In this work, we utilize Fourier transform infrared and temperature-jump (T-jump) infrared (IR) spectroscopy to investigate the melting thermodynamics and kinetics of a series of five DNA sequences ranging from 6 to 14 base pairs long. IR spectroscopy is well suited for the study of DNA because of its ability to distinguish base-specific information, and the nanosecond time resolution of the T-jump apparatus can access the relevant range of kinetics. Eyring analysis of a two-state model examines both the activation enthalpy and entropy, providing new insights into the energetic driving forces and physical processes behind the association and dissociation while also helping to clarify the commonly observed negative activation energy. Global analysis of the thermodynamic and kinetic data applying a linear dependence of activation barriers on oligo length provides a holistic result by producing reasonable agreement between our data and existing nearest-neighbor (NN) thermodynamic parameters blending the experimental results with established predictive models. By studying the trends in the thermodynamics and kinetics as a function of length, this work demonstrates a direct correlation between the effects additional dinucleotides have on the kinetics and the NN parameters for those dinucleotides. This result further supports the development of a kinetic analogue to the thermodynamic NN parameters.

Glycine betaine stabilizes folded protein structure due to its unfavorable thermodynamic interactions with amide oxygen and aliphatic carbon surface area exposed during protein unfolding. However, glycine betaine can attenuate nucleic acid secondary structure stability, although its mechanism of destabilization is not currently understood. In this work we quantify glycine betaine interactions with the surface area exposed during thermal denaturation of nine RNA dodecamer duplexes with guanine-cytosine (GC) contents of 17–100%. Hyperchromicity values indicate increasing glycine betaine molality attenuates stacking. Glycine betaine destabilizes higher GC content RNA duplexes to a greater extent than low GC content duplexes due to greater accumulation at the surface area exposed during unfolding. The accumulation is very sensitive to temperature and displays characteristic entropy-enthalpy compensation. Since the entropic contribution to the m-value (used to quantify GB interaction with the RNA solvent accessible surface area exposed during denaturation) is more dependent on temperature than the enthalpic contribution, higher GC content duplexes with their larger transition temperatures are destabilized to a greater extent than low GC content duplexes. The concentration of glycine betaine at the RNA surface area exposed during unfolding relative to bulk was quantified using the solute partitioning model. Temperature correction predicts a glycine betaine concentration at 25 °C to be nearly independent of GC content, indicating that glycine betaine destabilizes all sequences equally at this temperature.

In recent years, the importance of safety in academic research laboratories has gained considerable attention nationwide. The University of Chicago Joint Research Safety Initiative (JRSI) is a community of graduate students, postdoctoral researchers, and research assistants in the Department of Chemistry and Pritzker School of Molecular Engineering, whose focus is to facilitate a sustainable lab safety culture by providing educational tools, training, and resources that are presented in an organized, clear, and centralized fashion. Our organization was established in Fall 2017 to address the safety needs of our research community with a bottom-up approach. Here, we provide a brief account of how the JRSI designed activities around five themes: (1) Developing Organizational Structure, (2) Evaluating Safety Culture and Organizational Effectiveness, (3) Facilitating Open Dialogues and Collaborations, (4) Defragmenting Safety Efforts and Resources, and (5) Educating Researchers, Teachers, and Safety Contacts. In each of these areas, we discuss programs and highlight lessons learned that can assist in analogous student-led implementation strategies. This Case Study does not provide an exhaustive list of solutions for all safety-related deficiencies; rather, it strives to bring special attention to the general background, core ideas, reflections, and encountered challenges when forming a new researcher-led safety initiative.

In this work, we present a kinetic Markov state Monte Carlo model designed to complement temperature-jump (T-jump) infrared spectroscopy experiments probing the kinetics and dynamics of short DNA oligonucleotides. The model is designed to be accessible to experimental researchers in terms of both computational simplicity and expense while providing detailed insights beyond those provided by experimental methods. The model is an extension of a thermodynamic lattice model for DNA hybridization utilizing the formalism of the nucleation-zipper mechanism. Association and dissociation trajectories were generated utilizing the Gillespie algorithm and parameters determined via fitting the association and dissociation timescales to previously published experimental data. Terminal end fraying, experimentally observed following a rapid T-jump, in the sequence 5′-ATATGCATAT-3′ was replicated by the model that also demonstrated that experimentally observed fast dynamics in the sequences 5′-C(AT)nG-3′, where n = 2–6, were also due to terminal end fraying. The dominant association pathways, isolated by transition pathway theory, showed two primary motifs: initiating at or next to a G:C base pair, which is enthalpically favorable and related to the increased strength of G:C base pairs, and initiating in the center of the sequence, which is entropically favorable and related to minimizing the penalty associated with the decrease in configurational entropy due to hybridization.