Trial Proteomic Qualitative and Quantitative Analysis of the Protein Matrix of Submandibular Sialoliths.

Our studies aimed to explore the protein components of the matrix of human submandibular gland sialoliths. A qualitative analysis was carried out based on the filter aided sample preparation (FASP) methodology. In the protein extraction process, we evaluated the applicability of the standard demineralization step and the use of a lysis buffer containing sodium dodecyl sulfate (SDS) and dithiothreitol (DTT). The analysis of fragmentation spectra based on the human database allowed for the identification of 254 human proteins present in the deposits. In addition, the use of multi-round search in the PEAKS Studio program against the bacterial base allowed for the identification of 393 proteins of bacterial origin present in the extract obtained from sialolith, which so far has not been carried out for this biological material. Furthermore, we successfully applied the SWATH methodology, allowing for a relative quantitative analysis of human proteins present in deposits. The obtained results correlate with the classification of sialoliths proposed by Tretiakow. The performed functional analysis allowed for the first time the selection of proteins, the levels of which differ between the tested samples, which may suggest the role of these proteins in the calcification process in different types of sialoliths. These are preliminary studies, and drawing specific conclusions requires research on a larger group, but it provides us the basis for the continuation of the work that has already begun.

Deep blue autofluorescence reveals the instability of human transthyretin.

Wild-type human transthyretin (TTR) is a tetrameric protein that transports thyroxine and retinol in the blood and brain. However, a number of mutations or aging leads to destabilization of the quaternary structure of TTR, which results in dissociation of TTR tetramers to monomers, followed by oligomerization and subsequent amyloid formation. TTR amyloid is a pathogenic factor underlying several diseases. It has recently been documented that destabilization of the structure of TTR is driven by Ca2+. The present work shows that the in vitro redox conditions contribute to the destabilization and formation of the highly unstable substoichiometric population(s) of TTR molecules. Importantly, destabilized TTR forms acquire the ability to emit fluorescence in the blue range of the light spectrum. Dithiothreitol (DTT), in the presence of Ca2+, enhances the formation of complex autofluorophore which displays maxima at 417 nm and 438 nm in the emission spectrum of TTR.

The utility of dithiothreitol treatment of periprosthetic tissues and explanted implants in the diagnosis of prosthetic joint infection.

PURPOSE: The methods used for the processing of periprosthetic tissues and explanted implants to improve culture outcome especially in biofilm mediated prosthetic joint infections (PJIs) are still debated upon. Studies have reported that Dithiothreitol (DTT) pretreatment of infected devices gives similar results as sonication. However, none of them evaluated the DTT treatment of periprosthetic tissues and explanted implants in the same cohort. We evaluated the diagnostic utility of DTT treatment of periprosthetic tissue and explanted implants, as compared to the normal saline treatment of periprosthetic tissues and sonication of explanted implants for the diagnosis of PJI. METHODS: Seventy-three revision arthroplasty cases were prospectively included in this study. Three to five tissue specimens and the explanted implants were collected from each patient. Periprosthetic tissue samples were processed by both normal saline and DTT treatments. Explanted implants were subjected to both DTT treatment and sonication. Musculoskeletal Infection Society (MSIS) PJI criteria was used as the reference standard for the diagnosis of PJI. RESULTS: Of the 73 cases enrolled, 34 had PJI and 39 were aseptic failures. The sensitivity of DTT treated periprosthetic tissue culture (PTC) and saline treated PTC was similar (66.6% vs 58.8%, P = 0.25). The specificity of both was 100%. Sonication and DTT treatment of explanted implants showed comparable sensitivity (85.3% vs 82.4%) and specificity (100% vs 97.4%), P > 0.99. Compared to DTT treated PTC, culture of DTT treated explanted implants significantly improved the diagnosis of PJI (P = 0.03). CONCLUSIONS: We could verify that DTT can be used to improve culture outcome in laboratories where biofilm detaching sonication techniques are not available for infected implants. In addition, we showed that it is possible to use DTT for treating tissue biopsies, but larger studies are required to confirm our findings.

Unfolding and Aggregation of Lysozyme under the Combined Action of Dithiothreitol and Guanidine Hydrochloride: Optical Studies.

