The authors acknowledge Liyi Xu for providing MDA reagents and protocols. We also thank David Feldman and Navpreet Ranu for discussions relating to this work. This work was supported in part by a Burroughs Wellcome Career Award at the Scientific Interface to PCB.

Note: Fabricating the microfluidic device is not necessary for this assay, as droplets for this protocol can be formed with existing commercial droplet makers23,29.
1. Make the Droplet-forming Microfluidic Device
<ol>
	<li>Prepare master mold for the channels with the SU-8 Master Fabrication protocol outlined previously31, but with a droplet generator mask pattern32.</li>
	<li>Fabricate devices in PDMS using the techniques of soft lithography32,33.</li>
</ol>
2. Prepare Reaction Mix for Bulk Droplet Readout
 
Note: The protocol can be used to quantify nucleic acids using many types of amplification reactions. As an example, the reagents needed for MDA of several Lambda DNA concentrations are given. Reagent details are listed in the Table of Specific Reagents. The distribution of template within the droplets depends on sufficient mixing of the sample.
<ol>
	<li>Obtain or Purify Phi29 DNA polymerase.
	<ol>
		<li>Purify Phi29 as previously described7, or purchase from supplier. The Phi29 used for the shown experiments was purified.</li>
	</ol>
	</li>
	<li>Prepare 10 ml&#160;of Denaturation Buffer consisting of 65 mM KOH, 1.65 mM EDTA, and 14 mM DTT.</li>
	<li>Prepare 10 ml&#160;of Neutralization Buffer consisting of 65 mM HCl, 0.21 M Tris-Cl pH 7.0, and 9 mM Tris-Cl pH 8.0.</li>
	<li>Prepare two standards, one no template control (NTC) such as nuclease-free water, and one high template concentration (around 4 pg/&#181;l&#160;Lambda DNA). Denature 3.3 &#181;l&#160;of each standard with 3.3 &#181;l&#160;of Denaturation Buffer in a qPCR tube. Incubate at RT for 3 min. Quench each with 3.3 &#181;L of Neutralization Buffer.</li>
	<li>Denature 3.3 &#181;l&#160;of the template of interest with 3.3 &#181;l&#160;of Denaturation Buffer in a qPCR tube. Incubate at RT for 3 min. Quench with 3.3 &#181;l&#160;of Neutralization Buffer.</li>
	<li>Prepare 11 &#181;l&#160;of master mixture per sample on ice. The 2x MDA reaction master mixture consists of 2x double-stranded DNA (dsDNA) binding dye, 2x qPCR reference dye, 50 &#181;M randomized oligo, 2 mg/ml&#160;BSA, 2x Phi29 DNA Polymerase Reaction Buffer, 4.8 mM dNTPs, nuclease-free water, and 40 &#181;g/ml&#160;Phi29 DNA polymerase. Add Phi29 DNA polymerase last to ensure the polymerase does not encounter pH levels much higher or lower than 7.5.Mix well.</li>
	<li>Optional: For fewer false positives, expose master mix with UV light prior to forming droplets34.
	<ol>
		<li>Prepare 10 &#181;l&#160;of pre-mixture per sample in a 0.5 ml&#160;or 1.5 ml&#160;clear tube on ice. The pre-mix consists of 55 &#181;M randomized oligo, 2.2 mg/ml&#160;BSA, 1.1x Phi29 DNA Polymerase Reaction Buffer, 5.3 mM dNTPs, and nuclease-free water.</li>
		<li>Place the tube in water on ice as described34 and expose to UV light (254 nm) to an accumulated dose of 5.7 J/cm2.</li>
		<li>Add dsDNA-binding dye to 1x, reference dye to 1x, and Phi29 to 40 &#181;g/ml&#160;in the pre-mixture. Mix well.</li>
	</ol>
	</li>
	<li>Combine 10 &#181;l&#160;of denatured template or standard and 10 &#181;l&#160;of master mixture. Mix well.</li>
</ol>
3. Droplet Formation
Note: Droplets can be very sensitive to static electricity and shear stress. Remove clothes that may cause static electricity, and ground yourself before forming droplets. Handle tubes of emulsion from the top of the tube, as far from the emulsion as possible. Pipette emulsions very slowly, preferably with a wide bore pipet tip. When dispensing from a pipette tip, watch the emulsion on the side of the tip to determine pipetting speed.
