SPRI bead binding buffer

DNA: 20% PEG 8000 + 2.5 M NaCl + 10 mM Tris–HCl + 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

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.