Evidence map›Paper›PMID 37671922›Full record

ArticleACS synthetic biology2023

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.

Tuan M Pham, Terrel Miffin, Hongying Sun, Kenneth K Sharp, Xiaoyu Wang, Mingyi Zhu, Shuichi Hoshika, Raymond J Peterson, Steven A Benner, Jason D Kahn and 1 more

Abstract read
In one paragraph

Article in ACS synthetic biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Datasets for Benchmarking RNA Design Algorithms.Methods in molecular biology (Clifton, N.J.) · 2025
    Article
  8. Sequence Design Using RNAstructure.Methods in molecular biology (Clifton, N.J.) · 2025
    Article
  9. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Tuan M PhamDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, United States.
Terrel MiffinDepartment of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States.
Hongying SunDepartment of Surgery, University of Rochester Medical Center, Rochester, New York 14642, United States.
Kenneth K SharpDepartment of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States.
Xiaoyu WangDepartment of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States.
Mingyi ZhuDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, United States.
Shuichi HoshikaFoundation for Applied Molecular Evolution, Alachua, Florida 32615, United States.ORCID 0000-0001-9128-1183
Raymond J PetersonDNA Analytics, Greenbelt, Maryland 20770, United States.
Steven A BennerFoundation for Applied Molecular Evolution, Alachua, Florida 32615, United States.
Jason D KahnDepartment of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States.ORCID 0000-0001-5060-4724
David H MathewsDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, United States.ORCID 0000-0002-2907-6557

Funding

RNA Structure Modeling Using Physics and Sequence ComparisonR35GM145283 · NIGMS · UNIVERSITY OF ROCHESTER · PI DAVID H. MATHEWS · 2022 to 2026
$2.7M
Equipment Supplement to 1R01GM141391-01A1 (Easily Used Kits to Evolve Reagents that Covalently Tag and Inactivate Proteins)R01GM141391 · NIGMS · FOUNDATION FOR APPLIED MOLECULAR EVOLUTN · PI BENNER, STEVEN A · 2021 to 2024
$1.4M
NIGMS NIH HHS R01 GM141391NIGMS NIH HHS R35 GM145283
6 · The paper itself

Abstract

We show that

Indexed as

AlgorithmsDNABase PairingNucleotidesThermodynamicsDNANucleotidesDNA folding thermodynamicsDNA secondary structure designexpanded DNA alphabetsynthetic biology

Identifiers

PMID37671922
PMCPMC10510751

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.