Complete mitochondrial genome of the worm snail Thylacodes adamsii (Littorinimorpha: Vermetidae) from South Korea.

The worm snail Thylacodes adamsii (Mörch, 1859) (Littorinimorpha: Vermetidae) is a sessile gastropod that mainly inhabits rocky shores along the warm temperate to tropical ocean. Herein, the complete mitochondrial genome (mitogenome) of T. adamsii from South Korea was characterized. The genome is 14,913 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The genome organization and base composition of T. adamsii are similar to those of other vermetids. A phylogenetic tree was reconstructed using maximum likelihood based on the nucleotide sequences of the 13 PCGs; this tree supported the monophyly of Vermetidae. The complete mitogenome of T. adamsii can assist with molecular species identification and vermetid phylogenetic research in the future.

Longitudinal Trajectories of Depressive Symptoms and Their Associations With Risks of Underweight and Obesity in Women: A Population-Based Longitudinal Study in Korea.

Objective: We explored depressive symptom trajectories and their associations with underweight and obesity in Korean women.Methods: This prospective cohort study involved 7,691 women enrolled in the Korean Longitudinal Survey of Women and Families, with a follow-up period spanning from 2014 to 2020. Depressive symptoms were evaluated through the 10-item version of the Center of Epidemiologic Studies Depression Scale. Growth mixture modeling was employed to identify trajectories of depressive symptoms. Multinomial logistic regressions were conducted to investigate the correlation between depression trajectories and the evolving risks of underweight and obesity over the study period.Results: Five distinct trajectory classes were observed ("persistent low symptoms": N = 5,236, 68.1%; "decreasing symptoms": N = 930, 12.1%; "transient high symptoms": N = 421, 5.5%; "increasing symptoms" N = 825, 10.7%; and "persistent high symptoms": N = 279, 3.6%). Those with a low socioeconomic status, comorbidity, and who were divorced or widowed were more likely to follow the persistent high symptom trajectory. Among the 5 trajectories, the risks of underweight and obesity steadily increased in women following the trajectory with persistent high symptoms. For these women, the odds ratio (OR) of underweight increased from 2.27 (95% CI, 1.32-3.92) in 2014 to 3.39 (1.91-6.05) in 2020. They were not associated with obesity in 2014 (OR [95% CI]: 1.38 [0.61-3.11]) but exhibited an elevated risk of obesity in 2020 (3.76 [1.97-7.17]).Conclusion: We observed considerable heterogeneity in the trajectories of depressive symptoms among women, and individuals with persistent high depressive symptoms face an escalating risk of both underweight and obesity.

Sex differences in the association between social jetlag and hazardous alcohol consumption in Korean workers: A nationwide cross-sectional study.

BACKGROUND: Social jetlag, the misalignment between biological and social rhythms, can lead to adverse health outcomes. This study explored the association between social jetlag and hazardous alcohol consumption, as well as the sex differences in this association. METHODS: This study included a nationally representative sample of Korean workers consisting of 11,462 individuals (5479 women). Social jetlag was calculated as the difference in the mid-point between sleep onset and offset on free days and workdays. Hazardous alcohol consumption was determined using the Alcohol Use Disorder Identification Test-Consumption (range 0-12), with a cutoff of ≥6 for men, ≥5 for women, and ≥3 for those aged ≥65. Logistic regression analysis was used to estimate the odds ratios (ORs) and 95 % confidence intervals (CIs). RESULTS: Among men, 599 out of 5983 individuals (10.0 %) had ≥120 min of social jetlag. Among women, 550 out of 5479 individuals (10.0 %) had ≥120 min of social jetlag. The prevalence of hazardous alcohol use was 56.2 % for men and 27.3 % for women. In the regression analysis, there was a significant sex interaction, where social jetlag ≥120 min was associated with hazardous alcohol consumption in female workers (OR: 1.52, 95 % CI: 1.18-1.96), but not in male workers (OR: 1.04, 95 % CI: 0.84-1.29). CONCLUSION: High social jetlag was associated with an increased likelihood of hazardous alcohol consumption among women. Our findings underscore the importance of considering sex differences in future research and policy interventions regarding social jetlag and its associated behavior outcomes.

