Length-Dependent Melting Kinetics of Short DNA Oligonucleotides Using Temperature-Jump IR Spectroscopy

Kinetics and dynamics of oligonucleotide hybridization

The hybridization of short nucleic acid strands is a remarkable spontaneous process that is foundational to biotechnology and nanotechnology and plays a crucial role in gene expression, editing and DNA repair. Decades of research into the mechanism of hybridization have resulted in a deep understanding of its thermodynamics, but many questions remain regarding its kinetics and dynamics. Recent advances in experiments and molecular dynamics simulations of nucleic acids are enabling more direct insight into the structural dynamics of hybridization, which can test long-standing assumptions regarding its mechanism. In this Review, we summarize the current state of knowledge of hybridization kinetics, discuss the barriers to a molecular description of hybridization dynamics, and highlight the new approaches that have begun uncovering the dynamics of hybridization and the duplex ensemble. The kinetics and dynamics of hybridization are highly sensitive to the composition of nucleic acids, and we emphasize recent discoveries and open questions on the role of nucleobase sequence and chemical modifications.

A Fluorescence-Based Temperature-Jump Apparatus for Illustrating Protein Dynamics on the Millisecond Time Scale

A fluorescence-based temperature jump (T-jump) module was constructed to illustrate the large-domain motion of a given protein upon thermal stimulus on the millisecond time scale. The aqueous sample was readily heated by 5.0 °C in ca. 2 ms with a lasting high temperature plateau (>1 s) upon irradiation with the "optical Riemann sum" of the discrete infrared pulses of different energy sequences from a 1467 nm diode laser operated at 1k Hz. The temperature evolution was revealed by the time-evolved fluorescence intensity change of the dissolved tryptophan. Bovine serum albumin (BSA) and human serum albumin (HSA) were chosen as model proteins, and their fluorescence intensity evolutions were recorded at 36.6-39.9 °C upon T-jump from 35.0 °C, within the range of physiological temperatures. The observed protein dynamics of BSA was characterized with an apparent activation energy of 276 ± 23 kJ mol-1, whereas HSA did not manifest the dynamic component. In this measurement, only a tiny amount of sample, ca. 1 μL, was required due to the conjugation of the microspot objective, and the initial temperature was readily controlled by a homemade thermostatic pad. This millisecond-resolution technique is advantageous for illustrating the large-domain dynamics of the targeted protein, bridging the characterizations of the localized protein dynamics on nanosecond to microsecond time scales using the fast techniques and the steady-state protein conformational features by conventional methods, such as Fourier-transform infrared and circular dichroism spectroscopies.

Biocompatible DNA hydrogel composed of minimized Takumi-shaped DNA nanostructure exhibits sustained retention after in vivo administration

Our previous studies showed that DNA hydrogels containing unmethylated CpG motifs effectively induced antigen-specific immune responses when combined with the appropriate antigens. A potential drawback of existing DNA hydrogels for further applications is the need for many oligodeoxynucleotide (ODN) types. Therefore, in this study, we attempted to optimize and minimize the nanostructured DNA units for DNA hydrogels to reduce the preparation cost, design difficulty, and possible risk of sequence-dependent off-target effects, and prepare DNA hydrogels with sustained retention ability. A Takumi-shaped unit with a stem and four flanking cohesive parts was constructed using one type of ODN with a palindromic sequence. A DNA hydrogel was prepared by mixing two Takumi-shaped units with complementary cohesive parts. The required length of the cohesive part was first examined using ODNs with 14 or 18 bases of stem length. Electrophoresis, melting temperature measurements, and viscoelastic analysis showed that the properties of the cohesive part determined the hydrogel properties. ODNs with a cohesive part consisting of GC-rich 5'-ccgcaagacg-3' efficiently formed a hydrogel with sustained retention in mice after administration. Several ODNs with optimized cohesive sequences and different stem lengths and sequences were designed. Analyses showed that a stem of 10 bases or longer was required for efficient hydrogel formation, and ODNs with a 12-base stem part exhibited the most prolonged retention after subcutaneous injection into mice. Thus, the present study demonstrated the requirements of minimal DNA units for preparing DNA hydrogels with sustained retention ability.