<ol>
	<li>Form droplets. For the experiments shown, the microfluidic device has an oil inlet and two aqueous inlets with a flow-focusing junction for generating droplets. Use two syringe pumps to control the flow rates of 55 &#181;l&#160;of oil with surfactant and a 20 &#181;l&#160;of reaction mixture through the microfluidic chip to generate 20,000 1 nl droplets.</li>
	<li>Note: It is possible to produce droplets with many types of oil with surfactant, but the composition will greatly affect droplet stability at high temperatures and over time. One possible combination is fluorinated oil HFE 7500 with an anionic surfactant19,35.</li>
	<li>Produce droplets at any size with any method13,36, but the size variability in the droplet population will affect the bulk fluorescence, and therefore the accuracy of the assay. For the experiments shown, droplets were monodisperse with a volume of 1 nl.</li>
	<li>Collect all of the droplets and oil into PCR tubes. For each sample, aliquot 30 &#181;l&#160;of oil into fresh PCR tubes with optical caps, and transfer 20 &#181;l&#160;of droplets on top of the oil. The consistent volumes ensure the assay is as accurate as possible.</li>
	<li>Close tube caps tightly, as loose caps will allow the oil to evaporate.</li>
</ol>
4. Isothermal Amplification
<ol>
	<li>Using a PCR thermocycler, qPCR thermocycler, or hot plate, incubate the samples at 30 &#176;C for 7 hr, and inactivate for 1 min at 75 &#176;C. The tubes of droplets may be left in a fridge covered with foil for a few hours at this point.</li>
</ol>
5. Data Acquisition and Analysis
<ol>
	<li>Immediately following reaction inactivation, measure dye fluorescence levels for all samples using the qPCR thermocycler. Optimal filter settings will depend on dye excitation and emission spectra. For this example, use the 492 nm-516 nm filter set for the dsDNA-binding dye, and the 585 nm-610 nm filter set for the reference dye. Other fluorescent measurement techniques may be used to quantify the fluorescence.</li>
	<li>For each sample, divide the fluorescence intensity of the dsDNA-binding dye by the fluorescence intensity of the reference dye. Subtract the background fluorescence, or the normalized fluorescence of the no template control, from all samples.</li>
	<li>Create a linear standard curve using the corrected fluorescence measurements from the standards. The NTC standard represents the fluorescence for a sample with 0% fluorescent droplets (&#8220;all negative&#8221;), and the high template concentration fluorescence measurement is the expected fluorescence for a sample with 100% fluorescent droplets (&#8220;all positive&#8221;). Using the corresponding standard curve, predict the intermediate ratios of positive and negative droplets based on their bulk fluorescence.</li>
</ol>
6. Producing Droplets for Proof-of-Principle Measurements
<ol>
	<li>Make fluorescent (positive) droplets: Prepare a PCR reaction mixture consisting of 0.1 ng Lambda DNA, 1x dsDNA-binding dye, 1x reference dye, 1.5 units Taq DNA polymerase, 10 mM Tris-HCl, 50mM KCl, 1.5 mM MgCl2, 0.2 mM dNTP, and 0.5 &#181;M primers. Thermocycle the mixture 30 times (95 &#176;C for 20 sec, 55 &#176;C for 20 sec, 72 &#176;C for 1 min), then form droplets as described above.</li>
	<li>Make non-fluorescent (negative) droplets: Prepare a PCR reaction mixture consisting of 1x dsDNA-binding dye, 1x reference dye, 1.5 units Taq DNA polymerase, 10 mM Tris-HCl, 50mM KCl, 1.5 mM MgCl2, 0.2 mM dNTP, and 0.5 &#181;M primers. Thermocycle the mixture 30 times (95 &#176;C for 20 sec, 55 &#176;C for 20 sec, 72 &#176;C for 1 min), then form droplets.</li>
	<li>Forming pre-mixed droplet ratios
	<ol>
		<li>Distribute 20 &#181;l&#160;of fluorinated oil into qPCR tubes, cover with an optical cap to prevent evaporation.</li>
		<li>Gently pipette 10 &#181;l&#160;of well-mixed droplets in desired positive:negative ratios on top of the oil. In the results shown, positive:negative droplet ratios were 1 (all positive), 0.8, 0.5, 0.2, 0.1, 0.01, 0.001, 0.0001, and 0 (all negative).</li>
	</ol>
	</li>
	<li>Measure dye fluorescence levels for all samples using the qPCR thermocycler. For this protocol, use the 492 nm-516 nm filter set for the dsDNA-binding dye, and the 585 nm-610 nm filter set for the reference dye.
