Electric-field dependent conformations of single DNA molecules on a model biosensor surface

Small-Molecule Patterning via Prefunctionalized Alkanethiols

Interactions between small molecules and biomolecules are important physiologically and for biosensing, diagnostic, and therapeutic applications. To investigate these interactions, small molecules can be tethered to substrates through standard coupling chemistries. While convenient, these approaches co-opt one or more of the few small-molecule functional groups needed for biorecognition. Moreover, for multiplexing, individual probes require different surface functionalization chemistries, conditions, and/or protection/deprotection strategies. Thus, when placing multiple small-molecules on surfaces, orthogonal chemistries are needed that preserve all functional groups and are sequentially compatible. Here, we approach high-fidelity small-molecule patterning by coupling small-molecule neurotransmitter precursors, as examples, to monodisperse asymmetric oligo(ethylene glycol)alkanethiols during synthesis and prior to self-assembly on Au substrates. We use chemical lift-off lithography to singly and doubly pattern substrates. Selective antibody recognition of pre-functionalized thiols was comparable to or better than recognition of small molecules functionalized to alkanethiols after surface assembly. These findings demonstrate that synthesis and patterning approaches that circumvent sequential surface conjugation chemistries enable biomolecule recognition and afford gateways to multiplexed small-molecule functionalized substrates.

Direct Mapping of Heterogeneous Surface Coverage in DNA-Functionalized Gold Surfaces with Correlated Electron and Fluorescence Microscopy

The characterization of biofunctionalized surfaces such as alkanethiol self-assembled monolayers (SAMs) on gold modified with DNA or other biomolecules is a challenging analytical problem, and access to a routine method is desirable. Despite substantial investigation from structural and mechanistic perspectives, robust and high-throughput metrology tools for SAMs remain elusive but essential for the continued development of these devices. We demonstrate that scanning electron microscopy (SEM) can provide image contrast of the molecular interface during SAM functionalization. The high-speed, large magnification range, and ease of use make this widely available technique a powerful platform for measuring the structure and composition of SAM surfaces. This increased throughput allows for a better understanding of the nonideal spatial heterogeneity characteristic of SAMs utilized in real-world conditions. SEM image contrast is characterized through the use of fluorescently labeled DNA, which enables correlative SEM and fluorescence microscopy. This allows identification of the DNA-modified regions at resolutions that approach the size of the biomolecule. The effect of electron beam irradiation dose is explored, which leads to straightforward lithographic patterning of DNA SAMs with nanometer resolution and with control over the surface coverage of specifically adsorbed DNA.

Self-standing aptamers by an artificial defect-rich matrix

The classical alkanethiol post-passivation can prevent nonspecific binding of nucleotide bases onto supporting substrates and help aptamers transition from a "lying down" to a "standing up" orientation. However, the surface probes display lower binding affinity towards targets than those in bulk solutions due to unsatisfied hybridization spaces on the alkanethiol passivated substrate. To overcome this challenge, an artificial defect-rich matrix possessing an aptamer "self-standing" property created by chemical lift-off lithography (CLL) is demonstrated. This approach provided artificial defects on a hydroxyl-terminated alkanethiol self-assembled monolayer (SAM), which allowed the insertion of thiolated aptamers. The diluted surface molecular environment assisted aptamers not only to "self-stand" on the surface, but also to separate from each other, providing a suitable surface aptamer density and sufficient space for capturing targets. With this approach, the binding affinity of the aptamer towards a target was comparable to solution-type probes, showing higher recognition efficiency than that in conventional methods.

Molecular conformations of DNA targets captured by model nanoarrays

An open question in single molecule nanoarrays is how the chemical and morphological heterogeneities of the solid support affect the properties of biomacromolecules. We generated arrays that allowed individually-resolvable DNA molecules to interact with tailored surface heterogeneities and revealed how molecular conformations are impacted by surface interactions.

Arrays of Individual DNA Molecules on Nanopatterned Substrates

Arrays of individual molecules can combine the advantages of microarrays and single-molecule studies. They miniaturize assays to reduce sample and reagent consumption and increase throughput, and additionally uncover static and dynamic heterogeneity usually masked in molecular ensembles. However, realizing single-DNA arrays must tackle the challenge of capturing structurally highly dynamic strands onto defined substrate positions. Here, we create single-molecule arrays by electrostatically adhering single-stranded DNA of gene-like length onto positively charged carbon nanoislands. The nanosites are so small that only one molecule can bind per island. Undesired adsorption of DNA to the surrounding non-target areas is prevented via a surface-passivating film. Of further relevance, the DNA arrays are of tunable dimensions, and fabricated on optically transparent substrates that enable singe-molecule detection with fluorescence microscopy. The arrays are hence compatible with a wide range of bioanalytical, biophysical, and cell biological studies where individual DNA strands are either examined in isolation, or interact with other molecules or cells.

Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials

Unique electronic and ligand recognition properties of the DNA double helix provide basis for DNA applications in biomolecular electronic and biosensor devices. However, the relation between the structure of DNA at electrified interfaces and its electronic properties is still not well understood. Here, potential-driven changes in the submolecular structure of DNA double helices composed of either adenine-thymine (dAdT)₂₅ or cytosine-guanine (dGdC)₂₀ base pairs tethered to the gold electrodes are for the first time analyzed by in situ polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) performed under the electrochemical control. It is shown that the conformation of the DNA duplexes tethered to gold electrodes via the C₆ alkanethiol linker strongly depends on the nucleic acid sequence composition. The tilt of purine and pyrimidine rings of the complementary base pairs (dAdT and dGdC) depends on the potential applied to the electrode. By contrast, neither the conformation nor orientation of the ionic in character phosphate-sugar backbone is affected by the electrode potentials. At potentials more positive than the potential of zero charge (pzc), a gradual tilting of the double helix is observed. In this tilted orientation, the planes of the complementary purine and pyrimidine rings lie ideally parallel to each other. These potentials do not affect the integral stability of the DNA double helix at the charged interface. At potentials more negative than the pzc, DNA helices adopt a vertical to the gold surface orientation. Tilt of the purine and pyrimidine rings depends on the composition of the double helix. In monolayers composed of (dAdT)₂₅ molecules the rings of the complementary base pairs lie parallel to each other. By contrast, the tilt of purine and pyrimidine rings in (dGdC)₂₀ helices depends on the potential applied to the electrode. Such potential-induced mobility of the complementary base pairs can destabilize the helix structure at a submolecular level. These pioneer results on the potential-driven changes in the submolecular structure of double stranded DNA adsorbed on conductive supports contribute to further understanding of the potential-driven sequence-specific electronic properties of surface-tethered oligonucleotides.

Controlled DNA Patterning by Chemical Lift-Off Lithography: Matrix Matters

Nucleotide arrays require controlled surface densities and minimal nucleotide-substrate interactions to enable highly specific and efficient recognition by corresponding targets. We investigated chemical lift-off lithography with hydroxyl- and oligo(ethylene glycol)-terminated alkanethiol self-assembled monolayers as a means to produce substrates optimized for tethered DNA insertion into post-lift-off regions. Residual alkanethiols in the patterned regions after lift-off lithography enabled the formation of patterned DNA monolayers that favored hybridization with target DNA. Nucleotide densities were tunable by altering surface chemistries and alkanethiol ratios prior to lift-off. Lithography-induced conformational changes in oligo(ethylene glycol)-terminated monolayers hindered nucleotide insertion but could be used to advantage via mixed monolayers or double-lift-off lithography. Compared to thiolated DNA self-assembly alone or with alkanethiol backfilling, preparation of functional nucleotide arrays by chemical lift-off lithography enables superior hybridization efficiency and tunability.

Insertion approach: bolstering the reproducibility of electrochemical signal amplification via DNA superstructures

For more than a decade, the backfilling approach for the immobilization of DNA probes has been routinely adopted for the construction of functional interfaces; however, reliably reproducing electrochemical signal amplification by this method is a challenge. In this research, we demonstrate that the insertion approach significantly bolsters the reproducibility of electrochemical signal amplification via DNA superstructures. The combination of the backfilling approach and the DNA superstructure formation poses a big challenge to reliably reproducing electrochemical signal amplification. In order to use the detection of Hg(2+) as a prototype of this new strategy, a thymine-rich DNA probe that is specific to mercury ion was applied in this study. The presence of Hg(2+) induces the folding of the DNA probes and inhibits the formation of DNA superstructures. By using electroactive probes ([Ru(NH3)6](3+)) that are electrostatically adsorbed onto the double strands, differential pulse voltammetry (DPV) could quantitatively confirm the presence of Hg(2+). A limit of detection (LOD) and a limit of quantification (LOQ) (LOQ) as low as 0.3 and 9.5 pM, respectively, were achieved. Furthermore, excellent selectivity and real sample analysis demonstrated the promising potential of this approach in future applications.

Microarrays and single molecules: an exciting combination

Biomolecules positioned at interfaces have spawned many applications in bioanalysis, biophysics, and cell biology. This Highlight describes recent developments in the research areas of protein and DNA arrays, and single-molecule sensing. We cover the ultrasensitive scanning of conventional microarrays as well as the generation of arrays composed of individual molecules. The combination of these tools has improved the detection limits and the dynamic range of microarray analysis, helped develop powerful single-molecule sequencing approaches, and offered biophysical examination with high throughput and molecular detail. The topic of this Highlight integrates several disciplines and is written for interested chemists, biophysicists and nanotechnologists.

Covalent, sequence-specific attachment of long DNA molecules to a surface using DNA-templated click chemistry

We present a novel method that covalently and sequence-specifically attaches long DNA molecules to a surface that is compatible with high-resolution atomic force microscopy (AFM) imaging.

Nanoscale spatial distribution of thiolated DNA on model nucleic acid sensor surfaces

The nanoscale arrangement of the DNA probe molecules on sensor surfaces has a profound impact on molecular recognition and signaling reactions on DNA biosensors and microarrays. Using electrochemical atomic force microscopy, we have directly determined the nanoscale spatial distribution of thiolated DNA that are attached to gold via different methods. We discovered significant heterogeneity in the probe density and limited stability for DNA monolayers prepared by the backfilling method, that is, first exposing the surface to thiolated DNA then "backfilling" with a passivating alkanethiol. On the other hand, the monolayers prepared by "inserting" thiolated DNA into a preformed alkanethiol monolayer lead to a more uniformly distributed layer of DNA. With high-resolution images of single DNA molecules on the surface, we have introduced spatial statistics to characterize the nanoscale arrangement of DNA probes. The randomness of the spatial distribution has been characterized. By determining the local densities surrounding individual molecules, we observed subpopulations of probes with dramatically different levels of "probe crowding". We anticipate that the novel application of spatial statistics to DNA monolayers can enable a framework to understand heterogeneity in probe spatial distributions, interprobe interactions, and ultimately probe activity on sensor surfaces.