DNA and buffers

Are there any noninteracting, neutral pH buffers?

Nancy C. Stellwagen, Alessandra Bossi, Cecilia Gelfi, Pier Giorgio Righetti

Research output: Contribution to journalArticle

51 Citations (Scopus)

Abstract

The interaction of DNA with various neutral pH, amine-based buffers has been analyzed by free solution capillary electrophoresis, using a mixture of a plasmid-sized DNA molecule and a small DNA oligonucleotide as the reporter system. The two DNAs migrate as separate, nearly Gaussian-shaped peaks in 20-80 mM TAE (TAE, Tris-acetate-EDTA; Tris, tris[hydroxymethyl]aminomethane) buffer. The separation between the peaks gradually increases with increasing TAE buffer concentration because of differences in solvent friction between large and small DNA molecules. The two DNAs form complexes with the borate ions in TBE (Tris-borate-EDTA) buffer, with mobilities that depend on the DNA/borate ratio. In 45 mM TBE buffer, the two DNAs comigrate as a single sharp peak, with a mobility that is faster than either of the constituent DNAs in the same buffer. Hence, the mixed DNA-borate complex is stabilized by the binding of additional borate ions, possibly forming bridges between the different DNAs. The mixed DNA-borate complex is gradually dissociated into its component DNAs by increasing the TBE concentration, possibly because the borate binding sites become saturated at high buffer concentrations. Other neutral pH, amine-based buffers, such as Mops (3-[N-morpholino]propanesulfonic acid), Hepes (N-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid]), Bes (N,N-bis[2-hydroxyethyl]-2-aminoethanesulfonic acid), Tes (N-tris [hydroxymethyl]methyl-2-aminoethanesulfonic acid), and tricine (N-tris[hydroxymethyl]methylglycine) also form complexes with DNA, giving distorted peaks in the electropherograms. The combined results indicate that borate buffers and most neutral pH, amine-based buffers interact with DNA. (C) 2000 Academic Press.

Original languageEnglish
Pages (from-to)167-175
Number of pages9
JournalAnalytical Biochemistry
Volume287
Issue number1
DOIs
Publication statusPublished - Dec 1 2000

Fingerprint

Buffers
Borates
DNA
Amines
Edetic Acid
Acids
Sarcosine
Ions
Morpholinos
Capillary electrophoresis
Tromethamine
Molecules
Friction
Capillary Electrophoresis
Oligonucleotides
Acetates
Plasmids
Binding Sites

Keywords

  • Amine-based buffers
  • Borate buffers
  • Capillary electrophoresis
  • DNA-buffer interactions
  • Free solution electrophoretic mobility

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

Cite this

DNA and buffers : Are there any noninteracting, neutral pH buffers? / Stellwagen, Nancy C.; Bossi, Alessandra; Gelfi, Cecilia; Righetti, Pier Giorgio.

In: Analytical Biochemistry, Vol. 287, No. 1, 01.12.2000, p. 167-175.

Research output: Contribution to journalArticle

Stellwagen, Nancy C. ; Bossi, Alessandra ; Gelfi, Cecilia ; Righetti, Pier Giorgio. / DNA and buffers : Are there any noninteracting, neutral pH buffers?. In: Analytical Biochemistry. 2000 ; Vol. 287, No. 1. pp. 167-175.
@article{fb48b86ffe0449a3a1702215492b8b55,
title = "DNA and buffers: Are there any noninteracting, neutral pH buffers?",
abstract = "The interaction of DNA with various neutral pH, amine-based buffers has been analyzed by free solution capillary electrophoresis, using a mixture of a plasmid-sized DNA molecule and a small DNA oligonucleotide as the reporter system. The two DNAs migrate as separate, nearly Gaussian-shaped peaks in 20-80 mM TAE (TAE, Tris-acetate-EDTA; Tris, tris[hydroxymethyl]aminomethane) buffer. The separation between the peaks gradually increases with increasing TAE buffer concentration because of differences in solvent friction between large and small DNA molecules. The two DNAs form complexes with the borate ions in TBE (Tris-borate-EDTA) buffer, with mobilities that depend on the DNA/borate ratio. In 45 mM TBE buffer, the two DNAs comigrate as a single sharp peak, with a mobility that is faster than either of the constituent DNAs in the same buffer. Hence, the mixed DNA-borate complex is stabilized by the binding of additional borate ions, possibly forming bridges between the different DNAs. The mixed DNA-borate complex is gradually dissociated into its component DNAs by increasing the TBE concentration, possibly because the borate binding sites become saturated at high buffer concentrations. Other neutral pH, amine-based buffers, such as Mops (3-[N-morpholino]propanesulfonic acid), Hepes (N-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid]), Bes (N,N-bis[2-hydroxyethyl]-2-aminoethanesulfonic acid), Tes (N-tris [hydroxymethyl]methyl-2-aminoethanesulfonic acid), and tricine (N-tris[hydroxymethyl]methylglycine) also form complexes with DNA, giving distorted peaks in the electropherograms. The combined results indicate that borate buffers and most neutral pH, amine-based buffers interact with DNA. (C) 2000 Academic Press.",
keywords = "Amine-based buffers, Borate buffers, Capillary electrophoresis, DNA-buffer interactions, Free solution electrophoretic mobility",
author = "Stellwagen, {Nancy C.} and Alessandra Bossi and Cecilia Gelfi and Righetti, {Pier Giorgio}",
year = "2000",
month = "12",
day = "1",
doi = "10.1006/abio.2000.4848",
language = "English",
volume = "287",
pages = "167--175",
journal = "Analytical Biochemistry",
issn = "0003-2697",
publisher = "Academic Press Inc.",
number = "1",

}

TY - JOUR

T1 - DNA and buffers

T2 - Are there any noninteracting, neutral pH buffers?

AU - Stellwagen, Nancy C.

AU - Bossi, Alessandra

AU - Gelfi, Cecilia

AU - Righetti, Pier Giorgio

PY - 2000/12/1

Y1 - 2000/12/1

N2 - The interaction of DNA with various neutral pH, amine-based buffers has been analyzed by free solution capillary electrophoresis, using a mixture of a plasmid-sized DNA molecule and a small DNA oligonucleotide as the reporter system. The two DNAs migrate as separate, nearly Gaussian-shaped peaks in 20-80 mM TAE (TAE, Tris-acetate-EDTA; Tris, tris[hydroxymethyl]aminomethane) buffer. The separation between the peaks gradually increases with increasing TAE buffer concentration because of differences in solvent friction between large and small DNA molecules. The two DNAs form complexes with the borate ions in TBE (Tris-borate-EDTA) buffer, with mobilities that depend on the DNA/borate ratio. In 45 mM TBE buffer, the two DNAs comigrate as a single sharp peak, with a mobility that is faster than either of the constituent DNAs in the same buffer. Hence, the mixed DNA-borate complex is stabilized by the binding of additional borate ions, possibly forming bridges between the different DNAs. The mixed DNA-borate complex is gradually dissociated into its component DNAs by increasing the TBE concentration, possibly because the borate binding sites become saturated at high buffer concentrations. Other neutral pH, amine-based buffers, such as Mops (3-[N-morpholino]propanesulfonic acid), Hepes (N-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid]), Bes (N,N-bis[2-hydroxyethyl]-2-aminoethanesulfonic acid), Tes (N-tris [hydroxymethyl]methyl-2-aminoethanesulfonic acid), and tricine (N-tris[hydroxymethyl]methylglycine) also form complexes with DNA, giving distorted peaks in the electropherograms. The combined results indicate that borate buffers and most neutral pH, amine-based buffers interact with DNA. (C) 2000 Academic Press.

AB - The interaction of DNA with various neutral pH, amine-based buffers has been analyzed by free solution capillary electrophoresis, using a mixture of a plasmid-sized DNA molecule and a small DNA oligonucleotide as the reporter system. The two DNAs migrate as separate, nearly Gaussian-shaped peaks in 20-80 mM TAE (TAE, Tris-acetate-EDTA; Tris, tris[hydroxymethyl]aminomethane) buffer. The separation between the peaks gradually increases with increasing TAE buffer concentration because of differences in solvent friction between large and small DNA molecules. The two DNAs form complexes with the borate ions in TBE (Tris-borate-EDTA) buffer, with mobilities that depend on the DNA/borate ratio. In 45 mM TBE buffer, the two DNAs comigrate as a single sharp peak, with a mobility that is faster than either of the constituent DNAs in the same buffer. Hence, the mixed DNA-borate complex is stabilized by the binding of additional borate ions, possibly forming bridges between the different DNAs. The mixed DNA-borate complex is gradually dissociated into its component DNAs by increasing the TBE concentration, possibly because the borate binding sites become saturated at high buffer concentrations. Other neutral pH, amine-based buffers, such as Mops (3-[N-morpholino]propanesulfonic acid), Hepes (N-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid]), Bes (N,N-bis[2-hydroxyethyl]-2-aminoethanesulfonic acid), Tes (N-tris [hydroxymethyl]methyl-2-aminoethanesulfonic acid), and tricine (N-tris[hydroxymethyl]methylglycine) also form complexes with DNA, giving distorted peaks in the electropherograms. The combined results indicate that borate buffers and most neutral pH, amine-based buffers interact with DNA. (C) 2000 Academic Press.

KW - Amine-based buffers

KW - Borate buffers

KW - Capillary electrophoresis

KW - DNA-buffer interactions

KW - Free solution electrophoretic mobility

UR - http://www.scopus.com/inward/record.url?scp=0034548718&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0034548718&partnerID=8YFLogxK

U2 - 10.1006/abio.2000.4848

DO - 10.1006/abio.2000.4848

M3 - Article

VL - 287

SP - 167

EP - 175

JO - Analytical Biochemistry

JF - Analytical Biochemistry

SN - 0003-2697

IS - 1

ER -