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Nanodrop Applications

 

 

High Throughput Screening (HTS)

Innovadyne enables the HTS market by producing high precision, non-contact dispensing instruments capable of reducing total-assay test volumes by at least an order of magnitude. The Platemaker and Screenmaker’s direct 96-tip dispensing of 100 – 250 nL samples eliminates the need for intermediary dilutions, saving time and reducing consumables. The Nanodrop™ series’ highly precise, fast, non-contact reagent dispensing, not only reduces traditional assay costs tenfold, but also improves signal-to-noise and data quality.

In this application note “Using the Nanodrop to Reduce the Cost of Reagents in a Typical Luminescence Assay”, developed in collaboration with Chiron Corporation (Emeryville, CA), a simple side-by-side experiment was designed to show that the Nanodrop™ liquid handler was able to, not only reduce total-assay volumes five-fold, but also improve results in comparison to data obtained through classical liquid handling.
>>Application Overview
>> Reduction of Volume in a Typical Luminescence Assay

 

PCR

The Nanodrop liquid handlers address your requirements for miniaturizing PCR reactions (20 to 50 fold) without compromising data quality. Precisely delivered low volumes permit direct linear reduction of reaction volumes and reagent use without dilution, therefore, maintaining optimal kinetics and assay performance.
Flexible aspirate and dispense programmability, such as single-tip, random access pipetting, simple reagent additions, complex reagent and template map assemblies are possible and easily programmed.

In this application note “Miniaturizing PCR with the Nanodrop”, a traditional liquid handling robot dispensing 10 µL (total volume) amplification reactions in a 384-well format is compared against a Nanodrop assembling 1.25µL reactions using the same components. The data shows that the Nanodrop delivers comparable results while significantly reducing reagent costs and sample consumption.
>>Application Overview
>>Miniaturizing PCR with the Nanodrop
>>Robotics Worklists for Creating 1536-Well Real Time PCR Assays
>>Analysis on a LightCycler 480® and a Nanodrop ™ Express Low-Volume Dispenser
>>PCR Setup at TARRC

 

Protein Crystallography

The Screenmaker 96+8 and Platemaker units can set up either hanging or sitting drop crystallography plates from pre-prepared or custom screens in less than 10mins. Up to 4 different proteins or protein concentrations can be transferred to any well on a crystal plate.

In the application note “Combinatorial Screening for Protein Crystallization” the Screenmaker 96+8 was used with custom software to automate random combinatorial screening.

Nanodrop ExtY Crystallography Sequence
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>>Application Overview

 

Cell Dispensing

Traditional and flow-through liquid handlers can be destructive to live cells, and suffer contamination and clogging issues. The Nanodrop units have a valve-free fluid path capable of fast dispensing of live cells without stressing. Sensitive cell lines such as MV 411 Leukemia have been handled by the Nanodrop with no loss of viability. Dosage of cell assays can also be performed over a large dynamic volume of 50nl to 500µl.
The easily changed nozzle harness facilitates sterilization.

In the application note “High-Precision Dispensing of Live Cells in a 1536-Well Format”, CHO-K1 cells were dispensed at a density of 1000 cells/well into 1536-well Greiner plates using a Nanodrop II. 2 µL of cells and 2 µL CellTiter-Glo reagent were added to each well. The cell viability of hand-pipetted cells and cells dispensed by the Nanodrop was comparable to within about 5%. Whole-plate Cv's were in the range of 3.5% to 4.5%.
>>Application Overview
>>High-Precision Dispensing of Live Cells in a 1536-Well Format
>>Cell Media Dispensing using the Nanodrop™ CAS System

 

Bead Dispensing


Reliability is the primary challenge for any liquid handler when pipetting a bead suspension. Beads can become lodged in valves, reducing lifetime and increasing instrument downtime. The Nanodrop’s unique syringe and valve-free fluid pathway is ideal, as beads never come into contact with these parts.
Beads are kept in suspension using either a paddle-wheel stirrer or by placing a reagent tray containing beads on an orbital shaker. An optimized protocol ensures that beads are rapidly aspirated and dispensed before they settle in the dispense tubing.

