Probing high-affinity aptamer binding region and development of aptasensor platform for the detection of cylindrospermopsin

Label-Free Direct Detection of Cylindrospermopsin via Graphene-Enhanced Surface Plasmon Resonance Aptasensor

“…Still, additional efforts are needed to address proper selectivity, which can be effectively achieved using in silico methods [ 21 ]. The molecular docking method followed by molecular dynamics (MD) simulations were used to indicate potential binding sites of CYN with aptamers, described in detail in [ 22 ]. In the stated research, C1–T5 bases of the CY9T2 aptamer were proposed to be involved in the binding of the CYN.…”

“…We observed a decrease in the signal during the exchange of solutions, associated with the dynamic release of molecules. The high affinity of the aptamer to CYN results in a decrease in π-π stacking interactions between the aptamer and graphene [ 22 , 25 ], thus increasing the effective thickness of the aptamer layer. Nevertheless, the high roughness of the substrate that exceeds the Debye length can lead to interference of neighbouring aptamer molecules and decrease the signal while increasing the concentration of the analyte during its accumulation.…”

Selection and characterization of ssDNA aptamer targeting Macrobrachium rosenbergii nodavirus capsid protein: A potential capture agent in gold‐nanoparticle‐based aptasensor for viral protein detection

“…This adjustment would ensure efficient capture of the target molecule and increases the detection response. The full length aptamer could be truncated to increase binding affinity (Chinnappan et al., 2020; Hassan et al., 2021; Liu et al., 2023; Ma et al., 2021). Based on structure predictions, APT‐MrNV‐CP‐1 revealed two stem‐loop structures from C35 to G90, one of which included an internal loop at the positions T52‐A86 (Figure 5).…”

Fluorescent aptamers for detection and treatment of pathogenic bacteria and cancer

“…bispecific and humanized antibodies) are in demand till date, their relatively longer and costlier production, stability, and immunotoxicity during application along with other problems mentioned earlier make them less suitable for use in diagnostic kits as well as therapies (Lu et al, 2020;Helwick C, 2020;Glassy & Gupta, 2014;Chames et al, 2009). Contrastingly, the relative ease of production, the feasibility of synthesis to several conditions (including in vivo), the ability to target a varied range of biomolecules, and pliability in the structure are some of the many reasons that favor investing in aptamer development (Tantirungrotechai & Soontornworajit, 2016;Chinnappan et al, 2020;Zheng, Zou, & Lou, 2012). A continuous decrease in the cost of high-throughput example) into the already existing nanocrystal structure of another metal to enhance optical or electrochemical properties of the latter.…”

“…Aptamer cores are essentially a collection of 15 to 50 RNA or DNA nucleotides (target binding segment is 10-15nt long) arranged in a single strand that can exist in various folding states or conformations described above (Tantirungrotechai & Soontornworajit, 2016;Chinnappan et al, 2020). The superior affinity and specificity of aptamers provides the ability to exist in several combinations of the folding structures placed together via interaction of hydrophobic, electrostatic, van der Waals, or hydrogen bonds (Song, Lee, & Ban, 2012;Lodish et al, 2000).…”