Ned Lab's Protocols





The followings are some tips on how to protect our scanner from the damage:


1. The computer should be on whenever the controller is on! Turn the computer on before the nanoscope controller!


2. On the scan control panel, avoid OFFSET voltages outside of +/- 150V for periods of more than about an hour. Whenever its possible, reset them to zero.


3. Avoid using maximum scan size for long periods (for instance, size greater than 40- 120 um) if not necessary.


4. Avoid leaking when organic solvents were used (isopropanol) during imaging.


5. The right way to start and shut down the scope should be as following:

On:  Main power---computer--controller

Off: Controller--Computer--main power


(This will protects the DSP, digital signal processor, and interface boards from damage by large random current)


6. Fluid cell is a very fragile since it is made of the glass itself. Avoid dropping it to the floor when you load the tip or install it into the scope head. Please don't press the spring clip too hard when you load the tip. 


7. If you encounter with the extreme noising signal or the blurring during the imaging, you should check that the air table is functioning properly, the mica sticks tightly with the magnet plate and the magnet plate contact directly to the  tube scanner. (make sure that  the silicon seal does not get in the way)



Formation of Hydrogen-bonded Complexes:



1. Complexes are formed by mixing a stoichiometric quantity of each strand, as estimated by OD260. 


2. This mixture is then heated to 95 C for 5 minutes and cooled to the desired temperature by the following protocol:  20 minutes at 65 C, 15 minutes at 50 C, 20 minutes at 37 C, and if desired, 20 minutes at room temperature.


3. When slow annealing is desirable, the mixture is heated at 95 C for 5 minutes, then transferred to a 2-liter water bath, preheated to about 90C and placed inside a Styrofoam box, and allowed to cool slowly to the desired temperature over the period of two days.



3-D Crystal (DNA treatment before the setting-up)



1. Purify strands using standard purification. Overnight dialysis in 2L of dd water to help get rid of salt and EB.  Filter strands with 0.22um microcentrifuge filters. 


2. Filter dd water and 10X TAE/Mg buffer using 0.22um syringe filters. 


3. Add water, buffer, and DNA to the 1.5 ml tubes.  Vortex for at least 1 min, spin down.


4. For slow anneal:


Bring 2 L of d water to boil.  Place in styrofoam box.  After ~24hrs, place box in cold room for at least another 12 hrs.


5. For fast anneal:


5 min at 90, 30 min at 65, 30 min at 50, 30 min at 37 in heating blocks


Denaturing Gels: 


1. These gels contain 8.3 M urea and are run at 55 C.


2. The running buffer consists of 89 mM Tris.HCl, pH 8.0, 89 mM Boric acid, 2 mM EDTA (TBE). 


3. The sample buffer consists of 10 mM NaOH, 1 mM EDTA, containing trace amount of Xylene Cyanol FF and Bromophenol Blue tracking dye.


4. Gels are run on a Hoefer SE 600 electrophoresis unit at 55 C (31 V/cm, constant voltage). 


5. When further denaturation is required, a 6% acrylamide gel solutions containing 7.0 M urea and 41 % formamide, or a 4% acrylamide gel solutions containing 6.8 M urea and 47 % formamide is substituted for a regular denaturing gel.



EXO Digestion:


1. Mix DNA, EXO buffer and dd-H2O to bring to certain volume (30 ul, generally) of mixture which is equivalent to 1x EXO buffer.


2. Add 1ul Exo(I) and 1ul Exo(III) respectively.


3. Incubate at 37 oC for about 2 hours.


4. For some complicated molecule.


The special treatment before Exo is needed: Heating to 90 oC for 10min, then cooling to 0 oC quickly by put it on ice.  Then step 2-3.



Fe-EDTA Cutting


Solutions( All must be fresh):


I. EDTA(mw 372.2)

          20X (4mM),  0.0744g in 50ml water

               final cutting conc: 0.2mM

II. L-Ascorbic Acid ( Sodium Salt) (mw 198.1)

         10X soln (10mM),  0.09905g in 50ml water

          final cutting conc: 1mM


       10X=1.5% ,  50ul 30% to 1000ul

      final cutting conc: 0.15%

IV. Fe(II) (Ammonium iron(II) Sulfate Hexahydrate) (mw 392)

      20X = 2mM, 0.0392g in 50ml water

       final cutting conc=0.1mM

V. thiourea(mw 76.12)

           10X = 10 mM,  0.03806g in 50ml water

               final cutting conc: 1mM




1. Anneal complex, put it on ice.


2. Place 1ml of each of the following solns in 1.5 ml tubes and place on ice for 1 hr

    1.L-ascorbic acid

    2. Fe-EDTA(each 500ul)

    3. H2O2

    4. thiourea


3. Placing 6ul DNA in the tube, and add 1ul of solns I,II,III one by one to the wall of the tube. Do not mix I.II.III until III is added. Mixing soln with the pipette tip ( not vertex) and push the mixture into the DNA solution.


