This study investigates the contributions of base stacking and base pairing to the thermal stability of the DNA double helix. The researchers measure the temperature and salt dependence of the stacking free energy of DNA double helices using DNA molecules with solitary nicks and gaps. They directly determine DNA stacking parameters for temperatures from below room temperature to near melting temperature and for salt concentrations ranging from 15 to 100 mM Na⁺. By analyzing stacking parameters of individual base pairs, they calculate the base-stacking contribution to the stability of A•T- and G•C-containing DNA polymers. The results show that base-stacking interactions are the main stabilizing factor in the DNA double helix, while A•T pairing is destabilizing and G•C pairing contributes little stabilization. The temperature and salt dependence of the stacking term fully determine the stability of DNA. The study also shows that the salt dependence of the stacking term determines the salt dependence of DNA stability. The findings suggest that base-stacking interactions dominate the stability of the DNA double helix, and that the sequence dependence of DNA stability is significantly influenced by base-stacking interactions. The study also highlights the importance of base-stacking interactions in various biological processes, including DNA breathing, DNA repair, and DNA sequencing. The results have implications for understanding the stability of DNA and its role in biological processes. The study provides new insights into the fundamental understanding of DNA structure and energetics, and has significant implications for various biological processes. The study also demonstrates the importance of base-stacking interactions in DNA stability and their role in DNA sequence-dependent stability. The findings suggest that base-stacking interactions are the primary factor in DNA stability, and that the sequence dependence of DNA stability is largely due to the heterogeneity of base-stacking interactions. The study provides a new understanding of the role of base-stacking interactions in DNA stability and their contribution to the sequence-dependent stability of DNA. The results have implications for understanding the stability of DNA and its role in biological processes. The study also highlights the importance of base-stacking interactions in DNA stability and their role in DNA sequence-dependent stability. The findings suggest that base-stacking interactions are the primary factor in DNA stability, and that the sequence dependence of DNA stability is largely due to the heterogeneity of base-stacking interactions. The study provides a new understanding of the role of base-stacking interactions in DNA stability and their contribution to the sequence-dependent stability of DNA. The results have implications for understanding the stability of DNA and its role in biological processes.This study investigates the contributions of base stacking and base pairing to the thermal stability of the DNA double helix. The researchers measure the temperature and salt dependence of the stacking free energy of DNA double helices using DNA molecules with solitary nicks and gaps. They directly determine DNA stacking parameters for temperatures from below room temperature to near melting temperature and for salt concentrations ranging from 15 to 100 mM Na⁺. By analyzing stacking parameters of individual base pairs, they calculate the base-stacking contribution to the stability of A•T- and G•C-containing DNA polymers. The results show that base-stacking interactions are the main stabilizing factor in the DNA double helix, while A•T pairing is destabilizing and G•C pairing contributes little stabilization. The temperature and salt dependence of the stacking term fully determine the stability of DNA. The study also shows that the salt dependence of the stacking term determines the salt dependence of DNA stability. The findings suggest that base-stacking interactions dominate the stability of the DNA double helix, and that the sequence dependence of DNA stability is significantly influenced by base-stacking interactions. The study also highlights the importance of base-stacking interactions in various biological processes, including DNA breathing, DNA repair, and DNA sequencing. The results have implications for understanding the stability of DNA and its role in biological processes. The study provides new insights into the fundamental understanding of DNA structure and energetics, and has significant implications for various biological processes. The study also demonstrates the importance of base-stacking interactions in DNA stability and their role in DNA sequence-dependent stability. The findings suggest that base-stacking interactions are the primary factor in DNA stability, and that the sequence dependence of DNA stability is largely due to the heterogeneity of base-stacking interactions. The study provides a new understanding of the role of base-stacking interactions in DNA stability and their contribution to the sequence-dependent stability of DNA. The results have implications for understanding the stability of DNA and its role in biological processes. The study also highlights the importance of base-stacking interactions in DNA stability and their role in DNA sequence-dependent stability. The findings suggest that base-stacking interactions are the primary factor in DNA stability, and that the sequence dependence of DNA stability is largely due to the heterogeneity of base-stacking interactions. The study provides a new understanding of the role of base-stacking interactions in DNA stability and their contribution to the sequence-dependent stability of DNA. The results have implications for understanding the stability of DNA and its role in biological processes.