Alejandro Soto, Francesco Mambretti, Emanuele Locatelli, Iliya D Stoev
{"title":"Modelling the melting of DNA oligomers with non-inert dangling ends.","authors":"Alejandro Soto, Francesco Mambretti, Emanuele Locatelli, Iliya D Stoev","doi":"10.3389/fmolb.2025.1646428","DOIUrl":null,"url":null,"abstract":"<p><p>In this work, we investigate the dependence of the melting temperature of low-valency DNA constructs on the length of non-inert dangling ends, controlling their sequence composition. We compare two computational models to evaluate their effectiveness and limitations in predicting the melting behavior of DNA oligomers (bivalent linkers) and more complex structures (trivalent nanostars), benchmarking the results against experimental spectroscopic data. Our results suggest that the length of non-inert dangling ends has minimal impact on the melting point of the DNA duplex for the duplexes we studied, informing the future design of DNA supramolecular constructs.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1646428"},"PeriodicalIF":3.9000,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12380575/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Frontiers in Molecular Biosciences","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.3389/fmolb.2025.1646428","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
In this work, we investigate the dependence of the melting temperature of low-valency DNA constructs on the length of non-inert dangling ends, controlling their sequence composition. We compare two computational models to evaluate their effectiveness and limitations in predicting the melting behavior of DNA oligomers (bivalent linkers) and more complex structures (trivalent nanostars), benchmarking the results against experimental spectroscopic data. Our results suggest that the length of non-inert dangling ends has minimal impact on the melting point of the DNA duplex for the duplexes we studied, informing the future design of DNA supramolecular constructs.
期刊介绍：
Much of contemporary investigation in the life sciences is devoted to the molecular-scale understanding of the relationships between genes and the environment — in particular, dynamic alterations in the levels, modifications, and interactions of cellular effectors, including proteins. Frontiers in Molecular Biosciences offers an international publication platform for basic as well as applied research; we encourage contributions spanning both established and emerging areas of biology. To this end, the journal draws from empirical disciplines such as structural biology, enzymology, biochemistry, and biophysics, capitalizing as well on the technological advancements that have enabled metabolomics and proteomics measurements in massively parallel throughput, and the development of robust and innovative computational biology strategies. We also recognize influences from medicine and technology, welcoming studies in molecular genetics, molecular diagnostics and therapeutics, and nanotechnology.
Our ultimate objective is the comprehensive illustration of the molecular mechanisms regulating proteins, nucleic acids, carbohydrates, lipids, and small metabolites in organisms across all branches of life.
In addition to interesting new findings, techniques, and applications, Frontiers in Molecular Biosciences will consider new testable hypotheses to inspire different perspectives and stimulate scientific dialogue. The integration of in silico, in vitro, and in vivo approaches will benefit endeavors across all domains of the life sciences.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
