Surface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time that a DNA strand resides within the plasmonic hot spot. In fact, DNA molecules flow through the nanopores so rapidly that the SERS signals collected are not sufficient for single-molecule analysis. Here, we report an approach to control the residence time of molecules in the hot spot by an electro-plasmonic trapping effect. By directly adsorbing molecules onto a gold nanoparticle and then trapping the single nanoparticle in a plasmonic nanohole up to several minutes, we demonstrate single-molecule SERS detection of all four DNA bases as well as discrimination of single nucleobases in a single oligonucleotide. Our method can be extended easily to label-free sensing of single-molecule amino acids and proteins.

The SERS‐based detection of protein sequences with single‐residue sensitivity suffers from signal dominance of aromatic amino acid residues and backbones, impeding detection of non‐aromatic amino acid residues. Herein, we trap a gold nanoparticle in a plasmonic nanohole to generate a single SERS hot spot for single‐molecule detection of 2 similar polypeptides (vasopressin and oxytocin) and 10 distinct amino acids that constitute the 2 polypeptides. Significantly, both aromatic and non‐aromatic amino acids are detected and discriminated at the single‐molecule level either at individual amino acid molecules or within the polypeptide chains. Correlated with molecular dynamics simulations, our results suggest that the signal dominance due to large spatial occupancy of aromatic rings of the polypeptide sidechains on gold surfaces can be overcome by the high localization of the single hot spot. The superior spectral and spatial discriminative power of our approach can be applied to single‐protein analysis, fingerprinting, and sequencing.

Successful diagnosis and treatment of many diseases depends on the availability of sensitive, reliable and low cost tools for the detection of the biomarkers associated with the diseases. Simple methods that use non-invasive biological samples are especially suitable for the deployment in the clinical environment. In this paper we demonstrate the application of a method that employs a capped gold nanoslit surface plasmon resonance (SPR) sensor and a microfluidic chip for the detection of a urinary nucleic acid biomarker in clinical samples. This method detects low concentrations of the biomarker in a relatively large volume (∼1 mL) of the sample. The method utilizes magnetic nanoparticles (MNPs) for the isolation of target molecules and signal enhancement in conjunction with surface plasmon resonance (SPR) on capped gold nanoslits. The ability of the method to detect urinary miRNA-16-5p in AKI patients was tested and the result was compared with the data obtained with the polymerase chain reaction (PCR). miRNA-16-5p has been found to be a specific and noninvasive biomarker for acute kidney injury (AKI). Our method allows the detection of the biomarker in the urine of AKI patients without amplification and labeling of the target molecules.

We have demonstrated a detection method for the ultra-sensitive detection of an mRNA biomarker. The method utilizes functionalized magnetic nanoparticles (MNPs) for signal enhancement in conjunction with surface plasmon resonance (SPR) on gold nanoslits. The approach for detection includes double hybridization at two different specific locations in two steps. First, the biomarker target molecule is captured with MNPs, and second, MNPs carrying the target molecule are introduced to the SPR chip to hybridize with probes immobilized on the gold nanoslits. In this work, MNPs were applied for a dual purpose: to isolate the target molecule from the sample matrix to prevent non-specific binding and to enhance the SPR response. Gold nanoslits that provide SPR sensing were fabricated by nanoimprinting lithography on polycarbonate (PC) film. The film was integrated with a microliter volume microfluidic chip to form the SPR detection chip. This detection method was used to detect mRNA heterogeneous nuclear ribonucleoproteins (hnRNP B1) in two cancer cell lines, CL1-0 and CL1-5. hnRNP B1 is an mRNA biomarker that is overexpressed in lung cancer tissue in the early stage of cancer and can be found in the serum and plasma of lung cancer patients. A synthetic target molecule and extracted total RNA from the cell lines were used as samples. Without amplification and labeling of the target molecule, the SPR results demonstrate a specific and sensitive method for the detection of hnRNP B1 mRNA in extracted RNA from the two selected cell lines. The method is capable of measuring down to 30 fM of the target molecule in a 7 μl sample (corresponding to 1.26 × 10(5) molecules) without amplification and labeling of the target molecule.