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Small molecule contaminants pose a significant threat to the environment and human health. While regulations are in place for allowed limits in many countries, detection and remediation of contaminants in more resource-limited settings and everyday environmental sources remains a challenge. Functional nucleic acids, including aptamers and DNA enzymes, have emerged as powerful options for addressing this challenge due to their ability to non-covalently interact with small molecule targets. The goal of this perspective is to outline recent efforts toward the selection of aptamers for small molecules and describe their subsequent implementation for environmental applications. Finally, we provide an outlook that addresses barriers that hinder these technologies from being widely adopted in field friendly settings and propose a path forward toward addressing these challenges. 

Peptide nucleic acids (PNAs) are high-affinity synthetic nucleic acid analogs capable of hybridization with native nucleic acids. PNAs synthesized having amino acid sidechains installed at the γ-position along the backbone provide a template for a single biopolymer to simultaneously encode nucleic acid and amino acid sequences. Previously, we reported the development of “bilingual” PNAs through the synthesis of an amphiphilic sequence featuring separate blocks of hydrophobic and hydrophilic amino acid functional groups. These PNAs combined the sequence-specific binding activity of nucleic acids with the structural organization properties of peptides. Like other amphiphilic compounds, these γ-PNAs were observed to assemble spontaneously into micelle-like nanostructures in aqueous solutions and disassembly was induced through hybridization to a complementary sequence. Here, we explore whether assembly of these bilingual PNAs is possible by harnessing the nucleic acid code. Specifically, we designed an amphiphile-masking duplex system in which spontaneous amphiphile assembly is prevented through hybridization to a nucleic acid masking sequence. We show that the amphiphile is displaced upon introduction of a releasing sequence complementary to the masking sequence through toehold mediated displacement. Upon release, we observe that the amphiphile proceeds to assemble in a fashion consistent with our previously reported structures. Our approach represents a novel method for controlled stimuli-responsive assembly of PNA-based nanostructures. 

As technology moves rapidly forward and our world becomes more interconnected, we are seeing increases in the complexity and challenge associated with scientific problems. More than ever before, scientists will need to be resilient and able to cope with challenges and failures en route to success. However, we still understand relatively little about how these skills manifest in STEM contexts broadly, and how they are developed by STEM undergraduate students. While recent studies have begun to explore this area, no measures exist that are specifically designed to assess coping behaviors in STEM undergraduate contexts at scale. Fortunately, multiple measures of coping do exist and have been previously used in more general contexts. Drawing strongly from items used in the COPE and Brief COPE, we gathered a pool of items anticipated to be good measures of undergraduate students’ coping behaviors in STEM. We tested the validity of these items for use with STEM students using exploratory factor analyses, confirmatory factor analyses, and cognitive interviews. In particular, our confirmatory factor analyses and cognitive interviews explored whether the items measured coping for persons excluded due to ethnicity or race (PEERs).

Our analyses revealed two versions of what we call the STEM-COPE instrument that accurately measure several dimensions of coping for undergraduate STEM students. One version is more fine-grained. We call this the Coping Behaviors version, since it is more specific in its description of coping actions. The other contains some specific scales and two omnibus scales that describe what we call challenge-engaging and challenge-avoiding coping. This version is designated the Coping Styles version. We confirmed that both versions can be used reliably in PEER and non-PEER populations.

The final products of our work are two versions of the STEM-COPE. Each version measures several dimensions of coping that can be used in individual classrooms or across contexts to assess STEM undergraduate students’ coping with challenges or failures. Each version can be used as a whole, or individual scales can be adopted and used for more specific studies. This work also highlights the need to either develop or adapt other existing measures for use with undergraduate STEM students, and more specifically, for use with sub-populations within STEM who have been historically marginalized or minoritized.

 

Abstract Background The ability to navigate obstacles and embrace iteration following failure is a hallmark of a scientific disposition and is hypothesized to increase students’ persistence in science, technology, engineering, and mathematics (STEM). However, this ability is often not explicitly explored or addressed by STEM instructors. Recent collective interest brought together STEM instructors, psychologists, and education researchers through the National Science Foundation (NSF) research collaborative Factors affecting Learning, Attitudes, and Mindsets in Education network (FLAMEnet) to investigate intrapersonal elements (e.g., individual differences, affect, motivation) that may influence students’ STEM persistence. One such element is fear of failure (FF), a complex interplay of emotion and cognition occurring when a student believes they may not be able to meet the needs of an achievement context. A validated measure for assessing FF, the Performance Failure Appraisal Inventory (PFAI) exists in the psychological literature. However, this measure was validated in community, athletic, and general undergraduate samples, which may not accurately reflect the motivations, experiences, and diversity of undergraduate STEM students. Given the potential role of FF in STEM student persistence and motivation, we felt it important to determine if this measure accurately assessed FF for STEM undergraduates, and if not, how we could improve upon or adapt it for this purpose. Results Using exploratory and confirmatory factor analysis and cognitive interviews, we re-validated the PFAI with a sample of undergraduates enrolled in STEM courses, primarily introductory biology and chemistry. Results indicate that a modified 15-item four-factor structure is more appropriate for assessing levels of FF in STEM students, particularly among those from groups underrepresented in STEM. Conclusions In addition to presenting an alternate factor structure, our data suggest that using the original form of the PFAI measure may significantly misrepresent levels of FF in the STEM context. This paper details our collaborative validation process and discusses implications of the results for choosing, using, and interpreting psychological assessment tools within STEM undergraduate populations. 

Aptamers are widely employed as recognition elements in small molecule biosensors due to their ability to recognize small molecule targets with high affinity and selectivity. Structure-switching aptamers are particularly promising for biosensing applications because target-induced conformational change can be directly linked to a functional output. However, traditional evolution methods do not select for the significant conformational change needed to create structure-switching biosensors. Modified selection methods have been described to select for structure-switching architectures, but these remain limited by the need for immobilization. Herein we describe the first homogenous, structure-switching aptamer selection that directly reports on biosensor capacity for the target. We exploit the activity of restriction enzymes to isolate aptamer candidates that undergo target-induced displacement of a short complementary strand. As an initial demonstration of the utility of this approach, we performed selection against kanamycin A. Four enriched candidate sequences were successfully characterized as structure-switching biosensors for detection of kanamycin A. Optimization of biosensor conditions afforded facile detection of kanamycin A (90 μM to 10 mM) with high selectivity over three other aminoglycosides. This research demonstrates a general method to directly select for structure-switching biosensors and can be applied to a broad range of small-molecule targets.