Biomod/2014/ASU/Materials

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Biomod/2014/ASU

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Tile Assembly


· buffer stock (10x TAE/Mg2+)

· ssDNA strand stocks



Gel Electrophoresis (PAGE)


     · 40% acrylamide

     · water

     · 10x TAE/Mg2+ + 1M KCl buffer

     · Ammonium persulfate (APS)

     · Tetramethylethylenediamine (TEMED)

     · SYBR Green gel stain

     · Native dye

           - 0.2% bromophenol blue

           - 0.2% xylene cyanole

           - 5% glycerol

           - in 1x TAE/Mg2+ buffered solution


Gel electrophoresis (Agarose)


     · Agarose powder

     · water

     · SYBR Safe


PCR


New England Biolabs PCR kit:

     · Phusion High-Fidelity DNA polymerase

     · 10 mM dNTPs

     · DMSO

     · 5x Phusion buffer

     · Affinity column preparations:

     · NHS ester beads

     · PCR Buffer


Affinity Column Preparation


     · NHS modified agarose beads

     · Coupling buffer: HEPES 100 mM, pH 7.2, 150 mM NaCl

     · Quenching buffer: 1 M Tris, pH 7.4

     · Binding buffer: 1x TAE Mg2+, 100 mM KCl


Computer Simulation


     · CaDNAno

     · Cando

     · PyMol

     · Chimera

     · Avogadro


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