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United States Department of Agriculture

Agricultural Research Service

Research Project: Optical Detection of Food Safety and Food Defense Hazards

Location: Quality and Safety Assessment Research Unit

Title: Determining the elastic properties of aptamer-ricin single molecule multiple pathways

Authors
item Wang, Bin -
item Park, Bosoon
item Kwon, Yongkuk -
item Xu, Bingqian -

Submitted to: Applied Physics Letters
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 30, 2014
Publication Date: May 14, 2014
Citation: Wang, B., Park, B., Kwon, Y., Xu, B. 2014. Determining the elastic properties of aptamer-ricin single molecule multiple pathways. Applied Physics Letters. 104, 193702; doi:10.10631/1.4876603.

Interpretive Summary: Aptamers are oligonucleic acid or peptide molecules that bind to a specific target molecule. The single-molecule interactions between aptamers and their targets have been intensively investigated in recent years. Aptamer refers to short single-stranded deoxyribonucleic acid (ssDNA) or ribonucleic acid (RNA) sequences that have specific interactions to other biomolecules. It is a versatile model molecule in biophysical study of nucleic acid-protein interactions. Some aptamers have been used in biomedical and clinical research for the development of new treatments of diseases. The specific properties and relatively low cost have made aptamer a widely used regent in both fundamental research and applications. Especially, many critical biophysical processes in living cells are related to the single-molecule interactions between nucleic acids and proteins, and most of those reactions show complicated behaviors. The studies of aptamer structures and interactions will help researchers understand the mechanisms of those biophysical processes.

Technical Abstract: Ricin and an anti-ricin aptamer showed three stable binding conformations with their special chemomechanical properties. The elastic properties of the ricin-aptamer single-molecule interactions were investigated by the dynamic force spectroscopy (DFS). The worm-like-chain model and Hook’s law were used to evaluate the elastic behaviors of the aptamer and linker molecule polyethylene glycol (PEG). The apparent spring constants of the aptamer were estimated for each of these three unbinding pathways. The two reaction barriers in the unbinding pathways also influenced the apparent spring constant of the aptamer. This special elastic property of aptamer was used to distinguish the three unbinding pathways under different loading rates. This method can be used to significantly reduce the non-specific force measurements in single-molecule experiments.

Last Modified: 10/22/2014
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