DNA and buffers: are there any noninteracting, neutral pH buffers?

Area of Science:

• Biochemistry
• Analytical Chemistry
• Molecular Biology

Background:

• Understanding DNA-buffer interactions is crucial for accurate molecular biology techniques.
• Capillary electrophoresis (CE) is a powerful separation technique sensitive to buffer composition.
• Various amine-based buffers are widely used in molecular biology and electrophoresis.

Purpose of the Study:

• To investigate the interactions between DNA and neutral pH, amine-based buffers.
• To analyze the impact of buffer composition on DNA migration in free solution CE.
• To characterize the formation and dissociation of DNA-buffer complexes.

Main Methods:

• Free solution capillary electrophoresis (CE) was employed.
• A mixture of plasmid-sized DNA and a small DNA oligonucleotide was used as a reporter system.
• Analysis of DNA migration patterns in different buffer concentrations (TAE and TBE) and types.

Main Results:

• DNA molecules separated in Tris-acetate-EDTA (TAE) buffer, with separation increasing with buffer concentration due to solvent friction.
• In Tris-borate-EDTA (TBE) buffer, DNA formed complexes with borate ions, leading to altered mobilities.
• At 45 mM TBE, DNA-borate complexes migrated faster as a single sharp peak, indicating stabilization; higher TBE concentrations dissociated these complexes.
• Other amine-based buffers (Mops, Hepes, Bes, Tes, Tricine) also formed complexes with DNA, causing distorted peaks.

Conclusions:

• Borate buffers and most neutral pH, amine-based buffers interact with DNA.
• These interactions can significantly affect DNA mobility and separation in CE.
• Buffer selection is critical for optimizing DNA analysis and preventing artifactual results.