Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention.

Understanding the impact of genomic variants on transcription factor binding and gene regulation remains a key area of research, with implications for unraveling the complex mechanisms underlying various functional effects. Our study delves into the role of DNA's biophysical properties, including thermodynamic stability, shape, and flexibility in transcription factor (TF) binding. We developed a multi-modal deep learning model integrating these properties with DNA sequence data. Trained on ChIP-Seq (chromatin immunoprecipitation sequencing) data in vivo involving 690 TF-DNA binding events in human genome, our model significantly improves prediction performance in over 660 binding events, with up to 9.6% increase in AUROC metric compared to the baseline model when using no DNA biophysical properties explicitly. Further, we expanded our analysis to in vitro high-throughput Systematic Evolution of Ligands by Exponential enrichment (SELEX) and Protein Binding Microarray (PBM) datasets, comparing our model with established frameworks. The inclusion of DNA breathing features consistently improved TF binding predictions across different cell lines in these datasets. Notably, for complex ChIP-Seq datasets, integrating DNABERT2 with a cross-attention mechanism provided greater predictive capabilities and insights into the mechanisms of disease-related non-coding variants found in genome-wide association studies. This work highlights the importance of DNA biophysical characteristics in TF binding and the effectiveness of multi-modal deep learning models in gene regulation studies.

Examining DNA breathing with pyDNA-EPBD.

MOTIVATION: The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion. This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. RESULTS: We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo algorithm. AVAILABILITY AND IMPLEMENTATION: pyDNA-EPBD is supported across most operating systems and is freely available at https://github.com/lanl/pyDNA_EPBD. Extensive documentation can be found at https://lanl.github.io/pyDNA_EPBD/.

Examining DNA Breathing with pyDNA-EPBD.

Motivation: The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion.This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. Results: We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop- Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo (MCMC) algorithm.

Bubble Relaxation Dynamics in Homopolymer DNA Sequences.

Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard-Bishop-Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine-thymine (AT) and guanine-cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule's dynamics, for times between 0.5-500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.

The Relationship Between Partial and Full Range of Motion Deadlift 1-Repetition Maximum: A Technical Note.

ABSTRACT: Gillingham, B, Bishop, A, Higa, GK, Adams, KJ, and DeBeliso, M. The relationship between partial and full range of motion deadlift 1-repetition maximum: a technical note. J Strength Cond Res 37(4): 909-914, 2023-The full range of motion (FROM) or partial range of motion (PROM) deadlift (DL) are often included in resistance training (RT) programs and are performed by strength athletes in competition. This study examined the relationship between the FROM and PROM 1-repetition maximum (1RM) DL and if the PROM 1RM DL can be estimated by the FROM 1RM DL. Eighteen National Collegiate Athletic Association wrestlers (20.8 ± 1.2 years, 176.0 ± 5.2 cm, 78.9 ± 10.6 kg) performed a warm-up followed by the assessment of the FROM and PROM 1RM DLs. The FROM DLs were executed with a starting position of the bar resting on the lifting platform. Partial range of motion DLs were executed in a power rack with the bar starting position at ≈2.54 cm above the patella. Regression analysis was employed to estimate PROM 1RM DL based on FROM 1RM DL, body height, and mass. A Pearson's correlation coefficient ( r ) was used to compare the PROM 1RM DL with FROM 1RM DL. A dependent t test was used to compare the PROM 1RM DL and FROM 1RM DL scores (α < 0.05). The PROM 1RM DL scores (226.0 ± 40.6 kg) were significantly greater than the FROM 1RM DL scores (191.7 ± 37.2 kg) ( p < 0.05: effect size = 0.92). The PCC between the PROM and FROM 1RM DL was r = 0.85 ( p < 0.05). The regression coefficient for the FROM 1RM DL was significant ( p < 0.05; R = 0.85, R2 = 0.73). The regression coefficients for body mass and height were not significant ( p > 0.05). The PROM and FROM DL may be interchangeable modalities within an RT program, and the PROM 1RM DL can be accurately predicted by the FROM 1RM DL.

Impact of Graphene Quantum Dot Edge Morphologies on Their Optical Properties.

