Importantly, a set of sequences with a rank of 8 (or 9 for dumbbells) can be used to derive a set of the 10 NN dimer energies that are a linear least-squares fit of the data set, but the solution is not unique. To fully characterize the thermodynamics of oligonucleotide duplexes, parameters for all 10 NN dimers (plus initiation parameters) are required. For oligonucleotide dumbbells with fixed termini but different lengths, nine invariants can be determined ( 18, 19). Linear combinations of these eight invariants can be used to completely describe the behavior of any DNA polymer within the limits of the NN model. \( \begin\)In this set, P is a measurable property such as Δ G° 37, Δ H°, or Δ S°. An additional entropic penalty ( 26) for the maintenance of the C2 symmetry of self-complementary duplexes is also included. terminal G⋅C pairs, two initiation parameters are introduced ( 22, 23): “initiation with terminal G⋅C” and “initiation with terminal A⋅T”. To account for differences between duplexes with terminal A⋅T vs. Importantly, all other sequence-independent effects are also combined into the initiation parameter including differences between terminal and internal NNs ( 23) and counterion condensation ( 24, 25). For oligonucleotide duplexes, additional parameters for the initiation of duplex formation are introduced. Throughout this paper, the 10 NN dimer duplexes are represented with a slash separating strands in antiparallel orientation (e.g., AC/TG means 5′-AC-3′ Watson–Crick base-paired with 3′-TG-5′). The NN model for nucleic acids assumes that the stability of a given base pair depends on the identity and orientation of neighboring base pairs. Empirical salt dependencies are also derived for oligonucleotides and polymers. Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics. 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. As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA polymers and oligomers. 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. DNA NN ΔG° 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made. A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented.
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