SPRI bead binding buffer

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DNA: 20% PEG 8000 + 2.5 M NaCl + 10 mM TrisHCl + 1 mM EDTA + 0.05% Tween 20, pH 8.0 @ 25 °C

RNA: 20% PEG 8000 + 2.5 M NaCl + 1 mM citrate + 0.05% Tween 20, pH 6.4 @ 25 °C

Contents

Purpose

  • SPRI bead mix, such as AMPure XP and RNAClean XP, is an alternative to spin columns for purifying nucleic acids out of aqueous solutions.
  • After the DNA/RNA is purified on the beads, they can be resuspended in a reaction mix and left in during the reaction ("with-bead protocol"); afterward, this buffer will rebind them to the same beads, saving on the cost of bead mix (it is equivalent to the buffer used in the bead mix).
  • This recipe includes Tween 20 to reduce surface tension and bead clumping.
  • The DNA version uses TE to protect DNA from degradation; the RNA version uses citrate.

Recipe (DNA version)

Final concentrations
PEG 8000 20% (w/v)
Sodium chloride 2.5 M
Tris base 10 mM
Disodium EDTA 1 mM
Tween 20 0.05% (v/v)
HCl 3.36 mM
Preparing 50 mL of 1X working solution
Sodium chloride, 5 M 25.000 mL
Nuclease-free water 3.582 mL
Tris base, 1 M 0.500 mL
Disodium EDTA, 0.1 M 0.500 mL
HCl, 1 N 0.168 mL
PEG 8000, 50% (w/v) 20.000 mL
Tween 20, 10% (v/v) 0.250 mL

Recipe (RNA version)

Final concentrations
PEG 8000 20% (w/v)
Sodium chloride 2.5 M
Trisodium citrate 1 mM
Tween 20 0.05% (v/v)
HCl 0.56 mM
Preparing 50 mL of 1X working solution
Sodium chloride, 5 M 25.000 mL
Nuclease-free water 4.672 mL
Trisodium citrate, 1 M 0.050 mL
HCl, 1 N 0.028 mL
PEG 8000, 50% (w/v) 20.000 mL
Tween 20, 10% (v/v) 0.250 mL

Notes

  • HCl titration was calculated with the Python package ionize 0.8.0.
  • pH is temperature-dependent and this dependency is especially strong for Tris, so pH indicators may show a noticeably higher pH than 8.0 at temperatures lower than 25 °C.
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