Impact of Surface Adsorption on DNA Structure and Stability: Implications for Environmental DNA Interactions with Iron Oxide Surfaces

Environmental DNA (eDNA), i.e., DNA found in the environment, can interact with various geochemical surfaces, yet little is known about these interactions. Mineral surfaces may alter the structure, stability, and reactivity of eDNA, impacting the cycling of genetic information and the reliability of eDNA-based detection tools. Understanding how eDNA interacts with surfaces is crucial for predicting its fate in the environment. In this study, we examined the surface interaction and stability of herring testes DNA, a model system for eDNA, on two common iron oxide phases present in the environment: α-FeOOH (goethite) and α-Fe2O3 (hematite). Utilizing spectroscopic probes, including attenuated total reflection Fourier-transform infrared (ATR-FTIR) and UV-vis spectroscopy, we quantified the DNA adsorption capacity at pH 5 and determined its secondary structure. DNA adsorbed irreversibly at pH 5 and 25 °C, primarily through its phosphate groups, and retained the solution-phase B-form structure. However, the infrared data also indicated some distortion of the B-form likely due to additional interactions between nitrogenous bases when adsorbed on the α-Fe2O3 particle surfaces. The distortion in the double helical structure of adsorbed DNA on α-Fe2O3 led to a lower melting temperature (Tm) of 60 °C compared to 70 °C for DNA in solution. In contrast, DNA adsorbed on α-FeOOH melted at higher temperatures relative to solution-phase DNA and in two distinct phases. Upon testing adsorbed DNA stability at higher pH values, there were distinct differences between the two iron oxide phases. For α-FeOOH, nearly 50% of the DNA desorbed from the surface when the solution pH changed from 5 to 8, while less than 5% desorbed from α-Fe2O3 under the same conditions. Overall, these findings underscore the importance of mineral-specific eDNA-surface interactions and their role in adsorbed eDNA stability, in terms of DNA melting and the impact of solution-phase pH changes.

Isotope-Edited Variable Temperature Infrared Spectroscopy for Measuring Transition Temperatures of Single A-T Watson-Crick Base Pairs in DNA Duplexes

Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2═O stretching vibration when it is within the DNA duplex via isotopic substitutions at other atomic positions in the structure. First, we determined that this stretching state was localized enough to specific atoms in the molecule to make submolecular scale measurements of local structure and stability in high molecular weight complexes. Next, we develop a new isotope-edited variable temperature infrared method to measure melting transitions at various locations in a DNA structure. As an initial test of this "sub-molecular scale thermometer", we applied our T13C2 difference infrared signal to measure location-dependent melting temperatures (TmL) in a DNA duplex via variable temperature attenuated total reflectance Fourier transform infrared (VT-ATR-FTIR) spectroscopy. We report that the TmL of a single Watson-Crick A-T base pair near the end of an A-T rich sequence (poly T) is ∼34.9 ± 0.7°C. This is slightly lower than the TmL of a single base pair near the middle position of the poly T sequence (TmL ∼35.6±0.2°C). In addition, we also report that the TmL of a single Watson-Crick A-T base pair near the end of a 50% G-C sequence (12-mer) is ∼52.5 ± 0.3°C, which is slightly lower than the global melting Tm of the 12-mer sequence (TmL ∼54.0±0.9°C). Our results provide direct physical evidence for end fraying in DNA sequences with our novel spectroscopic methods.

Enhanced Detection of Novel Low-Frequency Gene Fusions via High-Yield Ligation and Multiplexed Enrichment Sequencing

Panel-based methods are commonly employed for the analysis of novel gene fusions in precision diagnostics and new drug development in cancer. However, these methods are constrained by limitations in ligation yield and the enrichment of novel gene fusions with low variant allele frequencies. In this study, we conducted a pioneering investigation into the stability of double-stranded adapter DNA, resulting in improved ligation yield and enhanced conversion efficiency. Additionally, we implemented blocker displacement amplification, achieving a remarkable 7-fold enrichment of novel gene fusions. Leveraging the pre-enrichment achieved with this approach, we successfully applied it to Nanopore sequencing, enabling ultra-fast analysis of novel gene fusions within one hour with high sensitivity. This method offers a robust and remarkably sensitive mean of analyzing novel gene fusions, promising the discovery of pivotal biomarkers that can significantly improve cancer diagnostics and the development of new therapeutic strategies.

Transient states during the annealing of mismatched and bulged oligonucleotides

Oligonucleotide hybridization is crucial in various biological, prebiotic and nanotechnological processes, including gene regulation, non-enzymatic primer extension and DNA nanodevice assembly. Although extensive research has focused on the thermodynamics and kinetics of nucleic acid hybridization, the behavior of complex mixtures and the outcome of competition for target binding remain less well understood. In this study, we investigate the impact of mismatches and bulges in a 12 bp DNA or RNA duplex on its association (kon) and dissociation (koff) kinetics. We find that such defects have relatively small effects on the association kinetics, while the dissociation kinetics vary in a position-dependent manner by up to 6 orders of magnitude. Building upon this observation, we explored a competition scenario involving multiple oligonucleotides, and observed a transient low specificity of probe hybridization to fully versus partially complementary targets in solution. We characterize these long-lived metastable states and their evolution toward equilibrium, and show that sufficiently long-lived mis-paired duplexes can serve as substrates for prebiotically relevant chemical copying reactions. Our results suggest that transient low accuracy states may spontaneously emerge within all complex nucleic acid systems comprising a large enough number of competing strands, with potential repercussions for gene regulation in the realm of modern biology and the prebiotic preservation of genetic information.

