Ultrasensitive Colorimetric Detection of 17β-Estradiol: The Effect of Shortening DNA Aptamer Sequences

Abstract

We report a strategy enabling ultrasensitive colorimetric detection of 17β-estradiol (E2) in water and urine samples using DNA aptamer-coated gold nanoparticles (AuNPs). Starting from an established sensor format where aggregation is triggered when target-bound aptamers dissociate from AuNP surfaces, we demonstrated that step-change improvements are easily accessible through deletion of excess flanking nucleotides from aptamer sequences. After evaluating the lowest energy two-dimensional configuration of the previously isolated E2 binding 75-mer aptamer (KD ∼25 nM), new 35-mer and 22-mer aptamers were generated with KD's of 14 and 11 nM by simply removing flanking nucleotides on either side of the inner core. The shorter aptamers were found to improve discrimination against other steroidal molecules and to improve colorimetric sensitivity for E2 detection by 25-fold compared with the 75-mer to 200 pM. In comparing the response of all sequences, we find that the excess flanking nucleotides suppress signal transduction by causing target-bound aptamers to remain adhered to AuNPs, which we confirm via surface sensitive electrochemical measurements. However, comparison between the 22-mer and 35-mer systems show that retaining a small number of excess bases is optimal. The performance advances we achieved by specifically considering the signal transduction mechanism ultimately resulted in facile detection of E2 in urine, as well as enabling environmental detection of E2 at levels approaching biological relevance.

The Bound Structures of 17β‐Estradiol‐Binding Aptamers

“…Previous research has demonstrated the extraordinary potential of sensor devices constructed from aptamers, single‐stranded DNA or RNA molecules attached to nanoparticles or nanotubes . These “aptasensors” combine the unique optical and electrical properties of the nanomaterials with the ability of aptamers to bind with high affinity and specificity to predefined targets .…”

Electrostatic gating in carbon nanotube aptasensors

“…2,4 However, this approach was restricted to a limited range of target proteins, and device fabrication and operation was subject to tight constraints to maintain antibody stability. [15][16][17] These short strands of DNA can be generated via a synthetic evolution process to bind with specificity for different types of targets, including cells, 18 proteins, 15,[19][20][21] molecules, [22][23][24][25] and even ions. 11,12 The emergence of synthetic receptors such as DNA aptamers 13,14 has stimulated new opportunities for CNT biosensors.…”

An innovative application of time-domain spectroscopy on localized surface plasmon resonance sensing

“…Mirkin’s group first reported the unique optical properties of an aggregate of GNPs, which induces interparticle plasmon coupling, resulting in a redshift in the LSPR spectrum21222324. The GNP aggregation causes a LSPR shift that is manifested as a useful spectrum-based biosensing platform1429. Meanwhile, it belongs to a homogeneous binding assay, which is carried out in solution without sophisticated processes, such as separation, immobilization, or washing steps.…”

“…The most commonly used method for spectral analysis in chemistry and biology is the measurement of a spectral peak position or a corresponding intensity value12131415. As with any traditional spectrometer, performance is highly affected by the spectral resolution.…”