Using a number of optical techniques (interferometry, dynamic light scattering, and spectroscopy), denaturation of hen egg white lysozyme (HEWL) by treatment with a combination of dithiothreitol (DTT) and guanidine hydrochloride (GdnHCl) has been investigated. The denaturing solutions were selected so that protein denaturation occurred with aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM) or without aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM, GdnHCl 6 M) and can be evaluated after 60 min of treatment. It has been found that denatured by solution with 6 M GdnHCl lysozyme completely loses its enzymatic activity after 30 min and the size of the protein molecule increases by 1.5 times, from 3.8 nm to 5.7 nm. Denaturation without of GdnHCl led to aggregation with preserving about 50% of its enzymatic activity. Denaturation of HEWL was examined using interferometry. Previously, it has been shown that protein denaturation that occurs without subsequent aggregation leads to an increase in the refractive index (Δn ~ 4.5 × 10-5). This is most likely due to variations in the HEWL-solvent interface area. By applying modern optical techniques conjointly, it has been possible to obtain information on the nature of time-dependent changes that occur inside a protein and its hydration shell as it undergoes denaturation.

Modulating the in vitro gastric digestion of heat-induced beta-lactoglobulin aggregates: Incorporation with polysaccharide.

Three heat-induced protein aggregates, beta-lactoglobulin fibrils (BLGF), nanoparticles (BLGN), and worm-like aggregates (BLGW) were chosen to probe the effect of disulfide bond and surface hydrophobicity on their gastric digestion behavior. Furthermore, the effect of polysaccharide (dextran sulfate sodium, DSS) on the digestion behavior of the protein aggregates was investigated. Results showed that disulfide bond had a mild restraint on the digestion extent (maximum up to 4.65%), especially when its content was below 1 mol/mol, while the surface hydrophobicity had a stronger influence (up to 8.96%), and there is definitive positive linear relationship between the surface hydrophobicity and the digestion extent. When incorporated with DSS, both the disulfide bond content and surface hydrophobicity of the aggregates decreased, consequently, and the digestion was impeded, confirming the stronger effect from the surface hydrophobicity. The digestion extent of the heat-induced protein aggregates could be modulated linearly by incorporation of polysaccharide.

Bell-Shaped Electron Transfer Kinetics in Gold Nanoclusters.

Although metal nanoclusters (MNCs) have shown great promise for the further development of photochemical techniques to be applied in diverse areas (e.g., photoelectronic devices, photochemical sensors, photocatalysts, and energy storage and conversion systems), the fundamental problem of their electron transfer behavior still remains unsolved. Herein, a driving force-dependent photoinduced electron transfer process of gold nanoclusters (AuNCs) is clarified for the first time from a rational-designed opposite-charged system. It was found that the electron transfer dynamic of carboxylated chitosan and dithiothreitol-commodified AuNCs (CC/DTT-AuNCs) can be satisfactorily described by the Marcus electron transfer theory. This proved model was applied to estimate the ultrafast charge separation process between CC/DTT-AuNCs and mitoxantrone, which was confirmed by fluorescence quenching and femtosecond transient absorption spectroscopy measurements. We envision that this work will open a new door for understanding the electron transfer behavior of MNCs and facilitate the design of advanced optoelectronic devices.

Effect of the drug cyclophosphamide on the activity of porcine kidney betaine aldehyde dehydrogenase.

The enzyme betaine aldehyde dehydrogenase (BADH EC 1.2.1.8) catalyzes the synthesis of glycine betaine (GB), an osmolyte and osmoprotectant. Also, it participates in several metabolic pathways in humans. All BADHs known have cysteine in the active site involved in the aldehyde binding, whereas the porcine kidney enzyme (pkBADH) also has a neighborhood cysteine, both sensitive to oxidation. The antineoplastic and immuno-suppressant pre-drug cyclophosphamide (CTX), and its bioactivation products, have two highly oxidating chlorine atoms. This work aimed to analyze the effect of CTX in the activity of porcine kidney betaine aldehyde dehydrogenase. PkBADH was incubated with varying CTX concentration (0 to 2.0 mM) at 25 °C and lost 50 % of its activity with 2.0 mM CTX. The presence of the coenzyme NAD+ (0.5 mM) decreased 95% the activity in 2.0 mM CTX. The substrate betaine aldehyde (0.05 and 0.4 mM, and the products NADH (0.1-0.5 mM) and GB (1 and 10 mM) did not have an effect on the enzyme inactivation by CTX. The reducing agents, dithiothreitol and ß-mercaptoethanol, reverted the pkBADH inactivation, but reduced glutathione (GSH) was unable to restore the enzyme activity. Molecular docking showed that CTX could enter at the enzyme active site, where its chlorine atoms may interact with the catalytic and the neighboring cysteines. The results obtained show that CTX inactivates the pkBADH due to oxidation of the catalytic cysteine or because it oxidizes catalytic and neighborhood cysteine, forming a disulfide bridge with a concomitant decrease in the activity of the enzyme.

