6EO7

X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine residue

Replaces:  5LUY

Summary for 6EO7

• Entry DOI: 10.2210/pdb6eo7/pdb
• Related PRD ID: PRD_000020
• Descriptor: GA68B2 - MODIFIED HUMAN THROMBIN BINDING APTAMER, Prothrombin, POTASSIUM ION, ... (8 entities in total)
• Functional Keywords: alpha thrombin, aptamer, thrombin-mtba, complex, hydrolase-dna complex, hydrolase, hydrolase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 39440.18

Authors

Dolot, R.M.,Nawrot, B.,Yang, X. (deposition date: 2017-10-09, release date: 2017-10-18, Last modification date: 2024-11-13)

Primary citation

Dolot, R.,Lam, C.H.,Sierant, M.,Zhao, Q.,Liu, F.W.,Nawrot, B.,Egli, M.,Yang, X.
Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity.
Nucleic Acids Res., 46:4819-4830, 2018

PubMed Abstract: Thrombin-binding aptamer (TBA) is a DNA 15-mer of sequence 5'-GGT TGG TGT GGT TGG-3' that folds into a G-quadruplex structure linked by two T-T loops located on one side and a T-G-T loop on the other. These loops are critical for post-SELEX modification to improve TBA target affinity. With this goal in mind we synthesized a T analog, 5-(indolyl-3-acetyl-3-amino-1-propenyl)-2'-deoxyuridine (W) to substitute one T or a pair of Ts. Subsequently, the affinity for each analog was determined by biolayer interferometry. An aptamer with W at position 4 exhibited about 3-fold increased binding affinity, and replacing both T4 and T12 with W afforded an almost 10-fold enhancement compared to native TBA. To better understand the role of the substituent's aromatic moiety, an aptamer with 5-(methyl-3-acetyl-3-amino-1-propenyl)-2'-deoxyuridine (K; W without the indole moiety) in place of T4 was also synthesized. This K4 aptamer was found to improve affinity 7-fold relative to native TBA. Crystal structures of aptamers with T4 replaced by either W or K bound to thrombin provide insight into the origins of the increased affinities. Our work demonstrates that facile chemical modification of a simple DNA aptamer can be used to significantly improve its binding affinity for a well-established pharmacological target protein.

PubMed: 29684204
DOI: 10.1093/nar/gky268

Experimental method

X-RAY DIFFRACTION (2.24 Å)