Evidence map›Paper›PMID 38915531›Full record

ArticlebioRxiv : the preprint server for biology2024

Tuning the stability of DNA tetrahedra with base-stacking interactions.

Jibin Abraham Punnoose, Dadrian Cole, Tristan Melfi, Vinod Morya, Bharath Raj Madhanagopal, Alan A Chen, Sweta Vangaveti, Arun Richard Chandrasekaran, Ken Halvorsen

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

5 · Who and what money

Authors and funding

9 authors.

Jibin Abraham PunnooseThe RNA Institute, University at Albany, State University of New York, Albany, NY, USA.ORCID 0000-0003-2367-6874
Dadrian ColeThe RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
Tristan MelfiDepartment of Chemistry, University at Albany, State University of New York, Albany, NY, USA.
Vinod MoryaThe RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
Bharath Raj MadhanagopalThe RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
Alan A ChenThe RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
Sweta VangavetiThe RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
Arun Richard ChandrasekaranThe RNA Institute, University at Albany, State University of New York, Albany, NY, USA.ORCID 0000-0001-6757-5464
Ken HalvorsenThe RNA Institute, University at Albany, State University of New York, Albany, NY, USA.ORCID 0000-0002-2578-1339

Funding

Manipulating nucleic acids: applications in RNA biosensing, single-molecule analysis, and DNA nanotechnologyR35GM124720 · NIGMS · STATE UNIVERSITY OF NEW YORK AT ALBANY · PI Ken A Halvorsen · 2017 to 2026
$4.6M
Thermodynamically Calibrated RNA Simulations to Decode Mechanisms of RNAMolecular RecognitionR35GM133469 · NIGMS · STATE UNIVERSITY OF NEW YORK AT ALBANY · PI Alan Austin Chen · 2019 to 2026
$2.9M
Programmable DNA Nanostructures as Biomedical and Structural ScaffoldsR35GM150672 · NIGMS · STATE UNIVERSITY OF NEW YORK AT ALBANY · PI Arun Richard Chandrasekaran · 2023 to 2026
$1.7M
NIGMS NIH HHS R35 GM124720NIGMS NIH HHS R35 GM133469NIGMS NIH HHS R35 GM150672
6 · The paper itself

Abstract

DNA nanotechnology relies on programmable anchoring of regions of single-stranded DNA through base pair hybridization to create nanoscale objects such as polyhedra, tubes, sheets, and other desired shapes. Recent work from our lab measured the energetics of base-stacking interactions and suggested that terminal stacking interactions between two adjacent strands could be an additional design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra held together with sticky ends that contain identical base pairing interactions but different terminal stacking interactions. Testing all 16 possible combinations, we found that the melting temperature of DNA tetrahedra varied by up to 10 °C from altering a single base stack in the design. These results can inform stacking design to control DNA tetrahedra stability in a substantial and predictable way. To that end, we show that a 4 bp sticky end with weak terminal stacking does not form stable tetrahedra, while strengthening the stacks confers high stability with a 46.8 ± 1.2 °C melting temperature, comparable to a 6 bp sticky end with weak stacking (49.7 ± 2.9 °C). The results likely apply to other types of DNA nanostructures and suggest that terminal stacking interactions play an integral role in formation and stability of DNA nanostructures.

Identifiers

PMID38915531
PMCPMC11195101

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Registered trials

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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.