Superior Proton-Transfer Catalytic Promiscuity of Cytochrome†c in Self-Organized Media.

Evolutionarily elderly proteins commonly feature greater catalytic promiscuity. Cytochrome c is among the first set of proteins in evolution to have known prospects in electron transport and peroxidative properties. Here, we report that cyt c is also a proficient proton-transfer catalyst and enhances the Kemp elimination (KE; model reaction to show proton transfer catalytic property) by ∼750-fold on self-organized systems like micelles and vesicles. The self-organized systems mimic the mitochondrial environment in vitro for cyt c. Using an array of biophysical and biochemical mutational assays, both acid-base and redox mechanistic pathways have been explored. The histidine moiety close to hemin group (His18) is mainly responsible for proton abstraction to promote the concerted E2 pathway for KE catalysis when cyt c is in its oxidized form; this has also been confirmed by a H18A mutant of cyt c. However, the redox pathway is predominant under reducing conditions in the presence of dithiothreitol over the pH range 6-7.4. Interestingly, we found almost 750-fold enhanced KE catalysis by cyt c compared to aqueous buffer. Overall, in addition to providing mechanistic insights, the data reveal an unprecedented catalytic property of cyt c that could be of high importance in an evolutionary perspective considering its role in delineating the phylogenic tree and also towards generating programmable designer biocatalysts.

The effects of dithiothreitol (DTT) on fluorescent qPCR dyes.

DNA extractions of semen samples commonly utilize dithiothreitol (DTT) to reduce and disrupt disulfide bonds. Although traditional extraction techniques remove DTT before downstream analyses, the forensic DNA community has recently explored Y-screening, direct amplification, and direct cell lysis assays that omit purification but employ reducing agents to lyse spermatozoa. This study examined the impact of residual DTT on downstream processes involving fluorescent dyes. Quantification using Investigator® Quantiplex HYres revealed a significant increase in the male DNA yield (p = 0.00056) and a >150,000,000-fold increase in the male:human DNA ratio when DTT remained in extracts versus when it was filtered out using a traditional purification method. When DTT was present with Quantifiler™ Trio, the true mean DNA yield for the large autosomal target significantly increased (p = 0.038) and the average reported DNA yields increased 1.1-fold, >9.5-fold, and 1.3-fold for the small autosomal, large autosomal, and male targets, respectively. DTT-spiked DNA standards from both kits were impacted similarly to samples with residual DTT, demonstrating that observed effects were related to DTT and not the extraction method. This study corroborates other reports that DTT adversely affects multiple dyes (e.g., Cy5, Quasar 670, SYBR Green I, TMR, and Mustang Purple® ). Overall, DTT causes inaccurate quantities and, consequently, inaccurate calculated male:female ratios when used in conjunction with these kits. Thus, implementation of newer direct-to-PCR assays incorporating DTT should either be avoided or used only with carefully evaluated, compatible dyes.

Rapid Oxidation Following Photoreduction in the Avian Cryptochrome4 Photocycle.

Avian magnetoreception is assumed to occur in the retina. Although its molecular mechanism is unclear, magnetic field-dependent formation and the stability of radical-containing photointermediate(s) are suggested to play key roles in a hypothesis called the radical pair mechanism. Chicken cryptochrome4 (cCRY4) has been identified as a candidate magnetoreceptive molecule due to its expression in the retina and its ability to form stable flavin neutral radicals (FADH●) upon blue light absorption. Herein, we used millisecond flash photolysis to investigate the cCRY4 photocycle, in both the presence and absence of dithiothreitol (DTT); detecting the anion radical form of FAD (FAD●-) under both conditions. Using spectral data obtained during flash photolysis and UV-visible photospectroscopy, we estimated the absolute absorbance spectra of the photointermediates, thus allowing us to decompose each spectrum into its individual components. Notably, in the absence of DTT, approximately 37% and 63% of FAD●- was oxidized to FADOX and protonated to form FADH●, respectively. Singular value decomposition analysis suggested the presence of two FAD●- molecular species, each of which was destined to be oxidized to FADOX or protonated to FADH●. A tyrosine neutral radical was also detected; however, it likely decayed concomitantly with the oxidation of FAD●-. On the basis of these results, we considered the occurrence of bifurcation prior to FAD●- generation, or during FAD●- oxidization, and discussed the potential role played by the tyrosine radical in the radical pair mechanism.

