Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures

被引:268
作者
Owczarzy, R [1 ]
You, Y [1 ]
Moreira, BG [1 ]
Manthey, JA [1 ]
Huang, LY [1 ]
Behlke, MA [1 ]
Walder, JA [1 ]
机构
[1] Integrated DNA Technol, Coralville, IA 52241 USA
关键词
D O I
10.1021/bi034621r
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Melting temperatures, T-m, were systematically studied for a set of 92 DNA duplex oligomers in a variety of sodium ion concentrations ranging from 69 mM to 1.02 M. The relationship between T-m and In [Na+] was nonlinear over this range of sodium ion concentrations, and the observed melting temperatures were poorly predicted by existing algorithms. A new empirical relationship was derived from UV melting data that employs a quadratic function, which better models the melting temperatures of DNA duplex oligomers as sodium ion concentration is varied. Statistical analysis shows that this improved salt correction is significantly more accurate than previously suggested algorithms and predicts salt-corrected melting temperatures with an average error of only 1.6 degreesC when tested against an independent validation set of T-m measurements obtained from the literature. Differential scanning calorimetry studies demonstrate that this T-m salt correction is insensitive to DNA concentration. The T-m salt correction function was found to be sequence-dependent and varied with the fraction of G(.)C base pairs, in agreement with previous studies of genomic and polymeric DNAs. The salt correction function is independent of oligomer length, suggesting that end-fraying and other end effects have little influence on the amount of sodium counterions released during duplex melting. The results are discussed in the context of counterion condensation theory.
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收藏
页码:3537 / 3554
页数:18
相关论文
共 101 条
[1]   The calculation of the energy of transition associated with inversions in double-stranded DNA using a rising temperature method [J].
Aggarwal, P ;
Dollimore, D .
THERMOCHIMICA ACTA, 1996, 284 (01) :109-114
[2]  
Alberti P. W., 1998, NOISE HEALTH, V1, P3
[3]  
ANDERSON CF, 1995, ANNU REV PHYS CHEM, V46, P657, DOI 10.1146/annurev.physchem.46.1.657
[4]  
[Anonymous], 1996, NUMERICAL RECIPES FO
[5]  
ASCOLI F, 1961, J MOL BIOL, V3, P302
[6]  
Bevington P., 2002, Data Reduction and Error Analysis for the Physical Sciences, V3rd ed.
[7]   EFFECT OF SODIUM-ION ON THE HIGH-RESOLUTION MELTING OF LAMBDA DNA [J].
BLAKE, RD ;
HAYDOCK, PV .
BIOPOLYMERS, 1979, 18 (12) :3089-3109
[8]   Thermal stability of DNA [J].
Blake, RD ;
Delcourt, SG .
NUCLEIC ACIDS RESEARCH, 1998, 26 (14) :3323-3332
[9]  
BLOOMFIELD VA, 2000, NUCL ACIDS STRUCTURE, P307
[10]   Watson-Crick base-pairing properties of bicyclo-DNA [J].
Bolli, M ;
Trafelet, HU ;
Leumann, C .
NUCLEIC ACIDS RESEARCH, 1996, 24 (23) :4660-4667