We report a complete thermodynamic characterization of the impact of abasic and anucleosidic lesions on the stability, conformation, and melting behavior of a DNA duplex. The requisite thermodynamic data were obtained by using a combination of spectroscopic and calorimetric techniques to investigate helix-to-coil transitions in a family of DNA duplexes of the form d(CGCATGAGTACGC)-d(GCGTA-CXCATGCG), where X corresponds to a thymidine residue in the parent Watson-Crick duplex and to an abasic or anucleosidic site in the modified duplexes. The data derived from these studies reveal that incorporation of an abasic site into a DNA duplex dramatically reduces the duplex stability, transition enthalpy, and transition entropy. The magnitudes of these lesion-induced effects are greater than one would expect based on simple nearest-neighbor considerations. Nearly identical thermodynamic data are obtained when the modified duplex contains an anucleosidic site rather than an abasic site. This observation suggests that the thermodynamic impact of these lesions primarily results from removal of the base rather than the sugar ring. Significantly, the melting cooperativities of the abasic and anucleosidic derivatives are identical with each other and with the corresponding unmodified Watson-Crick parent duplex. This result suggests that the phosphodiester backbone, rather than the base-sugar network, serves as the primary propagation path for the communication of cooperative melting effects. We propose molecular interpretations for the thermodynamic data based on the structural picture that has emerged from the NMR studies of Patel and coworkers on the same family of modified and unmodified DNA duplexes

The role of relativistic jets in unbinding the stellar envelope during a supernova (SN) associated with a gamma-ray burst (GRB) is unclear. To study that, we explore observational signatures of stellar explosions that are driven by jets. We focus on the final velocity distribution of the outflow in such explosions and compare its observational imprints to SN/GRB data. We find that jet driven explosions produce an outflow with a flat distribution of energy per logarithmic scale of proper velocity. The flat distribution seems to be universal as it is independent of the jet and the progenitor properties that we explored. The velocity range of the flat distribution for typical GRB parameters is γβ ≈ 0.03 − 3, where γ is the outflow Lorentz factor and β is its dimensionless velocity. A flat distribution is seen also for collimated choked jets where the highest outflow velocity decreases with the depth at which the jet is choked. Comparison to observations of SN/GRBs strongly disfavors jets as the sole explosion source in these events. Instead, in SN/GRB the collapsing star seems to deposit its energy into two channels - a quasi-spherical (or wide angle) channel and a narrowly collimated one. The former carries most of the energy and is responsible for the SN sub-relativistic ejecta while the latter carries 0.01-0.1 of the total outflow energy and is the source of the GRB. Intriguingly, the same two channels, with a similar energy ratio, were seen in the binary neutron star merger GW170817, suggesting that similar engines are at work in both phenomena.

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