PMID- 20681741
OWN - NLM
STAT- MEDLINE
DCOM- 20101201
LR  - 20100819
IS  - 1520-5207 (Electronic)
IS  - 1520-5207 (Linking)
VI  - 114
IP  - 33
DP  - 2010 Aug 26
TI  - Coulombic free energy of polymeric nucleic acid: low- and high-salt analytical 
      approximations for the cylindrical Poisson-Boltzmann model.
PG  - 10793-803
LID - 10.1021/jp908267c [doi]
AB  - An accurate analytical expression for the Coulombic free energy of DNA as a 
      function of salt concentration ([salt]) is essential in applications to nucleic 
      acid (NA) processes. The cylindrical model of DNA and the nonlinear 
      Poisson-Boltzmann (NLPB) equation for ions in solution are among the simplest 
      approaches capable of describing Coulombic interactions of NA and salt ions and 
      of providing analytical expressions for thermodynamic quantities. Three 
      approximations for Coulombic free energy G(u,infinity)(coul) of a polymeric 
      nucleic acid are derived and compared with the numerical solution in a wide 
      experimental range of 1:1 [salt] from 0.01 to 2 M. Two are obtained from the two 
      asymptotic solutions of the cylindrical NLPB equation in the high-[salt] and 
      low-[salt] limits: these are sufficient to determine G(u,infinity)(coul) of 
      double-stranded (ds) DNA with 1% and of single-stranded (ss) DNA with 3% accuracy 
      at any [salt]. The third approximation is experimentally motivated Taylor series 
      up to the quadratic term in ln[salt] in the vicinity of the reference [salt] 0.15 
      M. This expression with three numerical coefficients (Coulombic free energy and 
      its first and second derivatives at 0.15 M) predicts dependence of 
      G(u,infinity)(coul) on [salt] within 2% of the numerical solution from 0.01 to 1 
      M for ss (a = 7 A, b = 3.4 A) and ds (a = 10 A, b = 1.7 A) DNA. Comparison of 
      cylindrical free energy with that calculated for the all-atom structural model of 
      linear B-DNA shows that the cylindrical model is completely sufficient above 0.01 
      M of 1:1 [salt]. The choice of two cylindrical parameters, the distance of 
      closest approach of ion to cylinder axis (radius) a and the average axial charge 
      separation b, is discussed in application to all-atom numerical calculations and 
      analysis of experiment. Further development of analytical expression for 
      Coulombic free energy with thermodynamic approaches accounting for ionic 
      correlations and specific effects is suggested.
FAU - Shkel, Irina A
AU  - Shkel IA
AD  - Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 
      53706, USA. ishkel@wisc.edu
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
RN  - 0 (Salts)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - DNA/*chemistry
MH  - Models, Molecular
MH  - Nucleic Acid Conformation
MH  - Poisson Distribution
MH  - Salts/*chemistry
MH  - Surface Properties
MH  - Thermodynamics
EDAT- 2010/08/05 06:00
MHDA- 2010/12/14 06:00
CRDT- 2010/08/05 06:00
PHST- 2010/08/05 06:00 [entrez]
PHST- 2010/08/05 06:00 [pubmed]
PHST- 2010/12/14 06:00 [medline]
AID - 10.1021/jp908267c [doi]
PST - ppublish
SO  - J Phys Chem B. 2010 Aug 26;114(33):10793-803. doi: 10.1021/jp908267c.