Quantitative Analysis of Monovalent Counterion Binding to Random-Sequence, Double-Stranded DNA Using the Replacement Ion Method

Stellwagen, Earle; Dong, Qian; Stellwagen, Nancy C.

doi:10.1021/bi062132w

Cited by 58 publications

(82 citation statements)

References 73 publications

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“…2B. Hence, the Debye-Hückel-Onsager theory is obeyed for cacodylate-buffered solutions containing this neutral salt, as expected since TEA + and cacodylate do not bind to DNA [ 2,11 ].…”

Section: Nih Public Accesssupporting

confidence: 67%

“…2B. Hence, the Debye-Hückel-Onsager theory is obeyed for cacodylate-buffered solutions containing this neutral salt, as expected since TEA + and cacodylate do not bind to DNA [ 2,11 ].In summary, the decrease of the mobility observed for ds26 in cacodylate buffer solutions containing added TEA + Cl − , and the constant mobility of ds26 in cacodylate buffer solutions containing added tricine +/− , indicate that zwitterions do not contribute to the ionic strength of a solution. However, zwitterions have very large dipole moments [24][25][26] and interact electrostatically with the solvent and with other charged molecules in the solution [ 1,2,7,8,27,28 ].…”

supporting

confidence: 65%

“…The duplex, which was prepared by standard methods from single-stranded oligomers synthesized by Integrated DNA Technologies (Coralville, IA), was monodisperse when analyzed by polyacrylamide gel electrophoresis. The capillary zone electrophoresis experiments were carried out with a Beckman Coulter P/ACE MDQ Capillary Electrophoresis System (Fullerton, CA), run in the reverse polarity mode (anode on the detector side) with UV detection at 254 nm, as described previously [ 9,11 ]. Coated capillaries were used to minimize the electroosmotic flow of the solvent; the current in the capillary was kept below 30 μA to prevent Joule heating.…”

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Do zwitterions contribute to the ionic strength of a solution?

Stellwagen

Prantner

Stellwagen

2008

Analytical Biochemistry

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Capillary electrophoresis has been used to determine whether zwitterions contribute to the ionic strength of a solution, by measuring the mobility of a double-stranded DNA oligomer in cacodylatebuffered solutions containing various concentrations of the ionic salt tetraethylammonium chloride (TEA + Cl − ) or the zwitterion tricine +/− . The mobility of the DNA decreased as the square root of ionic strength, as expected by the Debye-Hückel-Onsager theory of electrophoresis, when TEA + Cl − was added to the buffer. However, the mobility was independent of the concentration of added tricine +/− . Hence, zwitterions do not contribute to the ionic strength of a solution. KeywordsZwitterions; ionic strength; DNA; capillary electrophoresis Very few experiments have been designed to directly test whether zwitterions contribute to the ionic strength of a solution. However, capillary electrophoresis measurements in free solution are ideal for this purpose. If an analyte, such as a small DNA oligomer, does not bind one of the ions in the background electrolyte, its electrophoretic mobility will decrease as the square root of ionic strength [ 9 ], as predicted by Debye-Hückel-Onsager theory of electrophoresis [ 10 ], regardless of whether the ionic strength is increased by increasing the buffer concentration or by adding a neutral salt to the buffer. The same result would be expected upon adding a zwitterion to the buffer, if zwitterions contribute to the ionic strength. By contrast, if a zwitterion does not contribute to the ionic strength (and does not bind to the analyte), the observed mobility will be independent of the concentration of the added zwitterion.Capillary electrophoresis experiments were therefore carried out using a random-sequence, 26 base-pair double-stranded DNA oligomer with the sequence 5′-CGCTTACTAGATACTACTAGTACTAG-3′, called ds26 for brevity, as the analyte. The duplex, which was prepared by standard methods from single-stranded oligomers synthesized by Integrated DNA Technologies (Coralville, IA), was monodisperse when analyzed by polyacrylamide gel electrophoresis. The capillary zone electrophoresis experiments were * Corresponding author. Tel: +319-335-7896; Fax: +319-335-9570; Email address: nancy-stellwagen@uiowa.edu (N.C. Stellwagen). a Present address: Department of Chemistry, University of Washington, Seattle, WA 98915.Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Since relatively high concentrations of TEA + Cl − and tricine +/− were used in some of the experiments, the increased viscosity of solutions containing high concentrations of added...

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“…2B. Hence, the Debye-Hückel-Onsager theory is obeyed for cacodylate-buffered solutions containing this neutral salt, as expected since TEA + and cacodylate do not bind to DNA [ 2,11 ].…”

Section: Nih Public Accesssupporting

confidence: 67%

supporting

confidence: 65%

mentioning

confidence: 99%

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Do zwitterions contribute to the ionic strength of a solution?

Stellwagen

Prantner

Stellwagen

2008

Analytical Biochemistry

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“…The population distribution at the beginning of step l + 1 can be derived from that of the step at the end: Pðl þ 1Þ begin ¼ PðlÞ end for a, b, & c; Pðl þ 1Þ begin ¼ 0 for d. Applying this method from the first step to the end of transcription, we compute the folding kinetics for the RNA chain during transcription. Metal ions would like to bind to negatively charged nucleic acids to neutralize the negatively charged RNAs/DNAs [128][129][130][131][132][133][134][135][136][137][138][139]. The number of binding ions is important to DNA/RNA structure and stability, and can be measured via several experimental methods such as the small angle X-ray scattering (SAXS) [128][129][130][131][132][133][134][135][136][137][138][139], the ion-counting method [132], and the thermodynamic method [133][134][135][136][137][138].…”

Section: Folding Kinetics During Transcriptionmentioning

confidence: 99%

“…Metal ions would like to bind to negatively charged nucleic acids to neutralize the negatively charged RNAs/DNAs [128][129][130][131][132][133][134][135][136][137][138][139]. The number of binding ions is important to DNA/RNA structure and stability, and can be measured via several experimental methods such as the small angle X-ray scattering (SAXS) [128][129][130][131][132][133][134][135][136][137][138][139], the ion-counting method [132], and the thermodynamic method [133][134][135][136][137][138]. The experimental methods have been applied to various RNAs/DNAs, including yeast 58-nt ribosomal RNA fragment [136], tRNA [137,138], poly(A.U) [133], beet western yellow virus pseudoknot fragment [135], polymeric calf thymus DNA [134], oligomeric DNA/RNA duplexes [132], and DNA triplex [132]; see Ref [72] for a collection on the experimental data for ion binding to RNAs/DNAs.…”

Section: Folding Kinetics During Transcriptionmentioning

confidence: 99%

RNA Folding: Structure Prediction, Folding Kinetics and Ion Electrostatics

Tan

Zhang

Shi

et al. 2014

Advances in Experimental Medicine and Biology

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Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

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