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. 2023 Jun 3;18(1):81.
doi: 10.1186/s11671-023-03846-0.

Oligonucleotide nanoassemblies with allyl bromide scaffold-based small molecules

Sk Jahir Abbas  1 , Sabina Yesmin  2 , Fangfang Xia  3 , Sk Imran Ali  4 , Zeyu Xiao  5   6 , Weihong Tan  7   8   9
Affiliations

Oligonucleotide nanoassemblies with allyl bromide scaffold-based small molecules

Sk Jahir Abbas et al. Discov Nano. .

Abstract

The development of oligonucleotide nanoassemblies with small molecules has shown great potential in bio-medical applications. However, the interaction of negatively charged oligonucleotides with halogenated small molecules represents a scientific challenge. Here, we introduced a distinct allyl bromide halogenated scaffold, which exhibits specific interaction with adenine nucleic bases of the oligonucleotides, thus leading to the formation of self-assembled nanostructures.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Schematic representation of self-assembled nanostructures between anionic small molecules and oligonucleotides
Fig. 2
Fig. 2
A Polyacrylamide gel electrophoresis (PAGE) of self-assemble nanoparticles (NPs-18nt, 36nt and 72nt) with ONs-18nt/36nt/72nt and C1/C2; Lane 1, corresponds to the 1 µM of ONs-18nt; Lane 2 corresponds to the mixed equivalent volume of ONs-18nt with C2; Lane 3 corresponds to the 2 µM of ONs-18nt, Lane 4 corresponds mixture of equivalent volume of ONs-18nt with C1; Lane 5, corresponds to the 1 µM of ONs-36nt; Lane 6 corresponds to the mixture of equivalent volume of ONs-36nt with C1; Lane 7 corresponds to the 1 µM of ONs-72nt, Lane 8 corresponds to the mixture of equivalent volume of ONs-72nt with C1; full version of the PAGE in the supporting information Figure S2A, Crosslink 19:1; B Nanoparticle tracking analysis (NTA) of NPs-18nt with ONs-18nt and C1; C Transmission electron microscopy (TEM) images of NPs-18nt with ONs-18nt and C1, and its D EDX mapping
Fig. 3
Fig. 3
A The interaction patterns between ONs-18nt and C1 contribute to the stability of the complex, B The atomic distance between small molecules and nucleic bases as a function of simulation time, C Per nucleotide-based de-composition of the binding free energy of ONs-18nt and C1 complexes calculated by MM/GBSA
See this image and copyright information in PMC

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