Multicomponent Deoxyribozyme Probes for Targeted Detection of Cancer Associated Gene Insertions

Author

• Samuel R. Veleke, University of Central FloridaFollow

Keywords

DNA; deoxyribozyme probe; glioblastoma; NANOG; cancer diagnostics; indels

Abstract

Insertions and deletions (indels) in DNA sequences of genes are linked with cancers such as glioblastoma (GB). Thus, indels may be used as potential cancer biomarkers. In the NANOG gene, its pseudogene NANOGP8 has a 22 base pair insertion sequence for GB patients. In this work, the NANOG gene and the insertion sequence were detected in one sample using a dual-fluorescent assay containing two multicomponent split deoxyribozyme (Dz) probe complexes. One complex used TXR fluorescence to detect the gene regardless of the insertion’s presence. The other complex used fluorescein (FAM) fluorophore to detect the insertion. The probes were able to effectively detect their respective targets and discriminate between targets with insertion (T_i) and targets without insertion (T_n). The 2S-11, 2S-6, 3S-11, and 3S-6 probes were created to determine whether shorter insertions of 11 and 6 nucleotides could be detected by the Dz sensors targeting part of the 22 nucleotides in the insertion. Decreasing the insertion length did not greatly affect sensitivity, but selectivity decreased between insertion lengths of 11 and 6 nucleotides. The 3S-6 and 3S-11 probes minimized the Dz strands used by fusing two Dz strands; they also targeted 6 or 11 nucleotides of the insertion to detect the insertion using fewer nucleotides. Compared to the 2S probes, the 3S probes exhibited higher sensitivity but lower selectivity at lower insertion lengths. The 3SC design minimized the number of complexes and Dz strands by using two Dz strands specific to T_i or T_n that compete for complexation with a third Dz strand to enable fluorescence. The probes that targeted more than 6 nucleotides of the insertion exhibited high selectivity with high discrimination factors indicating blank-level signal for nonspecific targets; the probes were sensitive with a limit of detection range of 26.9-102 pM for T_n and 11.3-22.5 pM for T_i.

Thesis Completion Year

2026

Thesis Completion Semester

Spring

Thesis Chair

Gerasimova, Yulia

College

College of Sciences

Department

Chemistry

Thesis Discipline

Chemistry

Language

English

Access Status

Open Access

Length of Campus Access

None

Campus Location

Orlando (Main) Campus

STARS Citation

Veleke, Samuel R., "Multicomponent Deoxyribozyme Probes for Targeted Detection of Cancer Associated Gene Insertions" (2026). Honors Undergraduate Theses. 606.
https://stars.library.ucf.edu/hut2024/606