as the oxidant and BCIP is the AP-substrate (and gives also dark blue dye). In immunohistochemistry the alkaline phosphatase is often used as a marker, conjugated to an antibody. The colored product can either be of the NBT/BCIP reaction reveals where the antibody is bound, or can be used in immunofluorescence.

21. Colorimetric blot

22. Chemiluminescent detection using CSPD • Dephosphorylation of CSPD by alkaline phosphatase to the metastable phenolate anion. • Phenolate anion decomposes and emits light at a wavelength of 477 nm. • Light emission is captured on X-rays. • chloro-5-substituted adamantyl-1,2-dioxetane phosphate (CSPD), formally disodium 3-(4-methoxyspiro{1,2-dioxetane-3,2'-(5'-chloro)tricyclo[3.3.1.13,7]decan}-4-yl)phenyl phosphate is a chemical substance with formula C18H20ClO7PNa2. It is a component of enhanced chemiluminescenceenzyme-linked immunosorbent assay (ELISA) kits, used for the detection of minute amounts of various substances. • In typical uses of ELISA kits, the enzymealkaline phosphatase removes the phosphate group from CSPD, yielding a reactiveanion (phenolate, which then splits itself in two components, adamantane and 1,2-dioxetane. This second reaction emitsturquoise-coloured light (λmax = 477 nm). The decomposition of the dioxetane generates a secondary glow.