The optoelectronic properties of functionalized graphene quantum dots (GQDs) have been explored by simulating electronic structure of three different shapes of GQDs containing exclusively zigzag or armchair edges in both pristine and functionalized forms. Absorption spectra and transition densities for the low-lying excited states are evaluated by using time-dependent density functional theory and compared for different functionalization species. The functionalization position dictates the optical properties of square GQDs, where isomers with CH2 in the intermediate positions (excluding corner and center positions) have higher electronic transition energies and exciton delocalization than other isomers. Rhombic GQDs with all armchair edges exhibit high steric flexibility, and their complete passivation results in the largest structural deformation from planarity and strongest red-shifts. A steady red-shift in the absorption energy is observed following the order F, CH3, Cl, and Br substitutions. This suggests that the steric effects due to large van der Waals radii overcome electronegative effects.

Thermalization in the one-dimensional Salerno model lattice.

The Salerno model constitutes an intriguing interpolation between the integrable Ablowitz-Ladik (AL) model and the more standard (nonintegrable) discrete nonlinear Schrödinger (DNLS) one. The competition of local on-site nonlinearity and nonlinear dispersion governs the thermalization of this model. Here, we investigate the statistical mechanics of the Salerno one-dimensional lattice model in the nonintegrable case and illustrate the thermalization in the Gibbs regime. As the parameter interpolating between the two limits (from DNLS toward AL) is varied, the region in the space of initial energy and norm densities leading to thermalization expands. The thermalization in the non-Gibbs regime heavily depends on the finite system size; we explore this feature via direct numerical computations for different parametric regimes.

Metabolomics and the pig model reveal aberrant cardiac energy metabolism in metabolic syndrome.

Although metabolic syndrome (MS) is a significant risk of cardiovascular disease (CVD), the cardiac response (MR) to MS remains unclear due to traditional MS models' narrow scope around a limited number of cell-cycle regulation biomarkers and drawbacks of limited human tissue samples. To date, we developed the most comprehensive platform studying MR to MS in a pig model tightly related to human MS criteria. By incorporating comparative metabolomic, transcriptomic, functional analyses, and unsupervised machine learning (UML), we can discover unknown metabolic pathways connections and links on numerous biomarkers across the MS-associated issues in the heart. For the first time, we show severely diminished availability of glycolytic and citric acid cycle (CAC) pathways metabolites, altered expression, GlcNAcylation, and activity of involved enzymes. A notable exception, however, is the excessive succinate accumulation despite reduced succinate dehydrogenase complex iron-sulfur subunit b (SDHB) expression and decreased content of precursor metabolites. Finally, the expression of metabolites and enzymes from the GABA-glutamate, GABA-putrescine, and the glyoxylate pathways significantly increase, suggesting an alternative cardiac means to replenish succinate and malate in MS. Our platform discovers potential therapeutic targets for MS-associated CVD within pathways that were previously unknown to corelate with the disease.

Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization.

The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer's J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. Here, we develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded "flexible hinges" to assist in loop formation. We combine the Czapla-Swigon-Olson structural model of DNA with our extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Further, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.

Development of a liquid chromatography/tandem mass spectrometry assay for the quantification of PM01183 (lurbinectedin), a novel antineoplastic agent, in mouse, rat, dog, Cynomolgus monkey and mini-pig plasma.

