A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.

A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented. DNA NN DeltaG degrees 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made. The seven studies used data from natural polymers, synthetic polymers, oligonucleotide dumbbells, and oligonucleotide duplexes to derive NN parameters; used different methods of data analysis; used different salt concentrations; and presented the NN thermodynamics in different formats. As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA polymers and oligomers. Herein I show that six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies remain. Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics. Empirical salt dependencies are also derived for oligonucleotides and polymers.

[1]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[2]  I. Tinoco,et al.  The stability of helical polynucleotides: base contributions. , 1962, Journal of molecular biology.

[3]  D. Crothers,et al.  THEORY OF THE MELTING TRANSITION OF SYNTHETIC POLYNUCLEOTIDES: EVALUATION OF THE STACKING FREE ENERGY. , 1964, Journal of molecular biology.

[4]  S. Lifson,et al.  Dependence of the melting temperature of DNA on salt concentration , 1965, Biopolymers.

[5]  Ignacio Tinoco,et al.  A new approach to the study of sequence‐dependent properties of polynucleotides , 1970 .

[6]  F. Frank-Kamenetskii,et al.  Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution. , 1971, Biopolymers.

[7]  D. Crothers,et al.  Improved estimation of secondary structure in ribonucleic acids. , 1973, Nature: New biology.

[8]  I. Tinoco,et al.  Stability of RNA hairpin loops: A6-Cm-U6 , 1973 .

[9]  I. Tinoco,et al.  Stability of ribonucleic acid double-stranded helices. , 1974, Journal of molecular biology.

[10]  D. Poland,et al.  Recursion relation generation of probability profiles for specific‐sequence macromolecules with long‐range correlations , 1974, Biopolymers.

[11]  Robert Zannetti,et al.  Landolt-bornstein, new series , 1974 .

[12]  N. Brown,et al.  The sequence of a region of bacteriophage phiX174 DNA coding for parts of genes A and B. , 1977, Journal of molecular biology.

[13]  M. Fixman,et al.  Theory of DNA melting curves , 1977, Biopolymers.

[14]  G. S. Manning.  The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides , 1978, Quarterly Reviews of Biophysics.

[15]  T. Lohman,et al.  A semiempirical extension of polyelectrolyte theory to the treatment of oligoelectrolytes: Application to oligonucleotide helix‐coil transitions , 1978 .

[16]  T. Lohman,et al.  Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity , 1978, Quarterly Reviews of Biophysics.

[17]  C. Cantor,et al.  Biophysical chemistry. Part III, The behavior of biologicalmacromolecules , 1980 .

[18]  R. A. Cox.  Biophysical Chemistry Part III: The Behavior of Biological Macromolecules , 1981 .

[19]  Yusaku Tagashira,et al.  Stabilities of nearest‐neighbor doublets in double‐helical DNA determined by fitting calculated melting profiles to observed profiles , 1981 .

[20]  R. Ornstein,et al.  Correlation of Tm and sequence of DNA duplexes with ΔH computed by an improved empirical potential method , 1983, Biopolymers.

[21]  B R Amirikyan,et al.  Allowance for heterogeneous stacking in the DNA helix-coil transition theory. , 1984, Journal of biomolecular structure & dynamics.

[22]  Albert S. Benight,et al.  Thermal denaturation of DNA molecules: A comparison of theory with experiment , 1985 .

[23]  H. Blöcker,et al.  Predicting DNA duplex stability from the base sequence. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[24]  D. Turner,et al.  Improved free-energy parameters for predictions of RNA duplex stability. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[25]  W. Olson,et al.  A dumbbell-shaped, double-hairpin structure of DNA: a thermodynamic investigation. , 1987, Biochemistry.

[26]  M. Aida,et al.  An ab initio molecular orbital study on the sequence-dependency of DNA conformation: an evaluation of intra- and inter-strand stacking interaction energy. , 1988, Journal of theoretical biology.

[27]  M. Record,et al.  Monte Carlo description of oligoelectrolyte properties of DNA oligomers: range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[28]  P. Otto,et al.  Investigation of the stability of oligonucleotides and oligodinucleotides , 1989 .

[29]  R. S. Quartin,et al.  Effect of ionic strength on the hybridization of oligodeoxynucleotides with reduced charge due to methylphosphonate linkages to unmodified oligodeoxynucleotides containing the complementary sequence. , 1989, Biochemistry.

[30]  William H. Press,et al.  Numerical recipes , 1990 .

[31]  K. Hall,et al.  Thermodynamic and structural properties of pentamer DNA.DNA, RNA.RNA, and DNA.RNA duplexes of identical sequence. , 1991, Biochemistry.

[32]  R. Blake,et al.  Stacking energies in DNA. , 1991, The Journal of biological chemistry.

[33]  A S Benight,et al.  How many numbers are required to specify sequence‐dependent properties of polynucleotides? , 1992, Biopolymers.

[34]  M. Schmitz,et al.  Base-pair probability profiles of RNA secondary structures , 1992, Comput. Appl. Biosci..

[35]  M J Doktycz,et al.  Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: Evaluation of the nearest‐neighbor stacking interactions in DNA , 1992, Biopolymers.

[36]  K. Breslauer,et al.  Thermodynamic characterization of daunomycin-DNA interactions: comparison of complete binding profiles for a series of DNA host duplexes. , 1993, Biochemistry.

[37]  L. Marky,et al.  Contribution of loops and nicks to the formation of DNA dumbbells: melting behavior and ligand binding. , 1993, Biochemistry.

[38]  G. Steger,et al.  Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. , 1994, Nucleic acids research.

[39]  J. Sturtevant,et al.  Significant discrepancies between van't hoff and calorimetric enthalpies. II , 1995, Protein science : a publication of the Protein Society.

[40]  N. Sugimoto,et al.  Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. , 1996, Nucleic acids research.

[41]  J. SantaLucia,et al.  Improved nearest-neighbor parameters for predicting DNA duplex stability. , 1996, Biochemistry.

[42]  D. Gray,et al.  Derivation of nearest-neighbor properties from data on nucleic acid oligomers. II. Thermodynamic parameters of DNA.RNA hybrids and DNA duplexes. , 1997, Biopolymers.

[43]  J. Bram,et al.  Encyclopedia of molecular biology and molecular medicine , 1997 .

[44]  J. SantaLucia,et al.  Thermodynamics and NMR of internal G.T mismatches in DNA. , 1997, Biochemistry.

[45]  J. Chaires.  Possible origin of differences between van't Hoff and calorimetric enthalpy estimates. , 1997, Biophysical chemistry.

[46]  J. Sturtevant,et al.  Significant discrepancies between van't Hoff and calorimetric enthalpies. III. , 1997, Biophysical chemistry.