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.

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

Base sequence information can be stored in the local structure of right-handed double-helical DNA (B-DNA). The question arises as to whether a set of rules for the three-dimensional readout of the B-DNA helix can be developed. This would allow the design of synthetic molecules that bind DNA of any specific sequence and site size. There are four stages of development for each new synthetic sequence-specific DNA-binding molecule: design, synthesis, testing for sequence specificity, and reevaluation of the design. This approach has produced bis(distamycin)fumaramide, a synthetic, crescent-shaped oligopeptide that binds nine contiguous adenine-thymine base pairs in the minor groove of double-helical DNA.

https://science.sciencemag.org/content/sci/232/4749/464.full.pdf

Design of sequence-specific DNA-binding molecules.

II. DNA BINDING ANTIBIOTICS 1. Pyrrole-Amidine Antibiotics and Synthetic Analogues (a) Structure and physical properties (b) Interactions with nucleic acids and synthetic polynucleotides (i) Netropsin (ii) Interaction of distamycin A (iii) Interactions of distamycin analogues (iv) Bifunctional netropsin-like compounds (c) Interactions with deoxyolioomers (d) Sequence specificity and mode of interaction (e) Association constants and thermodynamic aspects (f) Geometry and dynamics 2. Mithramycin and Structural Analogues 3. Anthramycin, Sibiromycin and Related Antibiotics 4. Other Antitumour Antibiotics

Nonintercalating dna binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material

We have studied electron transport in DNA duplexes, covalently bonded to two electrodes in aqueous buffer solutions, by repeatedly forming a large number of DNA junctions. The histogram of conductances reveals peaks at integer multiples of a fundamental value, which is used to identify with the conductance of a single DNA molecule. The measured conductance depends on the DNA sequence and length. For (GC)n sequences, the conductance is inversely proportional to the length (greater than eight base pairs). When inserting (A:T)m into GC-rich domains, it decreases exponentially with the length of A:T base pairs (m) with a decay constant of 0.43 A-1. This work provides an unambiguous determination of single DNA conductance and demonstrates different conduction mechanisms for different sequences.

Direct conductance measurement of single DNA molecules in aqueous solution

Differential scanning calorimetry (DSC), temperature-dependent uv-absorption spectroscopy, and temperature-dependent CD were used to monitor and characterize the salt-dependent, thermally induced structural transitions in the deoxydodecanucleotide d(CGCGAATTCGCG). At the high oligomer concentrations required for DSC, the calorimetric scans revealed a single, monophasic transition curve at all salt concentrations. Based on previous nmr melting studies under similar conditions, we conclude that these monophasic transitions correspond to the cooperative duplex-to-single-strand conversion of the dodecamer. By contrast, at the lower oligomer concentrations used for the spectroscopic studies, the shapes of the uv and CD melting curves were found to depend on the concentration of the added salt. At high salt (≥0.1M Na+), a single, monophasic transition curve was observed. At lower salt (⩽0.01M Na+), the CD and uv melting curves exhibit biphasic behavior. Based on the concentration dependence, the enthalpy, and the cooperativity of each transition in the biphasic curve, we conclude that at low salt and low oligomer concentrations, the dodecamer melts in a sequential manner involving initial disruption of a duplex structure and subsequent disruption of a hairpin structure.

Salt-dependent conformational transitions in the self-complementary deoxydodecanucleotide d(CGCAATTCGCG): evidence for hairpin formation.

We report the first calorimetric investigation of netropsin binding to poly d(AT). Temperature-dependent uv absorption, circular dichroism (CD), batch calorimetry, and differential scanning calorimetry (DSC) were used to detect, monitor, and thermodynamically characterize the binding process. The following results have been obtained: 1) Netropsin groove binding is accompanied by a large exothermic enthalpy of 9.2 kcal/mol of drug bound at 25 degrees C. This indicates that a large negative binding enthalpy may be a necessary but not a sufficient criterion for drug intercalation. We suggest that the exothermic binding might be correlated with specific H-bonding interactions. 2) From the difference in DSC transition enthalpies in the presence and absence of netropsin, we calculate a binding enthalpy of -10.7 kcal/mol of netropsin at 88 degrees C. 3) We calculate a positive delta S for netropsin binding to poly d(AT) at 25 degrees C. This positive entropy change may reflect netropsin-induced release of condensed cations and/or bound water. 4) The netropsin-saturated duplex monophasically melts 46 degrees C higher than the free duplex. The unsaturated duplex melts through two thermally-resolved transitions that correspond to netropsin-free and netropsin-bound regions. These two regions interact dynamically with no substantial influence on the thermal stabilities of the separate domains. 5) Netropsin binding decreases the cooperativity of the duplex to single strand transition.

Calorimetric and spectroscoptc Investigation of drug - DNA Interactions. I. The binding of netropsin to poly d(AT)

Temperature-dependent uv spectroscopy has been used to determine the differential salt effect of tetramethylammonium chloride (Me4NCl) and sodium chloride (NaCl) on the thermal stabilities of a series of deoxyoligonucleotide duplexes that systematically differ in base composition and sequence. This approach has allowed us to resolve the AT-specific effect of Me4N+ from the more general, non-specific cation effects of Me4N+ versus Na+. Our results reveal that in the absence of AT-specific effects, Me4N+ (relative to Na+) significantly reduces the thermal stability of duplex structures. We offer an interpretation of this differential salt effect in terms of the influence of the condensed cation on water structure at the surface of the duplex. We also observe an AT-specific effect of Me4N+ which results in an increased thermal stability for AT-containing duplexes in Me4NCl relative to NaCl. This specific effect which is governed by mass action is found to be uninfluenced by base sequence and to be a linear f...

Differential effect of tetramethylammonium chloride and sodium chloride on duplex melting temperatures of deoxyoligonucleotides: resolution of a salt effect into specific and non-specific components

Kenneth S. Blumenfeld

Papers

Salt-dependent conformational transitions in the self-complementary deoxydodecanucleotide d(CGCAATTCGCG): evidence for hairpin formation.

Calorimetric and spectroscoptc Investigation of drug - DNA Interactions. I. The binding of netropsin to poly d(AT)

Differential effect of tetramethylammonium chloride and sodium chloride on duplex melting temperatures of deoxyoligonucleotides: resolution of a salt effect into specific and non-specific components