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Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0].

ABSTRACT: Nucleic acids are highly charged macromolecules sensitive to their surroundings of water, salt, and other biomolecules. Molecular dynamics simulations with accurate biomolecular force fields provide a detailed atomistic view into DNA and RNA that has been useful to study the structure and dynamics of these molecules and their biological relevance. In this work we study the Drew-Dickerson dodecamer duplex with the sequence d(GCGCAATTGCGC)2 in three different salt concentrations and using different monvalent salt types to detect possible structural influence. Overall, the DNA shows no major structural changes regardless of amount or type of monovalent ions used. Our results show that only at very high salt conditions (5M) is a small structural effect observed in the DNA duplex, which mainly consist of narrowing of the grooves due to increased residence of ions. We also present the importance of sampling time to achieve a converged ensemble, which is of major relevance in any simulation to avoid biased or non-meaningful results.

SUBMITTER: Galindo-Murillo R

PROVIDER: S-EPMC7561045 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0].

Galindo-Murillo Rodrigo R Cheatham Thomas E TE

Living journal of computational molecular science 20190809 2

Nucleic acids are highly charged macromolecules sensitive to their surroundings of water, salt, and other biomolecules. Molecular dynamics simulations with accurate biomolecular force fields provide a detailed atomistic view into DNA and RNA that has been useful to study the structure and dynamics of these molecules and their biological relevance. In this work we study the Drew-Dickerson dodecamer duplex with the sequence d(GCGCAATTGCGC)<sub>2</sub> in three different salt concentrations and usi ...[more]

PMID: 33073182

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Project description:Simulation-based research has grown substantially over the past two decades; however, relatively few published simulation studies are multicenter in nature. Multicenter research confers many distinct advantages over single-center studies, including larger sample sizes for more generalizable findings, sharing resources amongst collaborative sites, and promoting networking. Well-executed multicenter studies are more likely to improve provider performance and/or have a positive impact on patient outcomes. In this manuscript, we offer a step-by-step guide to conducting multicenter, simulation-based research based upon our collective experience with the International Network for Simulation-based Pediatric Innovation, Research and Education (INSPIRE). Like multicenter clinical research, simulation-based multicenter research can be divided into four distinct phases. Each phase has specific differences when applied to simulation research: (1) Planning phase, to define the research question, systematically review the literature, identify outcome measures, and conduct pilot studies to ensure feasibility and estimate power; (2) Project Development phase, when the primary investigator identifies collaborators, develops the protocol and research operations manual, prepares grant applications, obtains ethical approval and executes subsite contracts, registers the study in a clinical trial registry, forms a manuscript oversight committee, and conducts feasibility testing and data validation at each site; (3) Study Execution phase, involving recruitment and enrollment of subjects, clear communication and decision-making, quality assurance measures and data abstraction, validation, and analysis; and (4) Dissemination phase, where the research team shares results via conference presentations, publications, traditional media, social media, and implements strategies for translating results to practice. With this manuscript, we provide a guide to conducting quantitative multicenter research with a focus on simulation-specific issues.

Project description:BACKGROUND:To develop effective and sustainable simulation training programs in low-resource settings, it is critical that facilitators are thoroughly trained in debriefing, a critical component of simulation learning. However, large knowledge gaps exist regarding the best way to train and evaluate debrief facilitators in low-resource settings. METHODS:Using a mixed methods approach, this study explored the feasibility of evaluating the debriefing skills of nurse mentors in Bihar, India. Videos of obstetric and neonatal post-simulation debriefs were assessed using two known tools: the Center for Advanced Pediatric and Perinatal Education (CAPE) tool and Debriefing Assessment for Simulation in Healthcare (DASH). Video data was used to evaluate interrater reliability and changes in debriefing performance over time. Additionally, twenty semi-structured interviews with nurse mentors explored perceived barriers and enablers of debriefing in Bihar. RESULTS:A total of 73 debriefing videos, averaging 18?min each, were analyzed by two raters. The CAPE tool demonstrated higher interrater reliability than the DASH; 13 of 16 CAPE indicators and two of six DASH indicators were judged reliable (ICC >?0.6 or kappa >?0.40). All indicators remained stable or improved over time. The number of 'instructors questions,' the amount of 'trainee responses,' and the ability to 'organize the debrief' improved significantly over time (p?<?0.01, p?<?0.01, p?=?0.04). Barriers included fear of making mistakes, time constraints, and technical challenges. Enablers included creating a safe learning environment, using contextually appropriate debriefing strategies, and team building. Overall, nurse mentors believed that debriefing was a vital aspect of simulation-based training. CONCLUSION:Simulation debriefing and evaluation was feasible among nurse mentors in Bihar. Results demonstrated that the CAPE demonstrated higher interrater reliability than the DASH and that nurse mentors were able to maintain or improve their debriefing skills overtime. Further, debriefing was considered to be critical to the success of the simulation training. However, fear of making mistakes and logistical challenges must be addressed to maximize learning. Teamwork, adaptability, and building a safe learning environment enhanced the quality enhanced the quality of simulation-based training, which could ultimately help to improve maternal and neonatal health outcomes in Bihar.

Dataset Information

Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0].

Publications

Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0].

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