Lurbinectedin (PM01183) is a new synthetic tetrahydroisoquinoline alkaloid that binds to selected sequences in the minor groove of DNA, inducing PM01183-DNA adducts that stall replication, DNA repair and transcription and gives rise to double-strand breaks and finally, caspase-dependent apoptotic cell death. PM01183 has demonstrated clinical antitumor activity in platinum resistant/refractory ovarian cancer patients. A rapid and sensitive liquid chromatography/tandem mass spectrometry assay was developed and validated to quantify PM01183 in plasma from nonclinical species. The bioanalysis consisted of a supported liquid extraction, followed by a gradient phase chromatography and, detection by positive ion electrospray tandem mass spectrometry. The calibration range for PM01183 was established using PM01183 standards from 0.1 to 100 ng/mL in blank plasma. The multiple reaction monitoring, based on the transition m/z 767.3→273.0, was specific for PM01183, and that based on the transition m/z 771.4→277.0 was specific for the internal standard (deuterated PM01183). No endogenous material interfered with the analysis of PM01183 and the internal standard from blank plasma. The limit of detection (LOD) of the assay was calculated as 0.025 ng/mL. The correlation coefficients for the calibration curves ranged from 0.9937 to 0.9987. The mean inter-day accuracies for all calibration standards ranged from 92 to 108% (≤8% bias), and the mean inter-day precision for calibration standards was always less than 12%. The mean intra and inter-day assay accuracy for all quality control replicates remained between 91 and 109%. The mean intra and inter-day assay precision was less than 10% for all QC levels. The method was validated to demonstrate the specificity, recovery, limit of quantification, accuracy and precision of measurements. The assay has been used to support preclinical pharmacokinetic and toxicokinetic studies of PM01183 in nonclinical species. The main PK parameters in dogs (3 male and 3 female, respectively) were calculated as follows: maximum concentration (Cmax, 12.9±0.6 and 10.2±3.0 ng/mL) and the area under the plasma concentration-time curve (AUC, 24.9±0.7 and 22.6±6.1 ng h/mL). The results showed that plasma samples could be monitored for PM01183 for long enough to accurately estimate pharmacokinetics information.

The role of structural parameters in DNA cyclization.

BACKGROUND: The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this study, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization. RESULTS: We calculate the cyclization rates of 86 DNA sequences with previously measured J factors and lengths between 57 and 325 bp as well as of 20,000 randomly generated DNA sequences with lengths between 350 and 4000 bp. Our comparison with experimental data is complemented with analysis of simulated data. CONCLUSIONS: Our data demonstrate that all sets of parameters yield very similar results for longer DNA fragments, regardless of the nucleotide sequence, which are in agreement with experimental measurements. However, for DNA fragments shorter than 100 bp, all sets of parameters performed poorly yielding results with several orders of magnitude difference from the experimental measurements. Our data show that DNA cyclization rates calculated using conformational parameters based on nucleosome packaging data are most similar to the experimental measurements. Overall, our study provides a comprehensive large-scale assessment of the role of structural parameters in calculating DNA cyclization rates.

Possible Demonstration of a Polaronic Bose-Einstein(-Mott) Condensate in UO2(+x) by Ultrafast THz Spectroscopy and Microwave Dissipation.

Bose-Einstein condensates (BECs) composed of polarons would be an advance because they would combine coherently charge, spin, and a crystal lattice. Following our earlier report of unique structural and spectroscopic properties, we now identify potentially definitive evidence for polaronic BECs in photo- and chemically doped UO2(+x) on the basis of exceptional coherence in the ultrafast time dependent terahertz absorption and microwave spectroscopy results that show collective behavior including dissipation patterns whose precedents are condensate vortex and defect disorder and condensate excitations. That some of these signatures of coherence in an atom-based system extend to ambient temperature suggests a novel mechanism that could be a synchronized, dynamical, disproportionation excitation, possibly via the solid state analog of a Feshbach resonance that promotes the coherence. Such a mechanism would demonstrate that the use of ultra-low temperatures to establish the BEC energy distribution is a convenience rather than a necessity, with the actual requirement for the particles being in the same state that is not necessarily the ground state attainable by other means. A macroscopic quantum object created by chemical doping that can persist to ambient temperature and resides in a bulk solid would be revolutionary in a number of scientific and technological fields.

A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder.

Schizophrenia (SZ) genome-wide association studies (GWASs) have identified common risk variants in >100 susceptibility loci; however, the contribution of rare variants at these loci remains largely unexplored. One of the strongly associated loci spans MIR137 (miR137) and MIR2682 (miR2682), two microRNA genes important for neuronal function. We sequenced ∼6.9 kb MIR137/MIR2682 and upstream regulatory sequences in 2,610 SZ cases and 2,611 controls of European ancestry. We identified 133 rare variants with minor allele frequency (MAF) <0.5%. The rare variant burden in promoters and enhancers, but not insulators, was associated with SZ (p = 0.021 for MAF < 0.5%, p = 0.003 for MAF < 0.1%). A rare enhancer SNP, 1:g.98515539A>T, presented exclusively in 11 SZ cases (nominal p = 4.8 × 10(-4)). We further identified its risk allele T in 2 of 2,434 additional SZ cases, 11 of 4,339 bipolar (BP) cases, and 3 of 3,572 SZ/BP study controls and 1,688 population controls; yielding combined p values of 0.0007, 0.0013, and 0.0001 for SZ, BP, and SZ/BP, respectively. The risk allele T of 1:g.98515539A>T reduced enhancer activity of its flanking sequence by >50% in human neuroblastoma cells, predicting lower expression of MIR137/MIR2682. Both empirical and computational analyses showed weaker transcription factor (YY1) binding by the risk allele. Chromatin conformation capture (3C) assay further indicated that 1:g.98515539A>T influenced MIR137/MIR2682, but not the nearby DPYD or LOC729987. Our results suggest that rare noncoding risk variants are associated with SZ and BP at MIR137/MIR2682 locus, with risk alleles decreasing MIR137/MIR2682 expression.

Comparing one repetition maximum and three repetition maximum between conventional and eccentrically loaded deadlifts.

This study determined if an eccentrically loaded deadlift yields a higher 1 repetition maximum (1RM) and 3RM than a conventional deadlift and if the 1RM conventional and eccentrically loaded deadlift can be accurately estimated from the 3RM (3RM = 93% of 1RM). Division 1 football players (n = 15; 20.3 ± 1.9 years; 95.8 ± 18.2 kg; 184.4 ± 6.6 cm) participated. Deadlift 1RM and 3RM were measured in the conventional and eccentrically loaded deadlift. Dependent t-tests showed no significant difference between the 3RM and 1RM conventional deadlift and the 3RM and 1RM eccentrically loaded deadlift (p = 0.30 and p = 0.20, respectively). Pearson correlation between the 1RM conventional deadlift estimate and 1RM conventional deadlift actual was r = 0.91 (p ≤ 0.01); a dependent t-test indicated the 1RM conventional deadlift estimate was significantly less than the 1RM conventional deadlift actual (p = 0.007). Pearson correlation between the 1RM eccentrically loaded deadlift estimate and 1RM eccentrically loaded deadlift actual was r = 0.84 (p ≤ 0.01); a dependent t-test indicated the 1RM eccentrically loaded deadlift estimate was nearly significantly less than the 1RM eccentrically loaded deadlift actual (p = 0.061). Results suggest that conventional and eccentrically loaded deadlifts may be interchangeable within a training program; this may elicit the benefits of using a broader variety of ground-based multijoint compound movements in an athlete's strength and power training. Additionally, because of differences between predicted and actual 1RM scores in the deadlift, strength coaches should prioritize actual 1RM testing of their athletes to optimize deadlift training loads across the RM continuum.

Specificity and heterogeneity of terahertz radiation effect on gene expression in mouse mesenchymal stem cells.

We report that terahertz (THz) irradiation of mouse mesenchymal stem cells (mMSCs) with a single-frequency (SF) 2.52 THz laser or pulsed broadband (centered at 10 THz) source results in irradiation specific heterogenic changes in gene expression. The THz effect depends on irradiation parameters such as the duration and type of THz source, and on the degree of stem cell differentiation. Our microarray survey and RT-PCR experiments demonstrate that prolonged broadband THz irradiation drives mMSCs toward differentiation, while 2-hour irradiation (regardless of THz sources) affects genes transcriptionally active in pluripotent stem cells. The strictly controlled experimental environment indicates minimal temperature changes and the absence of any discernable response to heat shock and cellular stress genes imply a non-thermal response. Computer simulations of the core promoters of two pluripotency markers reveal association between gene upregulation and propensity for DNA breathing. We propose that THz radiation has potential for non-contact control of cellular gene expression.

Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.

Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double helix) of double-stranded DNA, we simulated the dynamics of known binding sites of the TF and nucleoid-associated protein Fis in Escherichia coli. Our study involves simulations of breathing dynamics, analysis of large published in vitro and genomic datasets, and targeted experimental tests of our predictions. Our simulation results and available in vitro binding data indicate a strong correlation between DNA breathing dynamics and Fis binding. Indeed, we can define an average DNA breathing profile that is characteristic of Fis binding sites. This profile is significantly enriched among the identified in vivo E. coli Fis binding sites. To test our understanding of how Fis binding is influenced by DNA breathing dynamics, we designed base-pair substitutions, mismatch, and methylation modifications of DNA regions that are known to interact (or not interact) with Fis. The goal in each case was to make the local DNA breathing dynamics either closer to or farther from the breathing profile characteristic of a strong Fis binding site. For the modified DNA segments, we found that Fis-DNA binding, as assessed by gel-shift assay, changed in accordance with our expectations. We conclude that Fis binding is associated with DNA breathing dynamics, which in turn may be regulated by various nucleotide modifications.