Generation of DNA oligomers with similar chemical kinetics via in-silico optimization

Networks of interacting DNA oligomers are useful for applications such as biomarker detection, targeted drug delivery, information storage, and photonic information processing. However, differences in the chemical kinetics of hybridization reactions, referred to as kinetic dispersion, can be problematic for some applications. Here, it is found that limiting unnecessary stretches of Watson-Crick base pairing, referred to as unnecessary duplexes, can yield exceptionally low kinetic dispersions. Hybridization kinetics can be affected by unnecessary intra-oligomer duplexes containing only 2 base-pairs, and such duplexes explain up to 94% of previously reported kinetic dispersion. As a general design rule, it is recommended that unnecessary intra-oligomer duplexes larger than 2 base-pairs and unnecessary inter-oligomer duplexes larger than 7 base-pairs be avoided. Unnecessary duplexes typically scale exponentially with network size, and nearly all networks contain unnecessary duplexes substantial enough to affect hybridization kinetics. A new method for generating networks which utilizes in-silico optimization to mitigate unnecessary duplexes is proposed and demonstrated to reduce in-vitro kinetic dispersions as much as 96%. The limitations of the new design rule and generation method are evaluated in-silico by creating new oligomers for several designs, including three previously programmed reactions and one previously engineered structure.

Near-Infrared Fluorescent Biosensors Based on Covalent DNA Anchors

Semiconducting single-walled carbon nanotubes (SWCNTs) are versatile near-infrared (NIR) fluorophores. They are noncovalently modified to create sensors that change their fluorescence when interacting with biomolecules. However, noncovalent chemistry has several limitations and prevents a consistent way to molecular recognition and reliable signal transduction. Here, we introduce a widely applicable covalent approach to create molecular sensors without impairing the fluorescence in the NIR (>1000 nm). For this purpose, we attach single-stranded DNA (ssDNA) via guanine quantum defects as anchors to the SWCNT surface. A connected sequence without guanines acts as flexible capture probe allowing hybridization with complementary nucleic acids. Hybridization modulates the SWCNT fluorescence and the magnitude increases with the length of the capture sequence (20 > 10 ≫ 6 bases). The incorporation of additional recognition units via this sequence enables a generic route to NIR fluorescent biosensors with improved stability. To demonstrate the potential, we design sensors for bacterial siderophores and the SARS CoV-2 spike protein. In summary, we introduce covalent guanine quantum defect chemistry as rational design concept for biosensors.

Modeling the Infrared Spectroscopy of Oligonucleotides with 13C Isotope Labels

The carbonyl stretching modes have been widely used in linear and two-dimensional infrared (IR) spectroscopy to probe the conformation, interaction, and biological functions of nucleic acids. However, due to their universal appearance in nucleobases, the IR absorption bands of nucleic acids are often highly congested in the 1600-1800 cm-1 region. Following the fruitful applications in proteins, 13C isotope labels have been introduced to the IR measurements of oligonucleotides to reveal their site-specific structural fluctuations and hydrogen bonding conditions. In this work, we combine recently developed frequency and coupling maps to develop a theoretical strategy that models the IR spectra of oligonucleotides with 13C labels directly from molecular dynamics simulations. We apply the theoretical method to nucleoside 5'-monophosphates and DNA double helices and demonstrate how elements of the vibrational Hamiltonian determine the spectral features and their changes upon isotope labeling. Using the double helices as examples, we show that the calculated IR spectra are in good agreement with experiments and the 13C isotope labeling technique can potentially be applied to characterize the stacking configurations and secondary structures of nucleic acids.

Sequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy

Time-resolved temperature-jump/drop infrared (IR) spectroscopy has been used to measure the impact of stem base sequence on the melting and refolding dynamics of ribonucleic acid (RNA) tetraloops. A series of three 12-nucleotide RNA hairpin sequences were studied, each featuring a UACG tetraloop motif and a double-stranded stem containing four base pairs. In each case, the stem comprised three GC pairs plus a single AU base pair inserted at the closing point of the loop (RNA_loop), in the middle of the stem (RNA_mid), or at the stem terminus (RNA_end). Results from analogous DNA tetraloop (TACG) sequences were also obtained. Inclusion of AU or AT base pairs in the stem leads to faster melting of the stem-loop structure compared to a stem sequence featuring four GC base pairs while refolding times were found to be slower, consistent with a general reduction in stem-loop stability caused by the AU/AT pair. Independent measurement of the dynamic timescales for melting and refolding of ring vibrational modes of guanine (G_R) and adenine (A_R) provided position-specific insight into hairpin dynamics. The G_R-derived data showed that DNA sequences melted more quickly (0.5 ± 0.1 to 0.7 ± 0.1 μs at 70 °C) than analogous RNA sequences (4.3 ± 0.4 to 4.4 ± 0.3 μs at 70 °C). Position-sensitive data from the A_R modes suggests that DNA hairpins begin melting from the terminal end of the stem toward the loop while RNA sequences begin melting from the loop. Refolding timescales for both RNA and DNA hairpins were found to be similar (250 ± 50 μs at 70 °C) except for RNA_end and DNA_loop which refolded much more slowly (746 ± 36 and 430 ± 31 μs, respectively), showing that the refolding pathway is significantly impaired by the placement of AU/AT pairs at different points in the stem. We conclude that conformational changes of analogous pairs of RNA and DNA tetraloops proceed by different mechanisms.

Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain

The hybridization kinetic of an oligonucleotide to its template is a fundamental step in many biological processes such as replication arrest, CRISPR recognition, DNA sequencing, DNA origami, etc. Although single kinetic descriptions exist for special cases of this problem, there are no simple general prediction schemes. In this work, we have measured experimentally, with no fluorescent labelling, the displacement of an oligonucleotide from its substrate in two situations: one corresponding to oligonucleotide binding/unbinding on ssDNA and one in which the oligonucleotide is displaced by the refolding of a dsDNA fork. In this second situation, the fork is expelling the oligonucleotide thus significantly reducing its residence time. To account for our data in these two situations, we have constructed a mathematical model, based on the known nearest neighbour dinucleotide free energies, and provided a good estimate of the residence times of different oligonucleotides (DNA, RNA, LNA) of various lengths in different experimental conditions (force, temperature, buffer conditions, presence of mismatches, etc.). This study provides a foundation for the dynamics of oligonucleotide displacement, a process of importance in numerous biological and bioengineering contexts.

Measuring RNA UNCG Tetraloop Refolding Dynamics Using Temperature-Jump/Drop Infrared Spectroscopy

Determining the structural dynamics of RNA and DNA is essential to understanding their cellular function, but direct measurement of strand association or folding remains experimentally challenging. Here we illustrate a temperature-jump/drop method able to reveal refolding dynamics. Time-resolved temperature-jump/drop infrared spectroscopy is used to measure the melting and refolding dynamics of a 12-nucleotide RNA sequence comprising a UACG tetraloop and a four-base-pair double-stranded GC stem, comparing them to an equivalent DNA (TACG) sequence. Stem-loop melting occurred an order of magnitude more slowly in RNA than DNA (6.0 ± 0.1 μs versus 0.8 ± 0.1 μs at 70 °C). In contrast, the refolding dynamics of both sequences occurred on similar time scales (200 μs). While the melting and refolding dynamics of RNA and DNA hairpins both followed Arrhenius temperature dependences, refolding was characterized by an apparent negative activation energy, consistent with a mechanism involving multiple misfolded intermediates prior to zipping of the stem base pairs.

Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides

Hybridization and strand displacement kinetics determine the evolution of the base paired configurations of mixtures of oligonucleotides over time. Although much attention has been focused on the thermodynamics of DNA and RNA base pairing in the scientific literature, much less work has been done on the time dependence of interactions involving multiple strands, especially in RNA. Here we provide a study of oligoribonucleotide interaction kinetics and show that it is possible to calculate the association, dissociation and strand displacement rates displayed by short oligonucleotides (5nt–12nt) that exhibit no expected secondary structure as simple functions of oligonucleotide length, CG content, ΔG of hybridization and ΔG of toehold binding. We then show that the resultant calculated kinetic parameters are consistent with the experimentally observed time dependent changes in concentrations of the different species present in mixtures of multiple competing RNA strands. We show that by changing the mixture composition, it is possible to create and tune kinetic traps that extend by orders of magnitude the typical sub-second hybridization timescale of two complementary oligonucleotides. We suggest that the slow equilibration of complex oligonucleotide mixtures may have facilitated the nonenzymatic replication of RNA during the origin of life.

