We report the complete thermodynamic library of all 10 Watson-Crick DNA nearest-neighbor interactions. We obtained the relevant thermodynamic data from calorimetric studies on 19 DNA oligomers and 9 DNA polymers. We show how these thermodynamic data can be used to calculate the stability and predict the temperature-dependent behavior of any DNA duplex structure from knowledge of its base sequence. We illustrate our method of calculation by using the nearest-neighbor data to predict transition enthalpies and free energies for a series of DNA oligomers. These predicted values are in excellent agreement with the corresponding values determined experimentally. This agreement demonstrates that a DNA duplex structure thermodynamically can be considered to be the sum of its nearest-neighbor interactions. Armed with this knowledge and the nearest-neighbor thermodynamic data reported here, scientists now will be able to predict the stability (delta G degree) and the melting behavior (delta H degree) of any DNA duplex structure from inspection of its primary sequence. This capability should prove valuable in numerous applications, such as predicting the stability of a probe-gene complex; selecting optimal conditions for a hybridization experiment; deciding on the minimum length of a probe; predicting the influence of a specific transversion or transition on the stability of an affected DNA region; and predicting the relative stabilities of local domains within a DNA duplex.

https://www.pnas.org/content/pnas/83/11/3746.full.pdf

Predicting DNA duplex stability from the base sequence.

To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html
 .

/pdf/rnastructure-software-for-rna-secondary-structure-prediction-3e42o4sg6f.pdf

RNAstructure: software for RNA secondary structure prediction and analysis

Thermodynamic parameters for prediction of RNA duplex stability are reported. One parameter for duplex initiation and 10 parameters for helix propagation are derived from enthalpy and free-energy changes for helix formation by 45 RNA oligonucleotide duplexes. The oligomer sequences were chosen to maximize reliability of secondary structure predictions. Each of the 10 nearest-neighbor sequences is well-represented among the 45 oligonucleotides, and the sequences were chosen to minimize experimental errors in delta GO at 37 degrees C. These parameters predict melting temperatures of most oligonucleotide duplexes within 5 degrees C. This is about as good as can be expected from the nearest-neighbor model. Free-energy changes for helix propagation at dangling ends, terminal mismatches, and internal G X U mismatches, and free-energy changes for helix initiation at hairpin loops, internal loops, or internal bulges are also tabulated.

https://www.pnas.org/content/pnas/83/24/9373.full.pdf

Improved free-energy parameters for predictions of RNA duplex stability

Improved thermodynamic parameters for prediction of RNA duplex formation are derived from optical melting studies of 90 oligoribonucleotide duplexes containing only Watson−Crick base pairs. To test end or base composition effects, new sets of duplexes are included that have identical nearest neighbors, but different base compositions and therefore different ends. Duplexes with terminal GC pairs are more stable than duplexes with the same nearest neighbors but terminal AU pairs. Penalizing terminal AU base pairs by 0.45 kcal/mol relative to terminal GC base pairs significantly improves predictions of ΔG°37 from a nearest-neighbor model. A physical model is suggested in which the differential treatment of AU and GC ends accounts for the dependence of the total number of Watson−Crick hydrogen bonds on the base composition of a duplex. On average, the new parameters predict ΔG°37, ΔH°, ΔS°, and T M within 3.2%, 6.0%, 6.8%, and 1.3 °C, respectively. These predictions are within the limit of the model, based on...

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson - Crick base pairs

In this paper, we derive the general forms of the equations required to extract thermodynamic data from equilibrium transition curves on oligomeric and polymeric nucleic acids of any molecularity Significantly, since the equations and protocols are general, they also can be used to characterize thermodynamically equilibrium processes in systems other than nucleic acids We briefly review how the reduced forms of the general equations have been used by many investigators to evaluate mono- and bimolecular transitions, and then explain how these equations can be generalized to calculate thermodynamic parameters from common experimental observables for transitions of higher molecularities We emphasize the strengths and weaknesses of each method of data analysis so that investigators can select the approach most appropriate for their experimental circumstances We also describe how to analyze calorimetric heat capacity curves and noncalorimetric differentiated melting curves so as to extract both model-independent and model-dependent thermodynamic data for transitions of any molecularity The general equations and methods of analysis described in this paper should be of particular interest to laboratories that currently are investigating association and dissociation processes in nucleic acids that exhibit molecularities greater than two

Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves

A DNA-RNA hybrid oligonucleotide duplex, dC(pA) 5pG:rC(pU)5pG, which contains a (dA:rU) 5 sequence, is at least 200 times less stable at room temperature than the corresponding duplex containing an (rA:dT) 5 sequence, rC(pA)5pG:dC(pT)5pG. This result provides an explanation for the finding that most primary RNA transcripts terminate in several consecutive rU residues, but not rA residues. It strongly supports the idea that instability of the DNA-RNA hybrid at the growing point of transcription plays a role in termination of transcription.