Temporary Employment Is Associated with Poor Dietary Quality in Middle-Aged Workers in Korea: A Nationwide Study Based on the Korean Healthy Eating Index, 2013-2021.

Temporary employment is associated with an elevated risk of cardiovascular diseases and mortality. This study explored the association between temporary employment and dietary quality in middle-aged workers. This cross-sectional study included a nationwide sample of middle-aged Korean workers (n = 6467). Employment type was categorized into regular, fixed-term, and daily employment, based on labor contract duration. Dietary quality was assessed using the Korean Health Eating Index (KHEI), which ranges from 0 to 100, with higher scores indicating superior dietary quality. Linear regression was used to estimate beta coefficients (ß) and 95% confidence intervals (CI). The survey-weighted proportion of regular, fixed-term, and daily employment was 79.0%, 14.2%, and 6.8%, respectively. Fixed-term and daily employment were associated with a reduced KHEI compared with regular employment (ß [95% CI]: -1.07 [-2.11, -0.04] for fixed-term and -2.46 [-3.89, -1.03] for daily employment). In sex-stratified analysis, the association between temporary employment and dietary quality was more pronounced in men (ß [95% CI]: -1.69 [-3.71, 0.33] for fixed-term and -2.60 [-4.63, -0.53] for daily employment than in women. In conclusion, this study suggests that temporary employment is a social determinant of dietary quality in middle-aged workers.

Association between Dietary Quality and Non-Alcoholic Fatty Liver Disease in Korean Adults: A Nationwide, Population-Based Study Using the Korean Healthy Eating Index (2013-2021).

This study explored the relationship between the Korean Healthy Eating Index (KHEI) and non-alcoholic fatty liver disease (NAFLD). This cross-sectional study included 34,174 Korean adults. The KHEI was composed of three subcomponents (adequacy, moderation, and energy balance) and calculated based on a 24 h dietary recall. The total score ranged from 0 to 100, with a higher score indicating a greater adherence to the Korean dietary guidelines. The total KHEI scores were categorized into quartiles (Q1-Q4). NAFLD was classified using the hepatic steatosis index. Logistic regressions were used to estimate odds ratios (ORs) and 95% confidence intervals (CIs). The adjusted OR (95% CI) of NAFLD was 0.95 (0.87-1.03) for the Q2 group, 0.90 (0.83-0.98) for the Q3 group, and 0.79 (0.72-0.87) for the Q4 group, compared with the Q1 group. Among the subcomponents of the KHEI, individuals with high scores in the adequacy component, characterized by an abundant consumption of fruits, vegetables, and dairy products, exhibited the most pronounced association with NAFLD. A higher KHEI score was negatively associated with NAFLD in Korean adults. Therefore, the promotion of healthy dietary patterns can play a beneficial role in the prevention or management of NAFLD.

Long working hours, work-life imbalance, and poor mental health: a cross-sectional mediation analysis based on the sixth Korean Working Conditions Survey, 2020-2021.

Background There has been growing concern about the negative mental health impact of long working hours and overwork. Our study examined how work-life imbalance (WLI) could be a mediator between working hours and poor mental well-being.Methods We included 34,968 individuals from a nationwide cross-sectional survey in Korea. Self-reported working hours per week was collected, and mental health was assessed by the WHO-5 Well-Being Index. Counterfactual-based mediation models were employed to disentangle the total effects into a direct effect (work hour - poor mental health) and an indirect effect (work hour - WLI - poor mental health).Results Out of 34,968 participants, 52.6% worked 35-40 h/week, 20.0% worked 41-48 h/week, 11.7% worked 49-54 h/week, and 15.6% worked ≥55 h/week. The odds ratios (ORs) of the total impact of working hours on poor mental health were 1.08 (95% CI: 1.01-1.16) for 41-48 h/week, 1.28 (1.17-1.39) for 49-54 h/week, and 1.60 (1.48-1.74) for ≥55 h/week in comparison to 35-40 h/week. The ORs of the indirect effects were 1.04 (1.03-1.05) for 41-48 h/week, 1.08 (1.07-1.09) for 49-54 h/week, and 1.14 (1.12-1.16) for ≥55 h/week, accounting for 51%, 31%, and 28% of the total effects.Conclusion: Our findings suggest that WLI can partially mediate the association of long working hours with mental health deterioration. Policy efforts are required to mitigate the adverse mental health effects of overwork.