4. After 100 secs (exactly), add 1ul thiourea directly to soln and vortex. Then add 1ml 100% ETOH and place into dry ice


5. Ethanol Precipitation and recover DNA.


Fill-in Reaction by Klenow Fragment (Adding Cy3 fluorescence dye to a DNA strand)


Anneal the DNA template and primer in 1X Eco Pol buffer (polymerase reaction buffer). Then add the specified free dNTPs, dCTP-Cy3 and the desired amount of klenow fragment polymerase, place in the 37oC incubator for about one and half hours. Then perform ethanol precipitation and purification.



Kination (Radioactive labeling) by the Phosphorylation


10 ul reaction:


Step 1.        1 pmole DNA (1 ul)

                    10x kination buffer (1 ul)

                       2.2 pmol labeled ATP (1 ul)

                       1 ul kinase (Diluted, 3 units/ul)

                       6 ul dd water.

                       The reaction proceeds at 37 degree in about 1 hours.


Step 2. Kinase is inactivated at 90 degree in about 5 min and filtered through the G-25 microspin  column (Pharmacia) to remove unincorporated g-32P-ATP


Step 3. Phenol extraction and ethanol precipitation. Dry down the liquid and hot DNA is purified by 10 to 15 % denaturing gel. 


Step 4. Salts in eluted DNA is removed by. Purified DNA is ready for annealing.






1. Make reaction solutions ( total V ul ) :


    DNA strands

   V/10 ul 10X ligation buffer

   dd H2O to V ul


2. Annealing to 4 oC as the protocol described in the annealing protocol.


3. Add  ligase and stand at 16 oC for at least 16 hrs.


4. Add one more time ligase at  16 oC  if it is necessary.




Non-Denaturing Gels:


1. The running buffer consisting of 40 mM Tris-HCl (pH 8.0), 20 mM Boric acid, 2 mM EDTA and 12.5 mM magnesium acetate (TAE/Mg).


2. The DNA is dissolved in 10 uL of TAE/Mg buffer. 10X Tracking dye (1 uL) containing TAEMg, 50% glycerol and trace amount of Bromophenol Blue and Xylene Cyanol FF is added to  the sample buffer. 


3. Gels are run on a Hoefer SE-600 gel electrophoresis unit at 12-16 V/cm at  the desired temperature.



Phenol Extraction


1. Add an equal vol. of saturated phenol to the DNA solution.( 0.1 -0.4 ml, monovalent cation smaller than 0.5 M , high salt causes inversion of aqueous and organic phases , the organic phase should be yellow in this case. 50 -100 ul is too small, need to be diluted.


2.Vortex vigorously for 10 sec.


3. Spin 15 sec at room temp. in microcentrifuge.  If solution is viscous and contain a large amount of protein, spin longer ( 1 to 2 min ).


4. Carefully remove the top aqueous phase to a new tube.


5. Add an equal vol. of saturated phenol/ chloroform (1:1) to the DNA solution. Repeat 2-4.


6. Add an equal vol. of chloroform to the DNA solution. Repeat 2-4.




Purification of DNA:. 



1. DNA strands have been purified by denaturing gel electrophoresis.


2. Eithidium bromide stained bands are cut out of 10-20% denaturing gels and eluted in a solution containing 500 mM ammonium acetate, 10 mM magnesium acetate and 1 mM EDTA.


3. The eluates are subjected to extraction with n-butanol to remove the ethidium, followed by ethanol precipitation.




Recovering the DNA from the Gel


1. Cut out the band with a razor blade.


2. Chop the slice into fine pieces.


3. Transfer them into a 1.5 -ml microcentrifuge tube (Larger tube for larger volume)


4. Add the elution buffer (0.5M ammonium acetate,  1 mM EDTA, 10 mM Tris-HCl, pH=7.6),  at least twice of the volume of the gel.