/pdf/dna-rna-hybrid-duplexes-containing-oligo-da-ru-sequences-are-4nckbs7dmj.pdf

DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription.

/pdf/unpaired-cytosine-in-the-deoxyoligonucleotide-duplex-2st27as19q.pdf

Unpaired cytosine in the deoxyoligonucleotide duplex dCA3CA3G.cntdot.dCT6G is outside of the helix

The thermodynamic parameters for the double-strand formation of the molecules rCAmG + rCUnG, m,n = 5–7, and dCAmG + dCTnG, m,n = 5,6, were measured from optical melting curves. Normal helices are formed when m = n. The deoxyoligomers are more stable than the ribo-oligomers, due to a more favorable enthalpy. Double helices with mismatched bases can be formed by mixing oligomers with m ≠ n. Such helices may form several possible structures. A structure with a dangling base is favored over a structure with a bulged base. The destabilization of the double strands by the formation of a bulged base was determined to be greater than 1.6 kcal/mol at 10°C. The extent of aggregation in the oligomer double strand rCA7G·rCU7G was determined using ultracentrifugation equilibrium. The possible effects of aggregation on the determination of the thermodynamic parameters for double-strand formation are discussed.

/pdf/dna-and-rna-oligomer-thermodynamics-the-effect-of-mismatched-2qvkvo8g6h.pdf

DNA and RNA oligomer thermodynamics: the effect of mismatched bases on double-helix stability.

The nonexchangeable base protons and the hydrogen-bonding NH--N imino protons were used to study the conformations and the helix--coil transitions in the following oligonucleotides: (I) dCT5G + dCA5G, (II) rCU5G + rCA5G, (III) dCT5 G + rCA5G, (IV) rCU5G + dCA5G. The first three mixtures all form stable double-helical structures at 5 degrees C, whereas IV forms a triple strand with an rCU5G:dCA5G 2:1 ratio. The chemical shifts of the imino protons in the double strands indicate that I, II, and III have different conformations in solution. For example, the hydrogen-bonded proton of one of the C.G base pairs is more deshielded (a 0.4-ppm downfield shift) in helix I than in helix II or III. This implies a significant change in helical parameters, such as the winding angle, the distance between base pairs, or overlap of the bases. The coupling constants of the H1' sugar protons show that helix I has 90% 2'-endo sugar conformation, whereas helix III has greater than 85% 3'-endo conformation for the observed sugar rings. The sugar pucker data are consistent with helix I having B-family geometry; III has A-family geometry. The chemical shifts of the nonexchangeable base protons in system I were followed with increasing temperature. The midpoints for the transitions, Tm's, for all the base protons were 28--30 degrees C; this indicates an all-or-none transition.

Comparative study of ribonucleotides, deoxyribonucleotides, and hybrid oligonucleotide helixes by nuclear magnetic resonance

A series of ribo- and deoxyribo-oligonucleotides were synthesized with the sequences CAnG, CUmG AND CTmG (n and m = 5 or 6). These molecules can form RNA, DNA and hybrid double stranded helices containing either perfect base pairing (n = m), or mismatches (n ≠ m). The thermodynamics of formation of these helices has been measured and the destabilization caused by an extra uridylic, thymidylic or adenylic residue has been determined. Nuclear magnetic resonance of exchangeable imino protons has been used to study the conformations of the different helices. The binding of ethidium to the helices has been studies.

Francis H. Martin

Papers

DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription.

Unpaired cytosine in the deoxyoligonucleotide duplex dCA3CA3G.cntdot.dCT6G is outside of the helix

DNA and RNA oligomer thermodynamics: the effect of mismatched bases on double-helix stability.

Comparative study of ribonucleotides, deoxyribonucleotides, and hybrid oligonucleotide helixes by nuclear magnetic resonance

Mismatched bases in nucleic acids: their effects on structures and stability