Association between precarious employment and the onset of depressive symptoms in men and women: a 13-year longitudinal analysis in Korea (2009-2022).

AIMS: Increasing social concern surrounds the potential adverse health effects of precarious employment (PE). In this study, we explored the association between PE and the onset of depressive symptoms. METHODS: A total of 11,555 Korean waged workers (5700 females) contributed 62,217 observations from 2009 to 2022. PE was operationalized as a multidimensional construct, including employment insecurity, income inadequacy and lack of rights and protection. Depressive symptoms were evaluated using the Center for Epidemiological Studies-Depression Scale (11-item version). The association between PE and the onset of depressive symptoms in the subsequent year was estimated using generalized estimating equations. Effect sizes were reported as odds ratio (OR) and 95% confidence interval (CI). RESULTS: The overall incidence of depressive symptoms was 8.3% during the study period. In cross-sectional analysis, daily employment, disguised employment, lower monthly wages and lack of social insurance coverage were associated with concurrent depressive symptoms in both men and women. Longitudinally, fixed-term employment (OR: 1.17, 95% CI: 1.07-1.29), daily employment (OR: 1.64, 95% CI: 1.45-1.85) and disguised employment (OR: 1.36, 95% CI: 1.17-1.57) were associated with the onset of depressive symptoms among the overall sample. Among men, the lowest quartiles of wage were associated with the onset of depressive symptoms (OR: 1.34, 95% CI: 1.13-1.60), while the absence of a trade union was associated among women (OR: 1.18, 95% CI: 1.01-1.39). CONCLUSIONS: Employment insecurity, inadequate income and lack of rights and protection may contribute to depressive symptoms. Therefore, PE serves as a significant social determinant of mental health among workers in Korea. Active policy efforts are warranted to improve the overall quality of employment in the workforce.

Relationship between long working hours and smoking behaviors: Evidence from population-based cohort studies in Korea.

OBJECTIVES: Long working hours and overwork are growing public health concerns in the Western-Pacific region. We explored the relationship between working hours and smoking behaviors of Korean workers. METHODS: This study included 284 782 observations (50 508 workers) from four nationwide cohort studies in Korea. Using generalized estimating equations, we estimated the associations of working hours with current smoking status, smoking initiation, and smoking cessation within each cohort. Cohort-specific estimates were combined through random-effect meta-analysis. Effect sizes were presented as odds ratios (OR) and 95 confidence intervals (CI). RESULTS: The overall smoking prevalence was 26.8% within the cohorts. The adjusted OR (95% CI) of the association between working hours and current smoking were 1.01 (0.94-1.08) for <35 hours/week, 1.04 (1.01-1.09) for 41-48 hours/week, 1.06 (1.01-1.10) for 49-54 hours/week, and 1.07 (1.04-1.10) for ≥55 hours/week compared with 35-40 hours/week. The adjusted OR (95% CI) of the association between working hours and smoking cessation in the follow-up were 0.93 (0.85-1.02) for <35 hours/week, 0.89 (0.83-0.96) for 41-48 hours/week, 0.87 (0.81-0.95) for 48-54 hours/week, and 0.91 (0.85-0.98) for ≥55 hours/week compared with 35-40 hours/week. No clear associations were observed between working hours and smoking initiation. CONCLUSION: Long working hours are associated with high current smoking risk and reduced likelihood of smoking cessation among Korean workers. Policy interventions are required to promote smoking cessation and reduce excess overwork for individuals experiencing long working hours.

A multiplex real-time RT-qPCR assay for simultaneous detection of porcine epidemic diarrhea virus, porcine deltacoronavirus, and swine acute diarrhea syndrome coronavirus.

Porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV) cause intestinal diseases with similar manifestations in suckling piglets. In this study, we developed a multiplex real-time PCR for differential diagnosis of PEDV, PDCoV, and SADS-CoV. The assay demonstrated high specificity with a detection limit of 5 copies/µl for each virus. The assay specifically detected PEDV, PDCoV, and SADS-CoV and excluded all other swine pathogens circulating in pigs. Furthermore, the assay exhibited satisfactory performance in analyzing clinical samples. The data indicate that the newly developed multiplex real-time PCR method can be applied for differential diagnosis of porcine enteric coronaviruses.

Association between temporary employment and current smoking and change in smoking behaviors: A prospective cohort study from South Korea (2009-2018).

Background Previous studies have suggested that employment insecurity is associated with adverse health outcomes. We explored the association between temporary employment and smoking behaviors.Methods We analyzed 11,795 workers (51,867 observations) from the Korea Health Panel Study (2009-2018). Employment types were categorized as regular, fixed-term, or daily, based on the duration of labor contract. The outcomes were current smoking status and changes in smoking behavior (initiation or cessation) in the following year. Generalized estimating equations were used to estimate odds ratio (OR) and 95% confidence interval (CI).Results The proportions of fixed-term and daily workers were 41.2% and 16.4% for women and 23.6% and 12.4% for men, respectively. Temporary employment was associated with increased odds of current smoking, while also demonstrating prospective associations with changes in smoking behaviors. For instance, in prospective analyses, male workers with fixed-term and daily employments were associated with a decreased likelihood of smoking cessation (OR:0.77; 95% CI:0.65-0.91 for fixed-term employment and OR:0.66; 95% CI:0.52-0.83 for daily employment) in the following year compared to those with regular employment. Moreover, those experiencing consecutive temporary employment was most inversely associated with smoking cessation in both men (OR:0.56; 95% CI:0.44-0.71) and women (OR:0.37; 95% CI:0.16-0.85) compared to those experiencing consecutive regular employment. However, no clear association between temporary employment and smoking initiation was observed in both men and women.Conclusions Temporary employment is directly associated with current smoking and inversely associated with smoking cessation. Policies are needed to improve job insecurity among temporary employees.

Comparison of the Influence of Dual-Task Activities on Prefrontal Activation and Gait Variables in Older Adults with Mild Cognitive Impairment during Straight and Curved Walking.

Background and Objectives: Mild cognitive impairment (MCI) is an early stage of dementia in which everyday tasks can be maintained; however, notable challenges may occur in memory, focus, and problem-solving skills. Therefore, motor-cognitive dual-task training is warranted to prevent cognitive decline and improve cognition in aging populations. This study aimed to determine the influence of such dual-task activities during straight and curved walking on the activities of the prefrontal cortex and associated gait variables in older adults with MCI. Materials and Methods: Twenty-seven older adults aged ≥65 years and identified as having MCI based on their scores (18-23) on the Korean Mini-Mental State Examination were enrolled. The participants performed four task scenarios in random order: walking straight, walking straight with a cognitive task, walking curved, and walking curved with a cognitive task. The activation of the prefrontal cortex, which is manifested by a change in the level of oxyhemoglobin, was measured using functional near-infrared spectroscopy. The gait speed and step count were recorded during the task performance. Results: Significant differences were observed in prefrontal cortex activation and gait variables (p < 0.05). Specifically, a substantial increase was observed in prefrontal cortex activation during a dual task compared with that during a resting-state (p < 0.013). Additionally, significant variations were noted in the gait speed and step count (p < 0.05). Conclusions: This study directly demonstrates the impact of motor-cognitive dual-task training on prefrontal cortex activation in older adults with MCI, suggesting the importance of including such interventions in enhancing cognitive function.

Association between long working hours and diet quality and patterns: A latent profile analysis of a nationally representative sample of Korean workers.

