9ehe: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 9ehe is ~~ON HOLD until 2027~~-05-21

==Structure of short Lettuce aptamer (A5T variant) bound with TO1-biotin.==

== Structural highlights ==

<table><tr><td colspan='2'>[[9ehe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9EHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9EHE FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.63Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=HZD:4-[(3-{2,16-dioxo-20-[(3aR,4R,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium'>HZD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9ehe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ehe OCA], [https://pdbe.org/9ehe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ehe RCSB], [https://www.ebi.ac.uk/pdbsum/9ehe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ehe ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Fluorogenic aptamers (FAPs) are increasingly important tools for cellular sensing and pathogen diagnostics. However, enhancing their performance remains a significant challenge. Here, we introduce a massively parallel approach to optimize the DNA-based FAP Lettuce using repurposed next-generation sequencing flow cells. By replacing Lettuce's cognate fluorogen, DFHBI-1T, with TO1-biotin, we achieve a 4-fold ensemble fluorescence enhancement, and a broader fluorescence lifetime modulation range from 4.7 to 6.0 ns. Through screening 8821 Lettuce variants complexed with TO1-biotin on a MiSeq chip, we identify the C14T mutant which exhibits an improved dissociation constant, increased quantum yield, extended fluorescence lifetime, and enhanced emission intensity. Co-crystal structures of the aptamer/fluorogen complexes reveal that pi-pi stacking interactions are critical for the stable coordination of TO1-biotin within Lettuce. When tested in a cellular environment, both the screening-identified C14T mutant and a structure-guided rationally designed variant, C14dU, exhibit 15% and 18% stronger fluorescence intensities, respectively, compared with canonical Lettuce. Our massive screening and molecular dynamics simulation pipeline enable efficient FAP optimization without prior structural knowledge, yielding not only improved probes for fluorescence sensing but also deeper insights into aptamer-fluorogen interactions.

~~Authors~~:

Fluorogenic Aptamer Optimization on a Massively Parallel Sequencing Platform.,Kuo YA, Chen YI, Siraj N, He Y, Yang Z, Wang Y, Batchelder-Schwab EJ, Korkmaz Z, Yonas S, Nguyen TD, Hong S, Nguyen AT, Kim S, Seifi S, Fan PH, Wu Y, Liu HW, Lu Y, Ren P, Mao C, Yeh HC ACS Sens. 2026 May 22;11(5):3587-3600. doi: 10.1021/acssensors.5c04046. Epub 2026 , May 11. PMID:42112875<ref>PMID:42112875</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Synthetic construct]]

[[Category: Batchelder-Schwab E]]

[[Category: Koomullam N]]

[[Category: Mao C]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9ehe is ON HOLD  until 2027-05-21
+==Structure of short Lettuce aptamer (A5T variant) bound with TO1-biotin.==
+<StructureSection load='9ehe' size='340' side='right'caption='[[9ehe]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9ehe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9EHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9EHE FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.63&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=HZD:4-[(3-{2,16-dioxo-20-[(3aR,4R,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium'>HZD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9ehe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ehe OCA], [https://pdbe.org/9ehe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ehe RCSB], [https://www.ebi.ac.uk/pdbsum/9ehe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ehe ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Fluorogenic aptamers (FAPs) are increasingly important tools for cellular sensing and pathogen diagnostics. However, enhancing their performance remains a significant challenge. Here, we introduce a massively parallel approach to optimize the DNA-based FAP Lettuce using repurposed next-generation sequencing flow cells. By replacing Lettuce's cognate fluorogen, DFHBI-1T, with TO1-biotin, we achieve a 4-fold ensemble fluorescence enhancement, and a broader fluorescence lifetime modulation range from 4.7 to 6.0 ns. Through screening 8821 Lettuce variants complexed with TO1-biotin on a MiSeq chip, we identify the C14T mutant which exhibits an improved dissociation constant, increased quantum yield, extended fluorescence lifetime, and enhanced emission intensity. Co-crystal structures of the aptamer/fluorogen complexes reveal that pi-pi stacking interactions are critical for the stable coordination of TO1-biotin within Lettuce. When tested in a cellular environment, both the screening-identified C14T mutant and a structure-guided rationally designed variant, C14dU, exhibit 15% and 18% stronger fluorescence intensities, respectively, compared with canonical Lettuce. Our massive screening and molecular dynamics simulation pipeline enable efficient FAP optimization without prior structural knowledge, yielding not only improved probes for fluorescence sensing but also deeper insights into aptamer-fluorogen interactions.
-Authors:
+Fluorogenic Aptamer Optimization on a Massively Parallel Sequencing Platform.,Kuo YA, Chen YI, Siraj N, He Y, Yang Z, Wang Y, Batchelder-Schwab EJ, Korkmaz Z, Yonas S, Nguyen TD, Hong S, Nguyen AT, Kim S, Seifi S, Fan PH, Wu Y, Liu HW, Lu Y, Ren P, Mao C, Yeh HC ACS Sens. 2026 May 22;11(5):3587-3600. doi: 10.1021/acssensors.5c04046. Epub 2026 , May 11. PMID:42112875<ref>PMID:42112875</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9ehe" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Batchelder-Schwab E]]
+[[Category: Koomullam N]]
+[[Category: Mao C]]