A Grafting Strategy for the Design of Improved G-Quadruplex Aptamers and High-Activity DNAzymes

Nucleic acid aptamers are generally obtained by in vitro selection. Some have G-rich consensus sequences with ability to fold into the four-stranded structures known as G-quadruplexes. A few G-quadruplex aptamers have proven to bind hemin to form a new class of DNAzyme with the peroxidase-like activity, which can be significantly promoted by appending an appropriate base-pairing duplex onto the G-quadruplex structures of aptamers. Knowing the structural role of base pairing, here we introduce a novel grafting strategy for the design of improved G-quadruplex aptamers and high-activity DNAzymes. To demonstrate this strategy, three existing G-quadruplex aptamers are chosen as the first generation. A base-pairing DNA duplex is grafted onto the G-quadruplex motif of the first generation aptamers. Consequently, three new aptamers with the quadruplex/duplex DNA structures are produced as the second generation. The hemin-binding affinities and DNAzyme functions of the second generation aptamers are characterized and compared with the first generation. The results indicate three G-quadruplex aptamers obtained by the grafting strategy have more excellent properties than the corresponding original aptamers. Our findings suggest that, if the structures and functions of existing aptamers are thoroughly known, the grafting strategy can be facilely utilized to improve the aptamer properties and thereby producing better next-generation aptamers. This provides a simple but effective approach to the design of nucleic acid aptamers and DNAzymes

Science teachers’ experiences of inquiry-based learning through a serious game:a phenomenographic perspective

This study employed a phenomenographic approach to investigate science teachers’ conceptions of inquiry-based learning through a serious game. Simaula is a prototype game designed and used as a virtual practicum for eliciting understandings on how in-game inquiry was appeared to, or experienced by, the participating teachers. Group interviews with 20 secondary education science teachers revealed four qualitatively different ways of experiencing inquiry-based learning through Simaula: (a) as uncovering insights about student’s learning needs, interests and emotions; (b) as generating ideas and concepts for meaningful inquiry; (c) as a set of operations for designing and carrying out scientific research; and (d) as authentic inquiry for enabling knowledge building processes. Seven dimensions of variation have been identified viewed as contextual influences on conceptions of in-game inquiry constituting discernment of: epistemic inquiry-based learning modes; role of teacher; role of student; game-play focus; core mechanics focus; feedback and progress mechanics and game uncertainty. The results illuminated a partial in-game inquiry approach with distinct epistemic modes from developing empathy and meaning making to knowledge construction and knowledge building. The findings also indicated that game design elements played central role in shaping conceptions of in-game inquiry from focusing on rules and logic as means to completing the game’s level to understanding the complexity of core mechanics for developing and transferring in-game inquiry to the real classroom. This insinuates that distinct game design properties may be considered in terms of extending intrinsic in-game inquiry experiences to actual in-class inquiry practice

Nucleic acid-based fluorescent probes and their analytical potential

It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays