A Robust Method for Determining DNA Binding Constants Using Capillary Zone Electrophoresis

Li, Chunze; Martin, Lenore M.

doi:10.1006/abio.1998.2791

Cited by 37 publications

(25 citation statements)

References 24 publications

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“…Using the affinity capillary electrophoresis (ACE) method, many DNA⅐protein and metal⅐DNA complexes have been successfully identified (57)(58)(59)(60)(61). Because the charge-to-mass ratio of DNA⅐ligand complex is generally different from that of the unbound DNA and ligand separately, the complex migrates separately from the free ligand (59).…”

Section: Methodsmentioning

confidence: 99%

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Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(III)hexamine Studied by Fourier Transform Infrared and Capillary Electrophoresis

Ouameur

Tajmir-Riahi

2004

Journal of Biological Chemistry

283

234

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Biogenic polyamines, such as putrescine, spermidine, and spermine are small organic polycations involved in numerous diverse biological processes. These compounds play an important role in nucleic acid function due to their binding to DNA and RNA. It has been shown that biogenic polyamines cause DNA condensation and aggregation similar to that of inorganic cobalt(III)hexamine cation, which has the ability to induce DNA conformational changes. However, the nature of the polyamine⅐DNA binding at the molecular level is not clearly established and is the subject of much controversy. In the present study the effects of spermine, spermidine, putrescine, and cobalt(III)hexamine on the solution structure of calf-thymus DNA were investigated using affinity capillary electrophoresis, Fourier transform infrared, and circular dichroism spectroscopic methods. At low polycation concentrations, putrescine binds preferentially through the minor and major grooves of double strand DNA, whereas spermine, spermidine, and cobalt(III)hexamine bind to the major groove. At high polycation concentrations, putrescine interaction with the bases is weak, whereas strong base binding occurred for spermidine in the major and minor grooves of DNA duplex. However, major groove binding is preferred by spermine and cobalt(III)hexamine cations. Electrostatic attractions between polycation and the backbone phosphate group were also observed. No major alterations of B-DNA were observed for biogenic polyamines, whereas cobalt(III)hexamine induced a partial B 3 A transition. DNA condensation was also observed for cobalt(III)hexamine cation, whereas organic polyamines induced duplex stabilization. The binding constants calculated for biogenic polyamines are K Spm ‫؍‬ 2.3 ؋ 10 5 M ؊1 , K Spd ‫؍‬ 1.4 ؋ 10 5 M ؊1 , and K Put ‫؍‬ 1.02 ؋ 10 5 M ؊1 . Two binding constants have been found for cobalt(III)hexamine with K 1 ‫؍‬ 1.8 ؋ 10 5 M ؊1 and K 2 ‫؍‬ 9.2 ؋ 10 4 M ؊1 . The Hill coefficients indicate a positive cooperativity binding for biogenic polyamines and a negative cooperativity for cobalt(III)hexamine.The biogenic polyamines putrescine [NH 2 (CH 2 ) 4 NH 2 ], spermidine [NH 2 (CH 2 ) 4 NH(CH 2 ) 3 NH 2 ], and spermine [NH 2 (C-H 2 ) 3 NH(CH 2 ) 4 NH(CH 2 ) 3 NH 2 ] (Structure 1) are the most prevalent polyamines in mammalian cells. They are small aliphatic polycations involved in numerous diverse biological processes, such as the ability to modulate gene expression and enzyme activities, activation of DNA synthesis, cell proliferation and differentiation, and others (1-8). Other functions of polyamines have been related to DNA protection from external agents (9, 10) and against radiation damage (11, 12). In general, spermidine and spermine are present in millimolar concentrations in vivo, whereas putrescine levels are slightly lower (13-15). However, the most important characteristic of polyamines within the cells is to bind nucleic acids and DNA in particular (1, 6).Polyamines also have the ability to induce DNA conformational transitions. Their bindi...

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Section: Methodsmentioning

confidence: 99%

“…Because the charge-to-mass ratio of DNA⅐ligand complex is generally different from that of the unbound DNA and ligand separately, the complex migrates separately from the free ligand (59). ACE provides both qualitative and quantitative information on molecular interaction.…”

Section: Methodsmentioning

confidence: 99%

Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(III)hexamine Studied by Fourier Transform Infrared and Capillary Electrophoresis

Ouameur

Tajmir-Riahi

2004

Journal of Biological Chemistry

283

234

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show abstract

“…concerning the research of DNA-drug interactions Capillary electrophoresis (CE) has become a and even quantitative determination of the binding robust separation technique in the past few years constants using CE [17][18][19][20]. Small duplex oligoowing to its several advantages such as short analysis nucleotides can be used as appropriate molecules for time, low sample size requirement, high efficiency the investigation of binding properties.…”

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confidence: 99%

Interaction between netropsin and double-stranded DNA in capillary zone electrophoresis and affinity capillary electrophoresis

Liang

et al. 2002

Journal of Chromatography A

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“…[24][25][26] The Scatchard equation expresses the binding of DNA-AO in the presence of Lu(ARS) 3 . According to the Scatchard equation [27] :…”

Section: Scatchard Methodsmentioning

confidence: 99%

Study of Interaction Between Lu(III)–ARS Complex and Herring Sperm DNA

Liu

Wang

Ding

2012

Synthesis and Reactivity in Inorganic, Metal-Organic, and Nano-

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A Robust Method for Determining DNA Binding Constants Using Capillary Zone Electrophoresis

Cited by 37 publications

References 24 publications

Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(III)hexamine Studied by Fourier Transform Infrared and Capillary Electrophoresis

Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(III)hexamine Studied by Fourier Transform Infrared and Capillary Electrophoresis

Interaction between netropsin and double-stranded DNA in capillary zone electrophoresis and affinity capillary electrophoresis

Study of Interaction Between Lu(III)–ARS Complex and Herring Sperm DNA

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