ArticleScientific reports2016
Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 37 citations in OpenAlex.
- Selection and validation of novel DNA aptamer panel co-specific toMolecular therapy. Nucleic acids · 2026Article
- Aminated PET Thin Film as a Functionalized Insulating Layer for Capacitive Gliadin Aptasensor Construction.Biosensors · 2026Article
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- Probing three-dimensional cyclooctatetraene for nucleobase modification in aptamer selection.Communications chemistry · 2025Article
- Direct Modeling of DNA and RNA Aptamers with AlphaFold 3: A Promising Tool for Predicting Aptamer Structures and Aptamer-Target Interactions.ACS synthetic biology · 2025Article
- Protonated Glutamate and Aspartate Side Chains Can Recognize Phosphodiester Groups via Strong and Short Hydrogen Bonds in Biomacromolecular Complexes.Angewandte Chemie (International ed. in English) · 2025Article
- Recent Developments in Aptamer-Based Sensors for Diagnostics.Sensors (Basel, Switzerland) · 2024Review
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
- Selection of an Aptamer against the Enzyme 1-deoxy-D-xylulose-5-phosphate Reductoisomerase fromPharmaceutics · 2022Article
- A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers.PLoS computational biology · 2021Article
- Structural Biology for the Molecular Insight between Aptamers and Target Proteins.International journal of molecular sciences · 2021Review
- SELEX-based DNA Aptamer Selection: A Perspective from the Advancement of Separation Techniques.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2021Review
- High-efficiency enrichment enables identification of aptamers to circulating Plasmodium falciparum-infected erythrocytes.Scientific reports · 2020Article
- Recent Advances in Aptamer Discovery and Applications.Molecules (Basel, Switzerland) · 2019Review
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Structural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we determined a crystal structure of PvLDH in complex with a DNA aptamer called pL1. This aptamer folds into a hairpin-bulge contact by adopting three novel structural elements, viz, DNA T-loop-like motif, base-phosphate zipper, and DNA G·G metal ion zipper. Moreover, the pL1:PvLDH complex shows unique properties compared with other protein:nucleic acid complexes. Generally, extensive intermolecular hydrogen bonds occur between unpaired nucleotides and proteins for specific recognitions. Although most protein-interacting nucleotides of pL1 are unpaired nucleotides, pL1 recognizes PvLDH by predominant shape complementarity with many bridging water molecules owing to the combination of three novel structural elements making protein-binding unpaired nucleotides stable. Moreover, the additional set of Plasmodium LDH residues which were shown to form extensive hydrogen bonds with unpaired nucleotides of 2008s does not participate in the recognition of pL1. Superimposition of the pL1:PvLDH complex with hLDH reveals steric clashes between pL1 and hLDH in contrast with no steric clashes between 2008s and hLDH. Therefore, specific protein recognition mode of pL1 is totally different from that of 2008s.
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