PXD055115-1

PXD055115 is an original dataset announced via ProteomeXchange.

Title	The Cancer Cell Target Discovery. Comparing Laboratory Evolution of Expanded DNA Six-Nucleotide Alphabets with Standard Four-Nucleotide Alphabets
Description	Artificial evolvable genetic information systems (AEGIS) are DNA-like molecules that can be copied, support laboratory in vitro evolution (LIVE), and evolve to give AegisBodies, analogs of antibodies. However, unlike DNA aptamers built from four different nucleotides, AegisBodies are built from six. Thus, 6-letter AEGIS-LIVE delivers AegisBodies with greater stability in biological mixtures, more folds, and enhanced binding and catalytic potential. However, AEGIS has not benefitted from four billion years of biological evolution. To learn whether AEGIS can nevertheless perform as well as natural DNA, we compare two 6-letter AegisBodies (LZH5b and LZH8) with a standard 4-letter aptamer. Both were evolved to bind cancer cells after ~10 cycles of LIVE. Both have ~ 50 nM affinities. Both discovered proteins on their cancer cell surfaces thought to function only inside of cells. Both can be internalized. Internalizing of LZH5b attached to an AEGIS nanotrain brings attached drugs into the cell. These data show that AEGIS-LIVE can do what 4-letter LIVE can do at its limits of performance after four billion years of evolution. However, synthetic biologists continue to improve AEGIS, suggesting that AEGIS not be dismissed as an avenue for future biotechnology.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_01:02:23.780.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sharpkate Shaker
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-23 02:25:16	ID requested
⏵ 1	2025-05-07 01:02:24	announced

10.1093/nar/gkaf072;

Shaker S, Li J, Wan S, Xuan H, Long J, Cao H, Wei T, Liu Q, Xu D, Benner SA, Zhang L, Cancer cell target discovery: comparing laboratory evolution of expanded DNA six-nucleotide alphabets with standard four-nucleotide alphabets. Nucleic Acids Res, 53(4):(2025) [pubmed]

submitter keyword: Target determination, Aptamer, Molecular interactions, Cancer cell,Unnatural bases

Liqin Zhang
contact affiliation	State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
contact email	lqzhang@hsc.pku.edu.cn
lab head
Sharpkate Shaker
contact affiliation	Peking University
contact email	Sharpkate@163.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD055115

PRIDE project URI

• PRIDE
  1. PXD055115
     1. Label: PRIDE project
     2. Name: The Cancer Cell Target Discovery. Comparing Laboratory Evolution of Expanded DNA Six-Nucleotide Alphabets with Standard Four-Nucleotide Alphabets