In the application note “Solving the Challenges of Automated SPA YOx Bead Dispensing”, a Nanodrop II, with bead dispensing accessories, was used to dispense 1.25 µL of 80 mg/mL Streptavidin-coated YOx beads into all wells of 12 Greiner 1536-well plates. These beads were then reacted with 3H-biotin and their fluorescence measured. Whole plate Cv’s ran between 3.9% and 5.4% with no overall trends seen in the dispensing. Signal-to-noise values in excess of 10:1 were observed. Also, no tips or solenoids showed signs of clogging during this period, and no degradation of system performance was observed in the course of this study.
>>Application Overview
>>Solving the Challenges of Automated SPA YOx Bead Dispensing
>>High Precision Bead Dispensing using the Nanodrop

 

Assay Development

Low dead volumes and fast, effective washing make Innovadyne liquid handlers cost effective and versatile for the user who requires an instrument that can handle a wide range of media (cells, beads, membranes). All assay development platforms feature the Nanobuilder software that enables a wide range of applications and data manipulation.

In the application note "Developing a Sterile, Reliable Laboratory Setup for Low-Volume Tuberculosis Antibiotic Discovery Assays", a Nanodrop II, with its stage in a Biosafety Level II containment cabinet, was used to test potential antibiotics against proliferating tuberculosis bacteria. The precision and reproducibility of transfers of low volumes (down to 250 nL) of stock compounds into the assay plates without cross-contamination was demonstrated. The unit operated for relatively long periods of time in isolation without maintenance and without loss of precision.
>>Application Overview
>>Developing a Sterile, Reliable Laboratory Setup for Low-Volume Tuberculosis Antibiotic Discovery Assays

 

MALDI Plate Spotting

For protein characterization and quality control of synthetic oligonucleotides, MALDI-TOF has become the method of choice.

To perform MALDI-TOF mass spectrometry, compounds must be spotted on a flat, metal MALDI target plate. Positional accuracy and precise deposition of the spots is critical. Classical liquid handlers using contact methods are prone to failure due to plate and tip irregularities and poor positional accuracy (typically > 100 µm/axis).

Innovadyne’s platforms reliably fulfill critical MALDI spotting requirements with precisely manufactured motion control (<20 µm return to spot accuracy) and high-precision non-contact solenoid dispensing. The aspirate/dispense capabilities of the platform enable rigorous washing to be performed between samples.
The Nanodrop II includes two plate nests for source and MALDI target. Single tip dispensing can be used to conserve precious samples, whereas independent channel spotting enables spotting of unique plate maps.

In the application note "Improved Liquid Handling for MALDI Plate Spotting," MALDI spotting performance for oligo QC was compared between a Nanodrop II and a BioMek FX, under actual manufacturing use. It was determined that the Nanodrop generated higher quality spots (no missed or doughnut-shaped spots) and better spectra using 1/5 the volume of matrix and 1/10 the volume of oligo required by the Biomek. Laser desorption in five different positions was required for each Biomek spot, whereas one position was sufficient for a Nanodrop spot.
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>>Application Note: Improved Liquid Handling for MALDI Plate Spotting
  

 

IC50’s/Serial Dilutions

The Nanodrop’s technology is well suited to the performance of the dilution plates and IC50 screens due to the hybrid syringe/solenoid aspirate and dispense architecture. DMSO is readily handled with the use of double air gaps and an intermediary DMSO solvent plug that acts as a buffer between the DI water-based system fluid and the DMSO sample.


Integration with a Flexus automated liquid handler or other plate feeder, can increase throughput for large numbers of compound screens.
 

In the application note "Developing a Sterile, Reliable Laboratory Setup for Low-Volume Tuberculosis Antibiotic Discovery Assays", the Nanodrop II's performance was tested by dispensing 90% v/v DMSO/water. The average precision (% CV) was 6.19, 2.76 and 3.16 for 250, 500 and 1000nL volumes respectively and the accuracy for all volumes showed a deviation from expected volume transferred of less than 10%.
>>Application Overview
>>Developing a Sterile, Reliable Laboratory Setup for Low-Volume Tuberculosis Antibiotic Discovery Assays

 

Low Density Array Spotting/Medical Diagnostics

The Nanodrop liquid handlers address requirements for low-density array creation by performing precise deposition of multiple reagents, in complex dispense patterns, into microplates or onto substrates. Each model reliably fulfils critical spotting requirements with precisely manufactured motion control (<20 µm return to spot accuracy) and high-precision non-contact solenoid dispensing.

In the application note “Array Dispensing”, the Nanodrop’s ability to dispense a 50nl drop on top of another 50nl drop.
>>Application Overview