Star-Polymer-DNA Gels Showing Highly Predictable and Tunable Mechanical Responses

Dynamically crosslinked gels are appealing materials for applications that require time-dependent mechanical responses. DNA duplexes are ideal crosslinkers for building such gels because of their excellent sequence addressability and flexible tunability in bond energy. However, the mechanical responses of most DNA gels are complicated and unpredictable. Here, a DNA gel with a highly homogeneous gel network and well predictable mechanical behaviors is demonstrated by using a pair of star-polymer-DNA precursors with presimulated DNA sequences showing the two-state transition. The melting curve analysis of the DNA gels reveals the good correspondence between the thermodynamic potentials of the DNA crosslinkers and the presimulated values by DNA calculators. Stress-relaxation tests and dissociation kinetics measurements show that the macroscopic relaxation time of the DNA gels is approximately equal to the lifetime of the DNA crosslinkers over 4 orders of magnitude from 0.1-2000 s. Furthermore, a series of durability tests find the DNA gels are hysteresis-less and self-healable after the applications of repeated temperature and mechanical stimuli. These results demonstrate the great potential of star-polymer-DNA precursors for building gels with predictable and tunable viscoelastic properties, suitable for applications such as stress-response extracellular matrices, injectable solids, and soft robotics.

A stop-flow sample delivery system for transient spectroscopy

A stop-flow sample delivery system for transient spectroscopy is presented, which is, in particular, suited for laser-based instruments (quantum-cascade lasers or amplified femtosecond lasers) with excitation pulse repetition rates in the range 10-100 Hz. Two pulsing micro-valves are mounted onto a flow cuvette designed for transient IR spectroscopy, which is integrated into a flow cycle driven by a peristaltic pump. The performance of the system is demonstrated with transient IR experiments of the trans-to-cis photoisomerization of a water-soluble azobenzene derivative. The sample stands still when the micro-valves are closed and is pushed out from the probe beam focus on a 1 ms timescale when opening the micro-valves. The setup is extremely sample efficient. It needs only small sample volumes, and at the same time, it enables excitation of a large fraction of molecules in solution.

A General DNA-Gated Hydrogel Strategy for Selective Transport of Chemical and Biological Cargos

The selective transport of molecular cargo is critical in many biological and chemical/materials processes and applications. Although nature has evolved highly efficient in vivo biological transport systems, synthetic transport systems are often limited by the challenges associated with fine-tuning interactions between cargo and synthetic or natural transport barriers. Herein, deliberately designed DNA-DNA interactions are explored as a new modality for selective DNA-modified cargo transport through DNA-grafted hydrogel supports. The chemical and physical characteristics of the cargo and hydrogel barrier, including the number of nucleic acid strands on the cargo (i.e., the cargo valency) and DNA-DNA binding strength, can be used to regulate the efficiency of cargo transport. Regimes exist where a cargo-barrier interaction is attractive enough to yield high selectivity yet high mobility, while there are others where the attractive interactions are too strong to allow mobility. These observations led to the design of a DNA-dendron transport tag, which can be used to universally modify macromolecular cargo so that the barrier can differentiate specific species to be transported. These novel transport systems that leverage DNA-DNA interactions provide new chemical insights into the factors that control selective cargo mobility in hydrogels and open the door to designing a wide variety of drug/probe-delivery systems.

Single-molecule kinetic locking allows fluorescence-free quantification of protein/nucleic-acid binding

Fluorescence-free micro-manipulation of nucleic acids (NA) allows the functional characterization of DNA/RNA processing proteins, without the interference of labels, but currently fails to detect and quantify their binding. To overcome this limitation, we developed a method based on single-molecule force spectroscopy, called kinetic locking, that allows a direct in vitro visualization of protein binding while avoiding any kind of chemical disturbance of the protein’s natural function. We validate kinetic locking by measuring accurately the hybridization energy of ultrashort nucleotides (5, 6, 7 bases) and use it to measure the dynamical interactions of Escherichia coli/E. coli RecQ helicase with its DNA substrate.

Rieu et al. present a magnetic tweezers based single-molecule manipulation method, called kinetic locking, for direct detection of biomolecular binding without use of fluorescent probes. By measuring dynamical interactions of E. coli RecQ helicase with its DNA substrate, authors show that this method holds promise for studying DNA-DNA and DNA-protein interactions while avoiding the need for labelling.

