Evidence map›Paper›PMID 38260323›Full record

ArticlebioRxiv : the preprint server for biology2024

Compact RNA sensors for increasingly complex functions of multiple inputs.

Christian Choe, Johan O L Andreasson, Feriel Melaine, Wipapat Kladwang, Michelle J Wu, Fernando Portela, Roger Wellington-Oguri, John J Nicol, Hannah K Wayment-Steele, Michael Gotrik and 4 more

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

14 authors.

Christian ChoeDepartment of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-8871-9682
Johan O L AndreassonDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Feriel MelaineDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-5238-2184
Wipapat KladwangDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
Michelle J WuProgram in Biomedical Informatics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-1734-7994
Fernando PortelaDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-0238-9251
Roger Wellington-OguriDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-7818-2161
John J NicolDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
Hannah K Wayment-SteeleDepartment of Chemistry, Stanford University, Stanford, CA, USA.ORCID 0000-0003-4949-2010
Michael GotrikDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-1784-1837
Eterna ParticipantsEterna Massive Open Laboratory.ORCID 0000-0002-7508-6705
Purvesh KhatriStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA.ORCID 0000-0002-4143-4708
William J GreenleafDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-1409-3095
Rhiju DasDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-7497-0972

Funding

POSTDOCTORAL TRAINING IN MEDICAL INFORMATION SCIENCEST15LM007033 · NLM · STANFORD UNIVERSITY · PI SYLVIA KATINA PLEVRITIS · 1985 to 2026
$25.5M
Special EquipmentP50HG007735 · NHGRI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2014 to 2018
$15.2M
Next-generation computational/chemical methods for complex RNA structuresR35GM122579 · NIGMS · STANFORD UNIVERSITY · PI Rhiju Das · 2017 to 2026
$7.2M
Internet-scale discovery of RNA bioengineering rulesR01GM100953 · NIGMS · STANFORD UNIVERSITY · PI DAS, RHIJU · 2012 to 2015
$1.8M
Quantitative high-throughput nucleic acid assays on a sequencing chipR01GM111990 · NIGMS · STANFORD UNIVERSITY · PI GREENLEAF, WILLIAM JAMES · 2014 to 2018
$1.5M
Understanding RNA interactions through deep learning modeling of high-throughput biophysical measurementsF31GM125151 · NIGMS · STANFORD UNIVERSITY · PI WU, MICHELLE · 2018 to 2018
$31k
NHGRI NIH HHS P50 HG007735NIGMS NIH HHS F31 GM125151NIGMS NIH HHS R01 GM100953NIGMS NIH HHS R01 GM111990NIGMS NIH HHS R35 GM122579NLM NIH HHS T15 LM007033Wellcome Trust
6 · The paper itself

Abstract

Designing single molecules that compute general functions of input molecular partners represents a major unsolved challenge in molecular design. Here, we demonstrate that high-throughput, iterative experimental testing of diverse RNA designs crowdsourced from Eterna yields sensors of increasingly complex functions of input oligonucleotide concentrations. After designing single-input RNA sensors with activation ratios beyond our detection limits, we created logic gates, including challenging XOR and XNOR gates, and sensors that respond to the ratio of two inputs. Finally, we describe the OpenTB challenge, which elicited 85-nucleotide sensors that compute a score for diagnosing active tuberculosis, based on the ratio of products of three gene segments. Building on OpenTB design strategies, we created an algorithm Nucleologic that produces similarly compact sensors for the three-gene score based on RNA and DNA. These results open new avenues for diverse applications of compact, single molecule sensors previously limited by design complexity.

Identifiers

PMID38260323
PMCPMC10802310

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.