5. Shake at 4C overnight.


6. Spin 1 min and collect the supernatant.


7. Recover any residual DNA by rinsing with small volume of elution buffer. Spin and combine the supernatants.


8. The eluates are subjected to extraction with n-butanol to 1/3 of the original volume and add 1ml 100% ethanol.


9. Place the tube in dry ice for 45 mins.


10. Spin at 10,000 rpm (13,000 X g) for 30 min in microcentrifuge and discard the supernatant.


11. Wash the pellet with 1ml 70 % ethanol and spin 7 mins. Then dry and resuspend in TE buffer.





1. Mix:



restriction buffer,



2. Anneal DNA by keeping at


90 C for 5 min,

65 C for 15 min,

37 C for 20 min,

RT for 20 min.


3. Add certain amount of restriction enzyme (no more than 1/10 of reaction mixture).


4. Incubate at the recommended temperature for the desired time.



Maxam-Gilbert Sequencing


1. 20 ul labeled DNA in water( about 50k)


2. Keep it in 0 degree for 1 hr.


3. Add 50 ul Formic acid, votex, keep in RT 4 mins.


4. Add: 180 ul HZ-stop solution( 2ml includes 5 ul tRNA, 40 ul EDTA, 200 ul NaAc and 1750 ul water)


           1000 ul ethanol


5. Keep in dry ice 30 mins.


6. Spin 20 mins, 1ml 70% ethanol washing , spin 5 mins, dry down.


7. Add 1M peperidine 100 ul


    90 degree 20 mins.


8. Add 20 ul water and dry down. repeat several times.



SoxR Binding Assay          


1. Anneal DNA complex in 10mM Tris-HCl, 75mM KCl, 10% glycerol, 2mM DTT SoxR binding buffer first. Then add the desired amount of SoxR protein, stay 30 min. at r.t..


2. Gel running buffer: 20mM Tris-HCl, 3mM sodium acetate, 1mM EDTA



Streptavidin Paramagnetic Particles:



1. Take certain amount (depends on the quantity of DNA, calculated according to the binding capacity which is 0.75-1.25 nmole/mg) of magnetic particles (Promega , 1mg/ml), using sterile tip, put the tube on Magnetic Stand in which the particles stick on one side of  the tube.


2.  Discard the supernatant.


3. Wash the particles three times using PBS(1mg/ml BSA and 0.02% NaAzide).


4. Wash the particles three times using the desired 1x buffer.


5. Add the DNA samples with Biotin to the magnetic particles pellet, keep at R.T. for 20 mins for the coupling reaction.


6. Put the tube back on Magnetic Stand for 2 mins. Collect the supernatant which contains only DNA without the Biotin.


7. You may wash the particles once using 1x buffer and combine two solutions .



AFM Imaging (tapping in buffer)



1 Tip

For the tapping mode imaging in buffer, use the short cantilever (either skinny or fat) on the AFM chip.


2 Sample preparations

The protocol for preparing sample is to put 5ul DNA lattice in TAE/Mg or HEPES /Mg on the mica, let it sit for 0.5 - 1 min, then add 25ul of buffer. An additional 30ul buffer will be applied to the tip with fluid cell right side up so that the drop is hanging.    


3 Laser align

Make sure to align the photodiodes both side to side (horizontal difference signal) by align the laser in AFM & LFM mode and aligning the laser in top to bottom (vertical difference signal) in TM AFM mode. Both vertical and horizontal difference should be around 0. When laser is properly aligned, go to auto tune icon and ask for a amplitude of 0.5 volts. The resonance for the small skinny tip should fall between 9and 9.5 kHz. 


4 Imaging

Do the engage. 


Setting for tapping in buffer:


Scan control:


Scan size: 5um-10um

Scan angle : 0

Scan rate: 3-6 Hz


Feedback control:

Integral gain: 0.4-0.7

Proportional gain: 0.6-0.8

Channel 1: 6nm-10nm of height contrast (for DNA)

Channel 2: 1volt of amplitude contrast


5 Dont change other settings except the ones mentioned in 4 before you counsel the persons who charge of AFM.


6 Dont put back the used tips into the new tip box. Before concluding the tip is bad and changing it, make sure that you did everything right and every setting is correct.