Huaqiang Zeng

Ultrasensitive and Selective Colorimetric DNA Detection by Nicking Endonuclease Assisted Nanoparticle Amplification

The ability to sense and detect ultralow concentrations of specific DNA sequences by using simple and inexpensive assays is important in clinical diagnostics, mutation detection, and biodefense applications. Conventional methods that use radioactive [P]-labeled nucleic acid probes or the polymerase chain reaction (PCR) coupled with molecular fluorophore assays offer high sensitivity of detection, but they suffer from several drawbacks that include complex handling procedures, easy contamination, high cost, and lack of portability. In contrast, metal-nanoparticle-based homogeneous colorimetric detection of oligonucleotides holds great promise for low-cost, low-volume, and rapid readout of a target DNA sequence. Despite these attractions, a number of notable challenges associated with this detection system still exist, such as relatively low sensitivity (ca. 10 nm) and the need for stringent control over melting temperatures for the detection of a single-base mismatch in DNA. In addition, this system is generally limited to the detection of short singlestranded oligonucleotides. Herein, we describe homogeneous colorimetric DNA detection by a novel nicking endonucleaseassisted nanoparticle amplification (NEANA) process that is capable of recognizing long single-stranded oligonucleotides with single-base mismatch selectivity and a 10-fold improvement in amplification (ca. 10 pm). A three-component sandwich assay format that includes a target DNA and two sets of oligonucleotide-modified nanoparticle probes is typically used in conventional homogenous nanoparticle-based colorimetric DNA detection. The target DNA also serves as a linker strand that triggers particle aggregation and a concomitant color change. Thus, the colorimetric detection limit is directly associated with the minimum number of the linkers required to initiate particle aggregation that can be visualized with the naked eye. At low linker concentrations (ca. 10 nm), aggregation of 14 nm nanoparticles does not exhibit sharp colorimetric melting transitions (see the Supporting Information). Larger particle probes and reduced oligonucleotide surface coverages can improve assay sensitivities, but sedimentation becomes more dominant with increase in the particle size. To increase the sensitivity of homogeneous nanoparticlebased assays, we have developed a detection system that contains an additional oligonucleotide strand as the linker, and a nicking endonuclease (NEase; Figure 1). Unlike

Creating nanocavities of tunable sizes: Hollow helices

A general strategy for creating nanocavities with tunable sizes based on the folding of unnatural oligomers is presented. The backbones of these oligomers are rigidified by localized, three-center intramolecular hydrogen bonds, which lead to well-defined hollow helical conformations. Changing the curvature of the oligomer backbone leads to the adjustment of the interior cavity size. Helices with interior cavities of 10 Å to >30 Å across, the largest thus far formed by the folding of unnatural foldamers, are generated. Cavities of these sizes are usually seen at the tertiary and quaternary structural levels of proteins. The ability to tune molecular dimensions without altering the underlying topology is seen in few natural and unnatural foldamer systems.

Persistently Folded Circular Aromatic Amide Pentamers Containing Modularly Tunable Cation-Binding Cavities with High Ion Selectivity

In this work, we illustrated a novel design strategy that allows systematically tunable interior properties (effective cavity size, steric crowdedness, and hydrophobicity) contained within a novel class of shape-persistent aromatic pentamers to take place on a scale below 3 A. Such finely tunable structural features are complimented by experimentally observable functional variations in ion-binding potential. Results of the selective, differential binding affinities of three circular pentamers for Li(+), Na(+), K(+), Rb(+), and Cs(+), substantiated by metal-containing crystal structures and computational modeling, are detailed.

Five-fold-symmetric macrocyclic aromatic pentamers: high-affinity cation recognition, ion-pair-induced columnar stacking, and nanofibrillation.