Cautionary Tale of Using Tris(alkyl)phosphine Reducing Agents with NAD+-Dependent Enzymes.

Protein biochemistry protocols typically include disulfide bond reducing agents to guard against unwanted thiol oxidation and protein aggregation. Commonly used disulfide bond reducing agents include dithiothreitol, ß-mercaptoethanol, glutathione, and the tris(alkyl)phosphine compounds tris(2-carboxyethyl)phosphine (TCEP) and tris(3-hydroxypropyl)phosphine (THPP). While studying the catalytic activity of the NAD(P)H-dependent enzyme Δ1-pyrroline-5-carboxylate reductase, we unexpectedly observed a rapid non-enzymatic chemical reaction between NAD+ and the reducing agents TCEP and THPP. The product of the reaction exhibits a maximum ultraviolet absorbance peak at 334 nm and forms with an apparent association rate constant of 231-491 M-1 s-1. The reaction is reversible, and nuclear magnetic resonance characterization (1H, 13C, and 31P) of the product revealed a covalent adduct between the phosphorus of the tris(alkyl)phosphine reducing agent and the C4 atom of the nicotinamide ring of NAD+. We also report a 1.45 Å resolution crystal structure of short-chain dehydrogenase/reductase with the NADP+-TCEP reaction product bound in the cofactor binding site, which shows that the adduct can potentially inhibit enzymes. These findings serve to caution researchers when using TCEP or THPP in experimental protocols with NAD(P)+. Because NAD(P)+-dependent oxidoreductases are widespread in nature, our results may be broadly relevant.

An Integrated LC-MS/MS Strategy for Quantifying the Oxidative-Redox Metabolome in Multiple Biological Samples.

The cellular redox balance plays a significant role in cell fate decisions and in the regulation of responses to various kinds of stress. In this study, we defined a novel concept of the oxidative-redox metabolome, and established a method for the simultaneous quantification of 23 metabolites involved in the oxidative-redox metabolome, covering NAD+ pathway, FAD pathway, GSSG pathway, and ATP pathway by using the AB SCIEX 5500 QTRAP LC/MS/MS system. Corresponding oxidative-redox metabolomics analysis was performed in plasma of humans, hamsters and mice, and hamsters were demonstrated to display a stronger resemblance than mice to humans. The known reductant dithiothreitol (DTT) and oxidant hydrogen peroxide (H2O2) were selected to treat A549 and HeLa cells to validate the current method, showing that DTT moderately increased while H2O2 greatly decreased most analytes. Antibiotic treatment may disturb the oxidative-redox balance in vivo. By comparing the oxidative-redox metabolome in antibiotic-fed hamsters with that of control hamsters, we demonstrated a substantial metabolic disparity between the two, further verifying the applicability and reliability of our method.

Improved protein purification system based on C-terminal cleavage of Npu DnaE split intein.

A purification system was constructed with the N-segment of the Npu DnaE split intein as an affinity ligand immobilized onto an epoxy-activated medium and the C-segment used as the cleavable tag fusing target protein. The affinity properties of C-tagged proteins adsorbed on IN affinity chromatography medium were studied with GFP as a model target protein. The saturated adsorption capacity and dynamic adsorption capacity reached 51.9-21.0 mg mL-1, respectively. With this system, two model proteins, GFP and alcohol dehydrogenase (ADH), has been successfully taglessly purified with regulation of Zn2+ and DTT. The yield, purification factor and purity of purified tagless GFP reached 39, 11.7 and 97%, respectively; while these values for purified tagless ADH were 38.2, 6.8 and 91%, respectively. These results showed that the system for Npu DnaE split intein-mediated affinity adsorption and in situ cleavage is a potential platform for recombinant protein production.

Expression of recombinant apopholasin using a baculovirus-silkworm multigene expression system and activation via dehydrocoelenterazine.

