1.-Klapak D, Broadfoot S, Penner G, Singh A, Inapuri E (2018) Development of novel aptamers for low-density lipoprotein particle quantification. PLoS ONE 13(10): e0205460.

Abstract

Cardiovascular disease (CVD) remains the leading cause of death worldwide. Low-density lipoprotein cholesterol (LDL-C) is commonly used for CVD risk assessment; however, recent research has shown LDL particle (LDL-P) number to be a more sensitive indicator of CVD risk than both LDL-C and non-high-density lipoprotein cholesterol (HDL-C). Described herein are five single stranded DNA aptamers with dissociation constants in the low picomolar range specific to LDL-P and its subfractions. Furthermore, a set of antisense sequences have been developed and characterized that are capable of binding to the best aptamers and undergoing displacement by LDL-P for use in a simple, affordable diagnostic assay.

2.-Lecocq. S, Spinella K, Dubois B, Lista S, Hampel H, Penner G :  Aptamers as biomarkers for neurological disorders. Proof of concept in trangenic mice. Plos One, January 2018

Abstract

The act of selecting aptamers against blood serum leads to deep libraries of oligonucleotide sequences that bind to a range of epitopes in blood. In this study we developed an enriched aptamer library by performing positive selection against a pool of blood serum samples from transgenic mice (P301S) carrying the human tau gene and counter selecting against pooled blood serum from negative segregant (wild type) mice. We demonstrated that a large proportion of the aptamer sequences observed with next generation sequence (NGS) analysis were the same from selection round 5 and selection round 6. As a second step, we applied aliquots of the selection round 5 enriched library to blood serum from 16 individual mice for a single round of selection. Each of these individual libraries were characterized through NGS analysis and the changes in relative frequency in aptamers from transgenic mice versus wild type were used to construct a diagnostic fingerprint of the effect of the action of the transgene on the composition of blood serum. This study serves as a model for similar applications with human subjects.

Improved Aptamers for the Diagnosis and Potential Treatment of HER2-Positive Cancer Marlies Gijs, Gregory Penner , Garth B. Blackler , Nathalie R.E.N. Impens, Sarah Baatout , André Luxen  and An M. Aerts, Pharmaceuticals 2016, 9, 29;

Abstract

Aptamers provide a potential source of alternative targeting molecules for existing antibody diagnostics and therapeutics. In this work, we selected novel DNA aptamers targeting the HER2 receptor by an adherent whole-cell SELEX approach. Individual aptamers were identified by next generation sequencing and bioinformatics analysis. Two aptamers, HeA2_1 and HeA2_3, were shown to bind the HER2 protein with affinities in the nanomolar range. In addition, both aptamers were able to bind with high specificity to HER2-overexpressing cells and HER2-positive tumor tissue samples. Furthermore, we demonstrated that aptamer HeA2_3 is being internalized into cancer cells and has an inhibitory effect on cancer cell growth and viability. In the end, we selected novel DNA aptamers with great potential for the diagnosis and possible treatment of HER2-positive cancer

Determination of ochratoxin a with a DNA aptamer.Cruz-Aguado JA, Penner G.,J Agric Food Chem. 2008 Nov 26;56(22):10456-61

Abstract

This work describes the identification of an aptamer that binds with high affinity and specificity to ochratoxin A (OTA), a mycotoxin that occurs in wheat and other foodstuffs, and a quantitative detection method for OTA based on the use of this aptamer. Aptamers are single-stranded oligonucleotides selected in vitro to bind to molecular targets. The aptamer selected in this work exhibited a dissociation constant in the nanomolar range and did not bind compounds with structures similar to OTA such as N-acetylphenylalanine or warfarin. The aptamer bound with a 100-fold less affinity to ochratoxin B. The selected aptamers could be used for the determination of ppb quantities of OTA in naturally contaminated wheat samples. Further work is ongoing to broaden the application demonstrated here with the development of sensors, affinity columns, and other analytical systems for field and laboratory determination of this toxin in food and agricultural products.

Fluorescence polarization based displacement assay for the determination of small molecules with aptamers.Cruz-Aguado JA, Penner G.Anal Chem. 2008 Nov 15;80(22):8853-5

Abstract

The conversion of an aptamer-target binding event into a detectable signal is an important step in the development of aptamer-based sensors. In this work, we show that the displacement of a fluorescently labeled oligo from the aptamer by the target can be detected by fluorescence polarization (FP). We used Ochratoxin A (OTA), a small organic molecule (MW = 403) as a case study. A detection limit of 5 nM OTA was achieved. The method presented here provides an advantage over fluorophore-quenching systems and other steady-state fluorescence approaches in that no modification of the aptamer or the target is required. Additionally, the signal is produced by the displacement event itself, so no further aggregation or conformational events have to be considered. This analytical method is particularly useful for small targets, as for large targets a direct measurement of the FP change of a labeled aptamer upon binding can be used to determine the concentration of the target. The results presented here demonstrate that aptamers and inexpensive labeled oligos can be used for rapid, sensitive, and specific determination of small molecules by means of FP.

Detection of Breast Cancer Cells Using Acoustics Aptasensor Specific to HER2 Receptors, Biosensors2019, 9(2), 72

Abstract

Detection of the breast cancer cells is important for early diagnosis of the cancer. We applied thickness shear mode acoustics method (TSM) for detection of SK-BR-3 breast cancer cells using DNA aptamers specific to HER2 positive membrane receptors. The biotinylated aptamers were immobilized at the neutravidin layer chemisorbed at gold surface of TSM transducer. Addition of the cells resulted in decrease of resonant frequency, fs, and in increase of motional resistance, Rm. Using gold nanoparticles (AuNPs), modified by aptamers it was possible improving the limit of detection (LOD) that reached 550 cells/mL, while without amplification the sensitivity of the detection of SK-BR-3 cells was 1574 cells/mL. HER2 negative cell line MDA-MB-231 did not resulted in significant changes of fs. The viability studies demonstrated that cells are stable at experimental conditions used during at least 8 h. AuNPs were not toxic on the cells up to concentration of 1 μg/mL.