Free vascularized medial femoral condyle autograft for challenging upper extremity nonunions.

Free vascularized bone grafts from the medial femoral condyle have increasingly demonstrated utility in the successful treatment of challenging nonunions and bony defects. The consistent, robust vascular anatomy and the versatility to function as either a thin, flexible periosteal or corticoperiosteal graft or as a structural corticocancellous graft have made this graft a valuable option for addressing recalcitrant nonunions. The rationale, indications, vascular anatomy, and surgical technique of harvesting these grafts from the medial femoral condyle are presented.

DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells.

The genome-wide mapping of the major gene expression regulators, the transcription factors (TFs) and their DNA binding sites, is of great importance for describing cellular behavior and phenotypic diversity. Presently, the methods for prediction of genomic TF binding produce a large number of false positives, most likely due to insufficient description of the physiochemical mechanisms of protein-DNA binding. Growing evidence suggests that, in the cell, the double-stranded DNA (dsDNA) is subject to local transient strands separations (breathing) that contribute to genomic functions. By using site-specific chromatin immunopecipitations, gel shifts, BIOBASE data, and our model that accurately describes the melting behavior and breathing dynamics of dsDNA we report a specific DNA breathing profile found at YY1 binding sites in cells. We find that the genomic flanking sequence variations and SNPs, may exert long-range effects on DNA dynamics and predetermine YY1 binding. The ubiquitous TF YY1 has a fundamental role in essential biological processes by activating, initiating or repressing transcription depending upon the sequence context it binds. We anticipate that consensus binding sequences together with the related DNA dynamics profile may significantly improve the accuracy of genomic TF binding sites and TF binding-related functional SNPs.

Non-thermal effects of terahertz radiation on gene expression in mouse stem cells.

In recent years, terahertz radiation sources are increasingly being exploited in military and civil applications. However, only a few studies have so far been conducted to examine the biological effects associated with terahertz radiation. In this study, we evaluated the cellular response of mesenchymal mouse stem cells exposed to THz radiation. We apply low-power radiation from both a pulsed broad-band (centered at 10 THz) source and from a CW laser (2.52 THz) source. Modeling, empirical characterization, and monitoring techniques were applied to minimize the impact of radiation-induced increases in temperature. qRT-PCR was used to evaluate changes in the transcriptional activity of selected hyperthermic genes. We found that temperature increases were minimal, and that the differential expression of the investigated heat shock proteins (HSP105, HSP90, and CPR) was unaffected, while the expression of certain other genes (Adiponectin, GLUT4, and PPARG) showed clear effects of the THz irradiation after prolonged, broad-band exposure.

DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases.

Trinucleotide repeats sequences (TRS) represent a common type of genomic DNA motif whose expansion is associated with a large number of human diseases. The driving molecular mechanisms of the TRS ongoing dynamic expansion across generations and within tissues and its influence on genomic DNA functions are not well understood. Here we report results for a novel and notable collective breathing behavior of genomic DNA of tandem TRS, leading to propensity for large local DNA transient openings at physiological temperature. Our Langevin molecular dynamics (LMD) and Markov Chain Monte Carlo (MCMC) simulations demonstrate that the patterns of openings of various TRSs depend specifically on their length. The collective propensity for DNA strand separation of repeated sequences serves as a precursor for outsized intermediate bubble states independently of the G/C-content. We report that repeats have the potential to interfere with the binding of transcription factors to their consensus sequence by altered DNA breathing dynamics in proximity of the binding sites. These observations might influence ongoing attempts to use LMD and MCMC simulations for TRS-related modeling of genomic DNA functionality in elucidating the common denominators of the dynamic TRS expansion mutation with potential therapeutic applications.