Pholasin is a photoprotein derived from the glowing bivalve mollusk, Pholas dactylus. Even though the chemical structure of the prosthetic group (chromophore) responsible for the light emission character of the mollusk remains unknown, research has shown that the presence of dehydrocoelenterazine (DCL) increased light emission and that the dithiothreitol adduct of DCL was isolated from Pholasin®. To date, our research has been focused on activating apopholasin, the naturally occurring apoprotein of Pholasin®, using DCL. In the current study, the expression of recombinant apopholasin via a baculovirus-silkworm multigene expression system is reported. Additionally, the purification of apopholasin using a Flag®-affinity column, the activation of apopholasin using DCL, and the initiation of its luminescent character through the addition of a peroxidase-hydrogen peroxide mixture are reported. The peroxidase-H2O2-dependent luminescence was observed from the recombinant apopholasin activated with DCL.

NanoTPOT: Enhanced Sample Preparation for Quantitative Nanoproteomic Analysis.

With the ever-growing need for protein-level understanding in pathological research, proteomics researchers thrive to examine detailed proteome dynamics using crucial, yet often limited, primary and clinical samples. Aside from mass spectrometer instrumentation advancement, a single-tube-based high-throughput sample processing workflow is imperative to ensure sensitive, quantitative, and reproducible protein analysis for these increasingly sophisticated studies. Leveraging the benefits of an acid-cleavable detergent, RapiGest SF Surfactant (Waters Corporation), we developed and optimized a nanoproteomic workflow that we termed Nanogram TMT Processing in One Tube (NanoTPOT). Through the assessment of proteolytic digestion, tandem mass tag (TMT) labeling, online and offline fractionation strategies, our optimized workflow effectively eliminated the need for sample desalting and enabled compatible sample processing for mass spectrometry analysis. We further applied the NanoTPOT workflow to examine cellular response to stress caused by dithiothreitol in HeLa cells, where we identified and quantified 6935 and 5474 proteins in TMT 10-plex experiments with one microgram of lysate protein and 2000 sorted HeLa cells (roughly half microgram lysate protein) in each channel, respectively. Our workflow has been proven to be an effective alternative for current nanoproteomic sample processing to minimize sample loss in biological and clinical applications.

Effects of ionic and reductive atmosphere on the conformational rearrangement in hen egg white lysozyme prior to amyloid formation.

In this study, the combined effects of pH and salt concentration on the aggregation and amyloid formation of a charge-bearing protein (hen egg white lysozyme, HEWL) were investigated, as well as the inhibition of amyloid formation by using dithiothreitol (DTT) as a denaturing agent. Amyloid formation was found to depend on the ion strength and pH of the sample solution. Rather than the total charge, the partial charge of the amyloid related residues contributes to amyloid formation at pH < isoelectric point (pI). On the other hand, at pH> pI HEWL only undergoes alkaline denaturation regardless of the ionic strength. The effect of adding different amounts of DTT at different times on amyloid formation was also investigated. These results suggested that the positions of charges on a protein and the protein secondary structure are critical for protein aggregation and amyloid formation.

Integrated microfluidic chip for on-line proteome analysis with combination of denaturing and rapid digestion of protein.

A microfluidic platform based on the integration of denaturation and online immobilized enzyme reactor (IMER) digestion for protein pretreatment was first developed on a glass chip. The design of three inlet channels and two groups of snake channel in glass chip can allow the protein solution, the reducing reagent and the alkylating agent to be simultaneously injected into the chip channel and ensured the reaction solution on-line efficient mixing and sufficient reacting. By thiol-ene click chemistry, the capillary-based and glass chip-based trypsin IMER on the surface of poly(trimethylolpropane trimethacrylate) monolith were fabricated. The wide range of flow rate tolerance (0.8-5.0 µL/min), and the acceptable reproducibility (RSD% = 3.1%, n = 5) and stability (13.8% decrease of enzyme activity in 2 months) indicated the feasibility of using IMER for online digestion of proteins. Compared with the solution denaturation-offline IMER digestion, the integrated microfluidic platform of chip denaturation-chip IMER and chip denaturation-online IMER have comparable protein identification ability for mouse liver protein with a similar number of protein (798 or 826 vs. 843) and unique peptides (3923 or 4593 vs. 3916). More importantly, the easy and fast digestion of protein samples and possible combination with MS revealed that this microfluidic platform can be a potential method for rapid proteomics analysis.

Structure-function analyses of alkylhydroperoxidase D from Streptococcus pneumoniae reveal an unusual three-cysteine active site architecture.