Factors and methods to modulate DNA hybridization kinetics

DNA oligonucleotides are widely used in a diverse range of research fields from analytical chemistry, molecular biology, nanotechnology to drug delivery. In these applications, DNA hybridization is often the most important enabling reaction. Achieving control over hybridization kinetics and a high yield of hybridized products is needed to ensure high-quality and reproducible results. Since DNA strands are highly negatively charged and can also fold upon itself to form various intramolecular structures, DNA hybridization needs to overcome these barriers. Nucleation and diffusion are two main kinetic limiting steps although their relative importance differs in different conditions. The effects of length and sequence, temperature, pH, salt concentration, cationic polymers, organic solvents, freezing and crowding agents are summarized in the context of overcoming these barriers. This article will help researchers in the biotechnology-related fields to better understand and control DNA hybridization, as well as provide a landscape for future work in simulation and experiment to optimize DNA hybridization systems.

Combining steady state and temperature jump IR spectroscopy to investigate the allosteric effects of ligand binding to dsDNA

Changes in the structural dynamics of double stranded (ds)DNA upon ligand binding have been linked to the mechanism of allostery without conformational change, but direct experimental evidence remains elusive. To address this, a combination of steady state infrared (IR) absorption spectroscopy and ultrafast temperature jump IR absorption measurements has been used to quantify the extent of fast (∼100 ns) fluctuations in (ds)DNA·Hoechst 33258 complexes at a range of temperatures. Exploiting the direct link between vibrational band intensities and base stacking shows that the absolute magnitude of the change in absorbance caused by fast structural fluctuations following the temperature jump is only weakly dependent on the starting temperature of the sample. The observed fast dynamics are some two orders of magnitude faster than strand separation and associated with all points along the 10-base pair duplex d(GCATATATCC). Binding the Hoechst 33258 ligand causes a small but consistent reduction in the extent of these fast fluctuations of base pairs located outside of the ligand binding region. These observations point to a ligand-induced reduction in the flexibility of the dsDNA near the binding site, consistent with an estimated allosteric propagation length of 15 Å, about 5 base pairs, which agrees well with both molecular simulation and coarse-grained statistical mechanics models of allostery leading to cooperative ligand binding.

Folding Dynamics of DNA G-Quadruplexes Probed by Millisecond Temperature Jump Circular Dichroism

G-quadruplexes play important roles in cellular regulatory functions, but despite significant experimental and theoretical efforts, their folding mechanisms remain poorly understood. In this context, we developed a T-jump experiment to access the thermal denaturation and renaturation dynamics of short intramolecular G-quadruplexes in vitro, on the time scale of a few hundred milliseconds. With this new setup, we compared the thermal denaturation and renaturation kinetics of three antiparallel topologies made of the human telomeric sequences d[(5'-GGG(TTAGGG)₃-3']/Na⁺ and d[5'-AGGG(TTAGGG)₃-3']/Na⁺ and the thrombin-binding aptamer sequence d[5'-GGTTGGTGTGGTTGG-3']/K⁺, with those of the parallel topology made of the human CEB25 minisatellite d[5'-AAGGGTGGGTGTAAGTGTGGGTGGGT-3']/Na⁺. In all cases, exponential kinetics of the order of several hundred milliseconds were observed. Measurements performed for different initial temperatures revealed distinct denaturation and renaturation dynamics, ruling out a simple two-state mechanism. The parallel topology, in which all guanines adopt an anti conformation, displays much slower dynamics than antiparallel topologies associated with very low activation barriers. This behavior can be explained by the constrained conformational space due to the presence of the single-base propeller loops that likely hinders the movement of the coiled DNA strand and reduces the contribution of the entropy during the renaturation process at high temperatures.

Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy

Measuring the strength of the hydrogen bonds between DNA base pairs is of vital importance for understanding how our genetic code is physically accessed and recognized in cells, particularly during replication and transcription. Therefore, it is important to develop probes for these key hydrogen bonds (H-bonds) that dictate events critical to cellular function, such as the localized melting of DNA. The vibrations of carbonyl bonds are well-known probes of their H-bonding environment, and their signals can be observed with infrared (IR) spectroscopy. Yet, pinpointing a single bond of interest in the complex IR spectrum of DNA is challenging due to the large number of carbonyl signals that overlap with each other. Here, we develop a method using isotope editing and infrared (IR) spectroscopy to isolate IR signals from the thymine (T) C2=O carbonyl. We use solvatochromatic studies to show that the TC2=O signal’s position in the IR spectrum is sensitive to the H-bonding capacity of the solvent. Our results indicate that C2=O of a single T base within DNA duplexes experiences weak H-bonding interactions. This finding is consistent with the existence of a third, noncanonical CH···O H-bond between adenine and thymine in both Watson–Crick and Hoogsteen base pairs in DNA.

