Stabilizing liquid phenol
Distillation removes colored (oxidation) products from liquid phenol. Clear liquid phenol gradually oxidizes and the color returns. Neutralized phenol oxidizes more rapidly suggesting that oxidation involves the phenolate form of phenol. If so then adding acid should inhibit oxidation. This indeed seems to be the case (see below).
10mM HCl should reduce pH by 2-3 units increasing the lifetime "clear phenol"by a factor of at least 100.
Phenol is the major (hydrogen ion) buffer in phenol extractions. Although the pKa of phenol is ~10 its concentration is 10M. Adding base (NaOH, tris, etc.) to phenol raises its pH (along with salt concentration). Reproducible extractions are best achieved by maintaining a constant base/phenol ratio. Increasing this ratio will decrease ionic bonding (higher salt conc.). Most RNAs should extract readily at lower ratios and DNA (along with salt bonded RNAs (mRNA?)) should extract more efficiently at higher ratios. Neutralizing 10mM HCl requires an extra (negligible) amount of base.
