Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation

Abstract

A clear difference in the enthalpy changes derived from spectroscopic and calorimetric measurements has recently been shown. The exact interpretation of this deviation varied from study to study, but it was generally attributed to the non-two-state transition and heat capacity change. Although the temperature-dependent thermodynamics of the duplex formation was often implied, systemic and extensive studies have been lacking in universally assigning the appropriate thermodynamic parameter sets. In the present study, the 24 DNA/DNA and 41 RNA/DNA oligonucleotide duplexes, designed to avoid the formation of hairpin or slipped duplex structures and to limit the base pair length less than 12 bp, were selected to evaluate the heat capacity changes and temperature-dependent thermodynamic properties of duplex formation. Direct comparison reveals that the temperature-independent thermodynamic parameters could provide a reasonable approximation only when the temperature of interest has a small deviation from the mean melting temperature over the experimental range. The heat capacity changes depend on the base composition and sequences and are generally limited in the range of )160 to % )40 calAEmol )1 AEK )1 per base pair. In contrast to the enthalpy and entropy changes, the free energy change and melting temperature are relatively insensitive to the heat capacity change. Finally, the 16 NN-model free energy parameters and one helix initiation at physiological temperature were extracted from the temperature-dependent thermodynamic data of the 41 RNA/DNA hybrids.Keywords: heat capacity change; temperature-dependent thermodynamics; enthalpy-entropy compensation; the NN-model parameters.With the dramatic progress in the human genome project, many gene sequences are well known but their structure and function are not yet clearly understood, and therefore, thermodynamic optimization strategy plays more and more important role in understanding and predicting the sequence-dependent higher-ordered structures of nucleic acids [1][2][3][4]. Knowledge of the thermodynamics of nucleic acids will also be very useful for designing appropriate screening or scanning experiments for identifying the genetic markers for diseases [5], sequencing single nucleotide polymorphisms on a genome-wide scale [6], calculating hybridization equilibria for purposes of designing the PCR and rolling-cycle amplification [7,8], selecting optimal conditions for hybridization experiments, and determining the minimum length of a probe required for the hybridization and cloning experiments [9,10]. Moreover, the development of DNA chips for rapidly screening and sequencing unknown DNAs mainly relies on the ability to predict the thermodynamic stability of the complexes formed by the oligonucleotide probes [11,12].Spectroscopic and calorimetric measurements are two widely applied methods to determine the thermodynamic parameters of nucleic acids [13][14][15]. The UV measurement is highly sensitive and only small sample units are required for a full set of measure...

Entropy-Driven Folding of an RNA Helical Junction: An Isothermal Titration Calorimetric Analysis of the Hammerhead Ribozyme

“…In addition, fell well within the range of per base-pair ΔC P 's reported for nucleic acid duplexes elsewhere (34)(35)(36)(37).…”

“…This value is in the consensus range of other heat capacities reported for helix formation (31)(32)(33)(34)(35)(36)(37). From and , we calculate a of +0.5 ± 0.1 kcal mor 1 K −1 .…”

Thermodynamic and kinetic modeling of transcriptional pausing

“…Clearly, for real biological DNA templates the sequence dependence profoundly affects the free energy landscape. In particular, the free energy contributions from (i)-(iii) above involve the nucleic acid duplex stabilities, which are highly sequence-dependent (32,33); whereas the contribution from (iv) above includes the contacts of nucleic acid backbones with RNAP and is not expected to be strongly sequence-dependent.…”

“…32, whereas the RNA-RNA (folding) contribution is obtained from the VIENNARNA package (33). The number of hypertranslocated configurations is bounded by the length of the hybrid, whereas the backtracked ones are fixed at 9, to account for paused complexes known to backtrack by Ͼ6 nt (36).…”

Heat capacity changes associated with nucleic acid folding

“…Due in part to the limitations of older calorimeters, it has long been assumed that ΔC P s were insignificant for nucleic acid folding, 64,65 although at least one early calorimetric study discussed the possibility of cold denaturation of RNA. 66 Only recently has the occurrence and impact of ΔC P s associated with nucleic acid folding become the focus of systematic investigation (e.g., [67][68][69][70]. Attending the recent influx of ΔC P data for nucleic acid structural changes have been further predictions of the possibility of nucleic acid cold denaturation.…”