Described in this study is a conceptually new class of five-fold-symmetric cavity-containing planar pentameric macrocycles with their interior decorated by five convergently aligned, properly spaced carbonyl oxygen atoms. These cation-binding oxygens enclose a hydrophilic lumen of 2.85 Å in radius and thus display high-affinity binding toward alkali metal cations, and possibly many other cations, too. Arising from their high-affinity recognition of metal ions, these planar macrocycles form cation- or ion-pair-induced one-dimensional columnar aggregates, and subsequently fascinating fibrillation results.

Crystallographic evidence of an unusual, pentagon-shaped folding pattern in a circular aromatic pentamer.

Introduction of a continuous hydrogen-bonding network suppressed the conformational flexibility of an oligomeric backbone. Cyclization of a rigidified, suitably sized oligomer led to a circular aromatic pentamer. Its crystal structure determined by X-ray crystallography reveals a pseudo five-fold symmetric planarity in the solid state, which is quite unusual among all the previously described shape-persistent macrocycles and synthetic foldamers with biased conformations enforced by noncovalent forces.

Stable Three-Center Hydrogen Bonding in a Partially Rigidified Structure

The three-center hydrogen bond in diaryl amide 1 was examined by IR and 1H NMR spectroscopy, X-ray crystallography, and ab initio calculations. By comparing 1 with its structural isomers 2, 3 and 4, and with its conformational isomers 1a-c, it was found that the two two-center components of the three-center interaction reinforce each other, that is, the enhanced stability of the three-center hydrogen bond is a result of positive cooperativity between the two components. Substituents not involved in hydrogen bonding have little effect on the strength of the two- and three-center hydrogen bonds. To our knowledge, this is the first three-center hydrogen-bonding system that has been shown to exhibit positive cooperativity. Ab initio calculations of the geometries, vibrational modes, and 1H NMR chemical shifts also support the experimental findings. These results have provided a new insight into the three-center intramolecular hydrogen bonding in a partially rigidified structure and have provided a reliable motif for designing stably folded structures.

Planar macrocyclic fluoropentamers as supramolecular organogelators.

Despite their great diversities, 2D-shaped macrocycles that can serve as the organogelators have been surprisingly rare; two planar macrocyclic fluoropentamers designed by us were highly able to gelate organic solvents, largely derived from their strong tendency to form 1D stacked fibrillar structures stabilized by both interplanar H-bonds and π-π stacking forces.

Helical organization in foldable aromatic oligoamides by a continuous hydrogen-bonding network.

Introduction of a continuous internal hydrogen-bonding network suppressed the conformational flexibility of a series of oligoaromatic foldamers with a lengthened backbone. The helical ordering over up to six aromatic repeating units was established in solution by a 2D NOESY study and in the solid state by an X-ray diffraction method. Computational molecular modeling further corroborates the experimentally observed helical propagation in this class of foldable molecular strands.

Two‐Component Supramolecular Gels Derived from Amphiphilic Shape‐Persistent Cyclo[6]aramides for Specific Recognition of Native Arginine

A unique supramolecular two-component gelation system was constructed from amphiphilic shape-persistent cyclo[6]aramides and diethylammonium chloride (or triethylammonium chloride). This system has the ability to discriminate native arginine from 19 other amino acids in a specific fashion. Cyclo[6]aramides show preferential binding for the guanidinium residue over ammonium groups. This specificity was confirmed by both experimental results and theoretical simulations. These results demonstrated a new modular displacement strategy, exploring the use of species-binding hydrogen-bonded macrocyclic foldamers for the construction of two-component gelation systems for selective recognition of native amino acids by competitive host-guest interactions. This strategy may be amenable to developing a variety of functional two-component gelators for specific recognition of various targeted organic molecular species.

Encapsulation of Conventional and Unconventional Water Dimers by Water-Binding Foldamers

Water-binding foldamers have been rarely studied. By orienting both H-bond donors and acceptors toward their interior, two pyridine-derived crescent-shaped folding oligoamides were found to be capable of trapping both conventional and unconventional water dimer clusters in their cavity (∼2.5 Å radius). In the unconventional water dimer cluster, the two water molecules stay in contact via an unusual H-H interaction (2.25 Å) rather than the typical H-bond.