During aerobic growth, the Gram-positive facultative anaerobe and opportunistic human pathogen Streptococcus pneumoniae generates large amounts of hydrogen peroxide that can accumulate to millimolar concentrations. The mechanism by which this catalase-negative bacterium can withstand endogenous hydrogen peroxide is incompletely understood. The enzyme alkylhydroperoxidase D (AhpD) has been shown to contribute to pneumococcal virulence and oxidative stress responses in vivo We demonstrate here that SpAhpD exhibits weak thiol-dependent peroxidase activity and, unlike the previously reported Mycobacterium tuberculosis AhpC/D system, SpAhpD does not mediate electron transfer to SpAhpC. A 2.3-Å resolution crystal structure revealed several unusual structural features, including a three-cysteine active site architecture that is buried in a deep pocket, in contrast to the two-cysteine active site found in other AhpD enzymes. All single-cysteine SpAhpD variants remained partially active, and LC-MS/MS analyses revealed that the third cysteine, Cys-163, formed disulfide bonds with either of two cysteines in the canonical Cys-78-X-X-Cys-81 motif. We observed that SpAhpD formed a dimeric quaternary structure both in the crystal and in solution, and that the highly conserved Asn-76 of the AhpD core motif is important for SpAhpD folding. In summary, SpAhpD is a weak peroxidase and does not transfer electrons to AhpC, and therefore does not fit existing models of bacterial AhpD antioxidant defense mechanisms. We propose that it is unlikely that SpAhpD removes peroxides either directly or via AhpC, and that SpAhpD cysteine oxidation may act as a redox switch or mediate electron transfer with other thiol proteins.

High-performance sono/nano-catalytic system: Fe3O4@Pd/CaCO3-DTT core/shell nanostructures, a suitable alternative for traditional reducing agents for antibodies.

Herein, a novel heterogeneous nanoscale reducing agent for antibody cleavage, made of iron oxide nanoparticles, silica network, palladium on calcium carbonate (10%), and dithiothreitol (Fe3O4@Pd/CaCO3-DTT), is presented as a substantial alternative for traditional homogeneous analogues. Conventionally, antibody fragmentation is accomplished using reducing agents and proteases that digest or cleave certain portions of the immunoglobulin protein structure to provide active thiol sites for drug tagging aims. Then, dialysis process is needed to separate excess chemical structures and purify the reduced antibody. In this work, we have made an effort to design a suitable heterogeneous tool for protein cleavage and skip the dialysis process for purification of the reduced antibody. In this regard, firstly, various preparation methods including microwave irradiation, reflux and ultrasonication have been precisely compared, and it has been proven that the best result is obtained through 10 min ultrasound (US) irradiation using an US bath with 50 KHz frequency and 200 W L-1 power density. Then, all the necessary structural analyses have been done and thoroughly interpreted for the final product. Afterward, the catalytic performance of Fe3O4@Pd/CaCO3-DTT nanoscale system in the presence of US waves (50 KHz, 200 W) has been monitored using some disulphide derivatives. The NPs could be conveniently separated from the mixture through their substantial paramagnetic property. Thus, dialysis process in which various types of membranes are used is practically jumped after the reduction process. In this work, this is clearly demonstrated that there is a constructive synergistic effect between US waves and prepared Fe3O4@Pd/CaCO3-DTT nanoscale reducing agent. Ultimately, trastuzumab (anti HER-2) antibody has been used to test the performance of the prepared Fe3O4@Pd/CaCO3-DTT NPs in a real protein reduction reaction.

An analytical method to control the surface density and stability of DNA-gold nanoparticles for an optimized biosensor.

DNA functionalized gold nanoparticles (DNA-AuNPs) have shown great potential for biosensing as they combine the excellent optical properties of gold nanoparticles and the molecular recognition function of DNA. Since the DNA density determines the assay performance and the stability of the conjugate, a precise control of the surface density of DNA-AuNP is crucial for an optimized biosensor. Here we report a simple assay for quantifying multiple unlabeled DNAs on AuNPs. The assay relies on potassium cyanide (KCN) to first dissolve the AuNPs, which then releases surface bound DNA for quantification through a double-stranded DNA dye. Using this analytical quantification method, we investigated several strategies to control the surface density of DNA-AuNPs. Besides the precise control of DNA density, the stability of DNA-AuNPs after conjugation is also important in developing a biosensor with optimal performance. Without proper storing conditions, DNA-AuNPs are unstable and aggregate over time. To overcome this problem, we developed a long-term storage solution to ensure the stability and quality of DNA-AuNPs after conjugation which would benefit any DNA-AuNP-based biosensor.