BACKGROUND: Long working hours are associated with cardiovascular and metabolic diseases. This study investigated the relationship between the working hours and dietary qualities and patterns in Korean workers. METHODS: Data from 24,523 workers were extracted from the Korea National Health and Nutrition Examination Survey, 2013-2021. The Korean Healthy Eating Index (KHEI), which ranges from 0 to 100, with a higher score indicating greater adherence to Korean dietary guidelines and superior dietary quality, was used for dietary assessment. We identified dietary patterns and classified workers using latent profile analysis. Logistic regressions were used to estimate odds ratios (ORs) and 95% confidence intervals (CIs). RESULTS: Five distinct dietary patterns emerged: healthy diet (24.8%), low-vegetable diet (14.0%), average diet (7.8%), low-fruit diet (31.4%), and poor diet (22.0%). The mean KHEI score was 60.8, with the highest score observed in the healthy diet pattern (71.3) and the lowest, in the poor diet pattern (50.0). Compared with working 35-40 h/week, working ≥55 h/week was negatively associated with KHEI scores (ß: -1.08; 95% CI: -1.67, -0.49). Those working ≥55 h/week were less likely to have a healthy diet pattern (OR: 0.81; 95% CI: 0.72, 0.91) and more likely to have a low-fruit diet (OR: 1.36; 95% CI: 1.20, 1.55) or poor diet pattern (OR: 1.23; 95% CI: 1.05, 1.43) compared with those working 35-40 h/week. CONCLUSION: Long working hours are associated with undesirable dietary quality and patterns. Policy interventions aimed at enhancing dietary quality are needed to alleviate the health burdens associated with long working hours.

Association of precarious employment with depressive symptoms and suicidal ideation among female workers: Findings from a nationwide longitudinal study in Korea.

BACKGROUND: In this study, we examined the relationship of precarious employment (PE) with depressive symptoms and suicidal ideation among Korean women. METHODS: We included a nationwide sample of 4162 women drawn from the Korean Longitudinal Study of Women and Families, comprising 7566 observations. PE was assessed using three dimensions: employment insecurity, income inadequacy, and lack of rights and protection. Depressive symptoms were assessed using the 10-item version of the Center for Epidemiological Studies Depression Scale. Generalized estimating equations were used to estimate the association between each element of PE and the depressive symptoms and suicidal ideation over a two-year follow-up period, represented as odds ratios (ORs) and confidence intervals (CIs). RESULTS: The overall prevalence rates of depressive symptoms and suicidal ideation were 11.8 % and 1.9 %, respectively. Compared with permanent employment, fixed-term employment (OR [95 % CI]:1.29 [1.00-1.67]) or daily employment (OR [95 % CI]:1.53 [1.26-1.99]) was associated with the depressive symptoms at the follow-up. Additionally, lack of social benefits (OR [95 % CI]:1.40 [1.09-1.79]) and high perceived vulnerability (OR [95 % CI]:1.27 [1.08-1.49]) were associated with the depressive symptoms at the follow-up. Additionally, daily employment was associated with the suicidal ideation at the follow-up (OR [95 % CI]:1.94 [1.02-3.68]) and high perceived vulnerability was marginally associated with an increased suicidal ideation risk (OR [95 % CI]:1.49 [0.98-2.29]). LIMITATION: Causal effect of PE could not be asserted due to the observational nature of this study. CONCLUSIONS: PE is a social determinant of women's mental health and policy interventions are required to improve their employment conditions.

Clinical and radiological features of malformed mesiodens in the nasopalatine canal: an observational study.

OBJECTIVES: The purpose of this study is to investigate the morphological changes that occur when mesiodens is located within the nasopalatine canal, as well as clinical characteristics. METHODS: Clinical records and CT images of patients who had mesiodens in the nasopalatine canal were retrospectively analysed. In addition to demographic information, clinical symptoms and complications associated with extraction of mesiodens were recorded. Using CT images, number, location, size, and tooth morphology were evaluated. RESULTS: This study included 32 patients and 38 mesiodens within the nasopalatine canal. Supernumerary teeth exhibited a characteristic feature of thin and elongated shape in the canal (narrow width and elongation were observed in 96.6% and 53.3% of the patients, respectively). Fusion was found in 4 patients and dilaceration in 12. A complication occurred in 2 patients, which was tooth remnant, not a neurologic complication. Only 5 mesiodens could be detected in the nasopalatine canal on panoramic images. CONCLUSIONS: Morphological abnormalities in mesiodens within the nasopalatine canal were frequently detected, and these could be effectively diagnosed through 3D imaging analysis.

