Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs

Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes

Vibrational non-Condon effects, which describe how molecular vibrational transitions are influenced by a system's rotational and translational degrees of freedom, are often overlooked in spectroscopy studies of biological macromolecules. In this work, we explore these effects in the modeling of infrared (IR) spectra for nucleic acids in the 1600-1800 cm-1 region. Through electronic structure calculations, we reveal that the transition dipole moments of the C═O and C═C stretching modes in nucleobases are highly sensitive to solvation, hydrogen bonding, and base stacking conditions. To incorporate vibrational non-Condon effects into spectroscopy modeling, we use local electric fields on chromophore atoms as collective coordinates and leverage experimental IR spectra of oligonucleotides to develop deep neural network-based transition dipole strength (TDS) maps for the C═O and C═C chromophores. By integrating molecular dynamics simulations with a mixed quantum/classical treatment of the line shape theory, we apply the TDS maps to calculate the IR spectra of nucleoside 5'-monophosphates, DNA double helices and yeast phenylalanine tRNA. The resulting theoretical spectra show quantitative agreement with experimental measurements. While the predictions for nucleoside 5'-monophosphates are comparable to baseline performance, the TDS maps yield significantly improved IR peak intensities across all oligonucleotides. This theoretical framework effectively bridges atomistic simulations and IR spectroscopy experiments, offering molecular insights into how vibrational non-Condon effects impact the observed spectral features.

NAIRDB: a database of Fourier transform infrared (FTIR) data for nucleic acids

The Nucleic Acid InfraRed Data Bank (NAIRDB) serves as a comprehensive public repository dedicated to the archival and free distribution of Fourier transform infrared (FTIR) spectral data specific to nucleic acids. This database encompasses a collection of FTIR spectra covering diverse nucleic acid molecules, including DNA, RNA, DNA/RNA hybrids and their various derivatives. NAIRDB covers details of the experimental conditions for FTIR measurements, literature links, primary sequence data, information about experimentally determined structures for related nucleic acid molecules and/or computationally modeled 3D structures. All entries undergo expert validation and curation to maintain the completeness, consistency and quality of the data. NAIRDB can be searched by similarity of nucleic acid sequences or by direct comparison of spectra. The database is open for the submission of the FTIR data for nucleic acids. NAIRDB is available at https://nairdb.genesilico.pl.

Simulation-Guided Conformational Space Exploration to Assess Reactive Conformations of a Ribozyme

Self-splicing ribozymes are small ribonucleic acid (RNA) enzymes that catalyze their own cleavage through a transphosphoesterification reaction. While this process is involved in some specific steps of viral RNA replication and splicing, it is also of importance in the context of the (putative) first autocatalytic RNA-based systems that could have preceded the emergence of modern life. The uncatalyzed phosphoester bond formation is thermodynamically very unfavorable, and many experimental studies have focused on understanding the molecular features of catalysis in these ribozymes. However, chemical reaction paths are short-lived and not easily characterized by experimental approaches, so molecular simulation approaches appear as an ideal tool to unveil the molecular details of the reaction. Here, we focus on the model hairpin ribozyme. We show that identifying a relevant initial conformation for reactivity studies, which is frequently overlooked in mixed quantum-classical studies that predominantly concentrate on the chemical reaction itself, can be highly challenging. These challenges stem from limitations in both available experimental structures (which are chemically altered to prevent self-cleavage) and the accuracy of force fields, together with the necessity for comprehensive sampling. We show that molecular dynamics simulations, combined with extensive conformational phase space exploration with Hamiltonian replica-exchange simulations, enable us to characterize the relevant conformational basins of the minimal hairpin ribozyme in the ligated state prior to self-cleavage. We find that what is usually considered a canonical reactive conformation with active site geometries and hydrogen-bond patterns that are optimal for the addition-elimination reaction with general acid/general base catalysis is metastable and only marginally populated. The thermodynamically stable conformation appears to be consistent with the expectations of a mechanism that does not require the direct participation of ribozyme residues in the reaction. While these observations may suffer from forcefield inaccuracies, all investigated forcefields lead to the same conclusions upon proper sampling, contrasting with previous investigations on shorter timescales suggesting that at least one reparametrization of the Amber99 forcefield allowed to stabilize aligned active site conformations. Our study demonstrates that identifying the most pertinent reactant state conformation holds equal importance alongside the accurate determination of the thermodynamics and kinetics of the chemical steps of the reaction.

RNA Complexes with Nicks and Gaps: Thermodynamic and Kinetic Effects of Coaxial Stacking and Dangling Ends

Multiple RNA strands can interact in solution and assume a large variety of configurations dictated by their potential for base pairing. Although duplex formation from two complementary oligonucleotides has been studied in detail, we still lack a systematic characterization of the behavior of higher order complexes. Here, we focus on the thermodynamic and kinetic effects of an upstream oligonucleotide on the binding of a downstream oligonucleotide to a common template, as we vary the sequence and structure of the contact interface. We show that coaxial stacking in RNA is well correlated with but much more stabilizing than helix propagation over an analogous intact double helix step (median ΔΔG°37 °C ≈ 1.7 kcal/mol). Consequently, approximating coaxial stacking in RNA with the helix propagation term leads to large discrepancies between predictions and our experimentally determined melting temperatures, with an offset of ≈10 °C. Our kinetic study reveals that the hybridization of the downstream probe oligonucleotide is impaired (lower kon) by the presence of the upstream oligonucleotide, with the thermodynamic stabilization coming entirely from an extended lifetime (lower koff) of the bound downstream oligonucleotide, which can increase from seconds to months. Surprisingly, we show that the effect of nicks is dependent on the length of the stacking oligonucleotides, and we discuss the binding of ultrashort (1-4 nt) oligonucleotides that are relevant in the context of the origin of life. The thermodynamic and kinetic data obtained in this work allow for the prediction of the formation and stability of higher-order multistranded complexes.

Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics

Local perturbations to DNA base-pairing stability from lesions and chemical modifications can alter the stability and dynamics of an entire oligonucleotide. End effects may cause the position of a disruption within a short duplex to influence duplex stability and structural dynamics, yet this aspect of nucleic acid modifications is often overlooked. We investigate how the position of an abasic site (AP site) impacts the stability and dynamics of short DNA duplexes. Using a combination of steady-state and time-resolved spectroscopy and molecular dynamics simulations, we unravel an interplay between AP-site position and nucleobase sequence that controls energetic and dynamic disruption to the duplex. The duplex is disrupted into two segments by an entropic barrier for base-pairing on each side of the AP site. The barrier induces fraying of the short segment when an AP site is near the termini. Shifting the AP site inward promotes a transition from short-segment fraying to fully encompassing the barrier into the thermodynamics of hybridization, leading to further destabilization of the duplex. Nucleobase sequence determines the length scale for this transition by tuning the barrier height and base-pair stability of the short segment, and certain sequences enable out-of-register base-pairing to minimize the barrier height.