Nearest-neighbour transition-state analysis for nucleic acid kinetics

We used stopped-flow to monitor hypochromicity for 43 oligonucleotide duplexes to study nucleic acid kinetics and extract transition-state parameters for association and dissociation. Reactions were performed in 1.0 M NaCl (for literature comparisons) and 2.2 mM MgCl2 (PCR conditions). Dissociation kinetics depended on sequence, increased exponentially with temperature, and transition-state parameters inversely correlated to thermodynamic parameters (r = -0.99). Association had no consistent enthalpic component, varied little with temperature or sequence, and poorly correlated to thermodynamic parameters (r = 0.28). Average association rates decreased 78% in MgCl2 compared to NaCl while dissociation was relatively insensitive to ionic conditions. A nearest-neighbour kinetic model for dissociation predicted rate constants within 3-fold of literature values (n = 11). However, a nearest-neighbour model for association appeared overparameterized and inadequate for predictions. Kinetic predictions were used to simulate published high-speed (<1 min) melting analysis and extreme (<2 min) PCR experiments. Melting simulations predicted apparent melting temperatures increase on average 2.4°C when temperature ramp rates increased from 0.1 to 32°C/s, compared to 2.8°C reported in the literature. PCR simulations revealed that denaturation kinetics are dependent on the thermocycling profile. Simulations overestimated annealing efficiencies at shorter annealing times and suggested that polymerase interactions contribute to primer-template complex stability at extension temperatures.

Quantify the combined effects of temperature and force on the stability of DNA hairpin

OxDNA, as a successful coarse-grain model, has been applied to reproduce the thermodynamic and mechanical properties of both single- and double-stranded DNA. In current simulation, oxDNA is extended to explore the combined effects of temperature and force on the stability of DNA hairpin and its free energy landscape. Simulations were carried out at different forces and temperatures, at each temperature, a 18-base-pair DNA hairpin dynamically transited between folded state and unfolded state, and the separation between two states is consistent with the full contour length of single-stranded DNA in the unfolded state. Two methods were used to identify the critical force of DNA hairpin at each temperature and the critical forces obtained from two methods were consistent with each other and gradually decreased with the increasing temperature from 300 K to 326 K. The critical force at 300 K is reasonably consistent with the single molecule result of DNA hairpin with the same stem length. The two-state free energy landscape can be elucidated from the probability distribution of DNA hairpin extension and its dependence on the force and temperature is totally different. The increasing temperature not only reduces the free energy barrier, but also alters the position of transition point along the extension coordinate, resulting in the reduction of folding distance and the extension of unfolding distance, but their sum is not obviously dependent on the temperature. Generally, an assumption that the location of transition state in two-state energy landscape is independent of the stretching force is used to analyze the data of the single molecule experiment, but current simulation results indicate that effects of stretching forces on the location of transition state in two-state energy landscape are dependent on temperature. At relatively high temperature, stretching force can also change the location of transition state in the free energy landscape.

Investigation into the mechanism and dynamics of DNA association and dissociation utilizing kinetic Monte Carlo simulations

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.

Elementary processes of DNA surface hybridization resolved by single-molecule kinetics: implication for macroscopic device performance

Direct monitoring of single-molecule reactions has recently become a promising means of mechanistic investigation. However, the resolution of reaction pathways from single-molecule experiments remains elusive, primarily because of interference from extraneous processes such as bulk diffusion. Herein, we report a single-molecule kinetic investigation of DNA hybridization on a metal surface, as an example of a bimolecular association reaction. The tip of the scanning tunneling microscope (STM) was functionalized with single-stranded DNA (ssDNA), and hybridization with its complementary strand on an Au(111) surface was detected by the increase in the electrical conductance associated with the electron transport through the resulting DNA duplex. Kinetic analyses of the conductance changes successfully resolved the elementary processes, which involve not only the ssDNA strands and their duplex but also partially hybridized intermediate strands, and we found an increase in the hybridization efficiency with increasing the concentration of DNA in contrast to the knowledge obtained previously by conventional ensemble measurements. The rate constants derived from our single-molecule studies provide a rational explanation of these findings, such as the suppression of DNA melting on surfaces with higher DNA coverage. The present methodology, which relies on intermolecular conductance measurements, can be extended to a range of single-molecule reactions and to the exploration of novel chemical syntheses.

Hybridization of a single DNA molecule on a surface was investigated by electrical conductance measurements. The hybridization efficiency increases with increasing the DNA concentration, in contrast to preceding studies with ensemble studies.

Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange

5-Formylcytosine (5fC) is a chemically edited, naturally occurring nucleobase which appears in the context of modified DNA strands. The understanding of the impact of 5fC on dsDNA physical properties is to date limited. In this work, we applied temperature-dependent 1H Chemical Exchange Saturation Transfer (CEST) NMR experiments to non-invasively and site-specifically measure the thermodynamic and kinetic influence of formylated cytosine nucleobase on the melting process involving dsDNA. Incorporation of 5fC within symmetrically positioned CpG sites destabilizes the whole dsDNA structure-as witnessed from the ∼2°C decrease in the melting temperature and 5-10 kJ mol-1 decrease in ΔG°-and affects the kinetic rates of association and dissociation. We observed an up to ∼5-fold enhancement of the dsDNA dissociation and an up to ∼3-fold reduction in ssDNA association rate constants, over multiple temperatures and for several proton reporters. Eyring and van't Hoff analysis proved that the destabilization is not localized, instead all base-pairs are affected and the transition states resembles the single-stranded conformation. These results advance our knowledge about the role of 5fC as a semi-permanent epigenetic modification and assist in the understanding of its interactions with reader proteins.

A QCM-based rupture event scanning technique as a simple and reliable approach to study the kinetics of DNA duplex dissociation

Rupture Event Scanning (REVS) is applied for the first time within an approach based on dynamic force spectroscopy. Using model DNA duplexes containing 20 pairs of oligonucleotides including those containing single mismatches, we demonstrated the possibility of reliable determination of the kinetic parameters of dissociation of biomolecular complexes: barrier positions, the rate constants of dissociation, and the lifetime of complexes. Within this approach, mechanical dissociation of DNA duplexes occurs according to a mechanism similar to unzipping. It is shown that this process takes place by overcoming a single energy barrier. In the case where a mismatch is located at the farthest duplex end from the QCM surface, a substantial decrease in the position of the barrier between the bound and unbound states is observed. We suppose that this is due to the formation of an initiation complex containing 3-4 pairs of bases, and this is sufficient for starting duplex unzipping.

Elucidation of leak-resistance DNA hybridization chain reaction with universality and extensibility

Hybridization chain reaction (HCR) was a significant discovery for the development of nanoscale materials and devices. One key challenge for HCR is the vulnerability to background leakage in the absence of the initiator. Here, we systematically analyze the sources of leakage and refine leak-resistant rule by using molecular thermodynamics and dynamics, biochemical and biophysical methods. Transient melting of DNA hairpin is revealed to be the underlying cause of leakage and that this can be mitigated through careful consideration of the sequence thermodynamics. The transition threshold of the energy barrier is proposed as a testing benchmark of leak-resistance DNA hairpins. The universal design of DNA hairpins is illustrated by the analysis of hsa-miR-21-5p as biomarker when used in conjunction with surface-enhanced Raman spectroscopy. We further extend the strategy for specific signal amplification of miRNA homologs. Significantly, it possibly provides a practical route to improve the accuracy of DNA self-assembly for signal amplification, and that could facilitate the development of sensors for the sensitive detection of interest molecules in biotechnology and clinical medicine.

5-Carboxylcytosine and Cytosine Protonation Distinctly Alter the Stability and Dehybridization Dynamics of the DNA Duplex

Applications associated with nucleobase protonation events are grounded in their fundamental impact on DNA thermodynamics, structure, and hybridization dynamics. Of the canonical nucleobases, N3 protonation of cytosine (C) is the most widely utilized in both biology and nanotechnology. Naturally occurring C derivatives that shift the N3 pK_a introduce an additional level of tunability. The epigenetic nucleobase 5-carboxylcytosine (caC) presents a particularly interesting example since this derivative forms Watson-Crick base pairs of similar stability and displays pH-dependent behavior over the same range as the canonical nucleobase. However, the titratable group in caC corresponds to the exocyclic carboxyl group rather than N3, and the implications of these divergent protonation events toward DNA hybridization thermodynamics, kinetics, and base pairing dynamics remain poorly understood. Here, we study the pH dependence of these physical properties using model oligonucleotides containing C and caC with FTIR and temperature-jump IR spectroscopy. We demonstrate that N3 protonation of C completely disrupts duplex stability, leading to large shifts in the duplex/single-strand equilibrium, a reduction in the cooperativity of melting, and an acceleration in the rate of duplex dissociation. In contrast, while increasing 5-carboxyl protonation in caC-containing duplexes induces an increase in base pair fluctuations, the DNA duplex can tolerate substantial protonation without significant perturbation to the duplex/single-strand equilibrium. However, 5-carboxyl protonation has a large impact on hybridization kinetics by reducing the transition state free energy. Our thermodynamic and kinetic analysis provides new insight on the impact of two divergent protonation mechanisms in naturally occurring nucleobases on the biophysical properties of DNA.