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Titolo:
Modeling the electrophoresis of short duplex DNA: Counterions K+ and Tris(+)
Autore:
Mazur, S; Chen, CY; Allison, SA;
Indirizzi:
Georgia State Univ, Dept Chem, Atlanta, GA 30329 USA Georgia State Univ Atlanta GA USA 30329 Dept Chem, Atlanta, GA 30329 USA
Titolo Testata:
JOURNAL OF PHYSICAL CHEMISTRY B
fascicolo: 5, volume: 105, anno: 2001,
pagine: 1100 - 1108
SICI:
1520-6106(20010208)105:5<1100:MTEOSD>2.0.ZU;2-L
Fonte:
ISI
Lingua:
ENG
Soggetto:
CHARGED COLLOIDAL CYLINDERS; UNIVALENT SALT-SOLUTIONS; FREE SOLUTION MOBILITY; CAPILLARY-ELECTROPHORESIS; ELECTRIC BIREFRINGENCE; RIGID POLYIONS; ION RELAXATION; FRAGMENTS; FIELD; POLARIZABILITY;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
52
Recensione:
Indirizzi per estratti:
Indirizzo: Allison, SA Georgia State Univ, Dept Chem, Atlanta, GA 30329 USA Georgia State Univ Atlanta GA USA 30329 Atlanta, GA 30329 USA
Citazione:
S. Mazur et al., "Modeling the electrophoresis of short duplex DNA: Counterions K+ and Tris(+)", J PHYS CH B, 105(5), 2001, pp. 1100-1108

Abstract

The electrophoretic mobility of short 18 and 20 bp duplex DNAs is modeled by an iterative boundary element procedure that numerically solves the coupled Poisson, low Reynolds Number Navier-Stokes, and ion transport equations. Both capped cylinder (CC) and "detailed" models derived from the secondary structure of the fragments are examined. Translation-rotation coupling isexamined with regard to the transport of the detailed models, and it is concluded that this coupling has very little effect on either diffusion or electrophoresis. When the buffer consists primarily of KCI, the calculated mobility is about 4-6% larger than the experimental mobility for either the CC or "detailed" models, but when the buffer is Tris acetate, the descrepancy is significantly larger. This indicates that there is an association between Tris(+) and DNA beyond the classical electrostatic interactions accounted for in modeling. For 18 bp DNA in 0.03 M Tris acetate, a model in which the phosphate charges of DNA are reduced from -1.0 to -0.45 gives good agreement with experiment. Alternatively, a model in which 40% of the DNA phosphates are neutralized by Tris+ cations specifically bound to the fragment also gives a mobility consistent with experiment.

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Documento generato il 03/04/20 alle ore 08:01:21