A strategy based on oligonucleotide hybridization and surface plasmon resonance for truncation of PDGF-BB aptamer

Name: Paphada Watcharapo

Organization : Thammasat University. Faculty of Science and Technology

Name: Pichayanoot Rotkrua

Organization : Thammasat University. Faculty of Medicine

Name: Boonchoy Soontornworajit

Organization : Thammasat University. Faculty of Science and Technology

Email : sbooncho@tu.ac.th

keyword: Aptamers (Nucleic acids)

LCSH: Oligonucleotides

; Surface plasmon resonance spectroscopy

LCSH: Surface plasmon resonance

LCSH: Platelet-derived growth factor

Abstract: Truncation is an essential step in aptamer generation because certain nucleotides in the full-length aptamer may interfere with the aptamer’s binding function. We proposed a truncation strategy relying on oligonucleotide hybridization and surface plasmon resonance (SPR). Model molecules were platelet-derived growth factor-BB (PDGF-BB) and its aptamer. The full-length aptamer underwent hybridization with all tested complementary oligonucleotides (COs), as demonstrated by electrophoresis. Based on the association kinetics characterized by SPR, the aptamer was truncated to a number of sequences: T38-antiPDGF, T36-antiPDGF, T34-antiPDGF, and T32-antiPDGF. In particular, T38-antiPDGF and T36-antiPDGF exhibited apparent dissociation constants (KD,app) within the nanomolar scale, which were comparable to the KD,app of the original sequence. The binding of the truncated sequences was confirmed by forming binding complexes with PDGF-BB and then characterized by electrophoresis. This strategy could be applied to the truncation of other aptamers and may also provide insights into the interactions between aptamers and their targets.

King Mongkut's University of Technology North Bangkok. Central Library

Address: BANGKOK

Email: library@kmutnb.ac.th

Created: 2025

Modified: 2025-10-28

Issued: 2025-10-28

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BibliograpyCitation : In The Chemical Society of Thailand under the Patronage of Professor Dr. Her Royal Highness Princess Chulabhorn Krom Phra Srisavangavadhana and Suranaree University of Technology. Institute of Science. School of Chemistry. Pure and Applied Chemistry International Conference 2025 (PACCON 2025) (pp.570-576). Bangkok : The Chemical Society of Thailand under the Patronage of Professor Dr. Her Royal Highness Princess Chulabhorn Krom Phra Srisavangavadhana in association with the School of Chemistry, Institute of Science, Suranaree University of Technology, 2025

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