Association between long working hours and engagement in preventive healthcare services in Korean workers: Findings from the Korean National Health and Nutrition Examination Survey.

BACKGROUND: Engagement in preventive healthcare services is crucial for preventing diseases. We explored how working hours are associated with engagement in preventive healthcare services, with a focus on gender differences. METHODS: This cross-sectional study used data from the 2007-2012 Korean National Health and Nutrition Examination Survey. The dependent variable was engagement in each of the five preventive healthcare services (health check-ups, influenza vaccination, and stomach, breast, and cervical cancer screenings). We estimated the prevalence ratios (PRs) and 95% confidence intervals (CIs) using robust Poisson regression. RESULTS: The study analyzed 19,819 workers (9119 women). The adjusted PRs (95% CI) of the association between working ≥55 h per week and engagement in preventive healthcare services among men were 0.95 (0.90-1.00) for health check-ups, 0.86 (0.77-0.96) for influenza vaccination, and 0.95 (0.87-1.03) for stomach cancer screening compared to working 35-40 h per week. Among women, the adjusted PRs (95% CI) of the association between working ≥55 h per week and engagement in preventive healthcare services were 0.84 (0.78-0.91) for health check-ups, 0.82 (0.73-0.92) for influenza vaccination, and 0.88 (0.80-0.97) for stomach, 0.85 (0.78-0.94) for breast, and 0.82 (0.74-0.91) for cervical cancer screenings. CONCLUSION: Long working hours were negatively associated with engagement in preventive healthcare services, and the association was pronounced among female workers. Efforts to promote preventive healthcare participation among individuals with long working hours are necessary, and it is essential to consider the unique vulnerabilities of women when developing such policies.

Association between long working hours and the development of suicidal ideation among female workers: An 8-year population-based study using the Korean Longitudinal Survey of Women & Family (2012-2020).

Long working hours and overwork have recently emerged as pressing public health concerns. We explored the association between long working hours and suicidal ideation in female workers. A total of 8017 women (24,331 observations) from the fourth to eighth waves of the Korean Longitudinal Survey of Women and Families (2012-2020) were analyzed. To address the repeated measurements within each participant, we employed a generalized estimating equation to estimate the odds ratio (OR) and 95% confidence intervals (CIs). The prevalence of suicidal ideation was 1.9% for those working 35-40 h/week and 4.4% for those working ≥55 h/week. Compared to individuals working 35-40 h/week, those working ≥55 h/week were more likely to experience concurrent suicidal ideation (OR [95% CI]:1.85 [1.43-2.39]). The OR (95% CI) of the association between long working hours and onset of suicidal ideation in the subsequent wave was 1.69 (1.20-2.38) for ≥55 h/week. In subgroup analysis, this association was pronounced among workers with low-income levels (OR [95% CI]: 1.97 [1.29-3.02]) and blue-collar occupations (OR [95% CI]: 2.27 [1.41-3.66]). Policy efforts are required to protect the mental health of female workers exposed to long working hours.

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.

Multicolor Conjugated Polymer Thin Films with Tunable Responsivity to Oxidative and Reductive Environments.

Dynamic colors that respond to environmental changes are of great interest for diverse areas of science and technology ranging from chemical and biological sensors to smart information display. Here, we demonstrate a multitude of responsive colors from a conjugated polymer film arising from a thin-film interference. This mechanism provides an excellent control over the thin-film color by varying the film thickness, type of substrate, and degree of polaron population and is generally applicable to various conjugated polymers for further color variation. Furthermore, multiple sets of responsive colors are achieved from a single polymer layer by patterning the underlying substrate to spatially modify the interference conditions. Using this system, we demonstrate the reversible color changes induced by an oxidative or reductive environment with color responsivity controllable with the nature of the polaron state.

Molecular insight into how the position of an abasic site and its sequence environment influence 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 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.

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

Hybridization of short nucleic acid segments (<4 nt) to single-strand templates occurs as a critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood because of the experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential noncanonical base-pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2-40 µs depending on the template and temperature. Dinucleotide hybridization and dehybridization involve a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.