Evidence map›Paper›PMID 40880986›Full record

ArticleFrontiers in molecular biosciences2025

Modelling the melting of DNA oligomers with non-inert dangling ends.

Alejandro Soto, Francesco Mambretti, Emanuele Locatelli, Iliya D Stoev

Abstract read
In one paragraph

Article in Frontiers in molecular biosciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Alejandro SotoInstitute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Karlsruhe, Germany.
Francesco MambrettiIstituto Italiano di Tecnologia, Atomistic Simulations Group, Genoa, Italy.
Emanuele LocatelliDepartment of Physics and Astronomy, University of Padua, Padua, Italy.
Iliya D StoevInstitute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Karlsruhe, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

DNA nanotechnologymelting curvesmolecular dynamicsNUPACKoxDNAumbrella sampling

Identifiers

PMID40880986
PMCPMC12380575

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.