	<ol>
		<li>Normalize dsDNA binding dye fluorescence using reference dye fluorescence. Further normalize by the fluorescence of the &#8220;all positive&#8221; sample.</li>
	</ol>
	</li>
	<li>Create a linear standard curve using the normalized fluorescence measurements from the &#8220;all positive&#8221; and &#8220;all negative&#8221; samples. Using the corresponding standard curve, predict the intermediate ratios of positive and negative droplets based on their bulk fluorescence.</li>
	<li>Repeat the experiment for each ratio (n = 3) with independent droplet formation and mixing for each replicate.</li>
</ol>
7. Proof-of-Principle MDA Experiment
<ol>
	<li>Measure the concentration of Lambda DNA stock solution with a spectrophotometer.
	<ol>
		<li>Calculate the template concentration necessary to average 10 template molecules per droplet. For this protocol, assume droplet volumes are 1 nl&#160;and 1 ng of Lambda DNA contains approximately 1.9 x 107 copies. Therefore, 10 templates per droplet will be 10 copies per nl, or 526 fg Lambda DNA per &#181;l. The template will be diluted ~6x when droplets are formed, therefore the initial highest template concentration will be 3.2 pg/&#181;l.</li>
	</ol>
	</li>
	<li>Serially dilute the Lambda DNA to 3.2 pg/&#181;l&#160;with Denaturation Buffer and equal volume Neutralization Buffer. For a dilution factor of 0.1, combine 10 &#181;l&#160;sample with 45 &#181;l&#160;of Denaturation Buffer and incubate at RT for 3 min. Add 45 lL of Neutralization Buffer to quench.</li>
	<li>Further dilute the sample as described in step 7.2 to make the rest of the samples for the experiment. The initial template concentrations in the reactions shown were 3.2 pg, 320 fg, 160 fg, 32 fg, 16 fg, 3.2 fg, and 1.6 fg per microliter. 
	Note: The final template concentrations after mastermix addition were 526 fg, 52.6 fg, 26.3 fg, 5.26 fg, 2.63 fg, 526 ag, and 263 ag per microliter. 10, 1, 0.5, 0.1, 0.05, 0.01, and 0.005 expected Lambda copies per droplet, respectively.</li>
	<li>Generate and analyze droplets from each sample as described in steps 2.5-5.3.</li>
	<li>Acquire the fluorescence images shown (Figure 2,3) using a digital camera mounted to an epi-fluorescence microscope with a 10x objective at RT. Acquire twelve fields of view for each sample. Correct fluorescence images by a background image obtained with a fluorescent slide.</li>
	<li>Use a contained chamber for imaging37 as the emulsion oil will evaporate quickly.</li>
	<li>Analyze individual droplet intensities using an ImageJ macro (Supplemental code file).
	<ol>
		<li>Choose a threshold fluorescence intensity that best separates non-fluorescent droplets in the NTC images from the fluorescent droplets in the high template concentration images. For each unknown sample, calculate the fraction of droplets with a fluorescence intensity above the threshold.</li>
	</ol>
	</li>
</ol>
8. PCR and MDA bulk reactions
<ol>
	<li>Prepare PCR reaction.
	<ol>
		<li>Serially dilute template DNA with a dilution factor of 0.1. For each dilution, combine 10 &#181;l&#160;of template with 45 &#181;l&#160;of Denaturation Buffer and incubate at RT for 3 min. Combine the dilution with 45 &#181;l&#160;of Neutralization Buffer.</li>
		<li>Prepare 20 &#181;l&#160;of PCR mastermix per sample. The 1.1x PCR reaction master mixture consists of 60 units/&#181;l Taq DNA polymerase, 11 mM Tris-HCl, 55mM KCl, 1.65 mM MgCl2, 0.22 mM dNTP, 1.1x dsDNA-binding dye, 1.1x reference dye, and 550 nM each primer.</li>
		<li>Combine 2 &#181;l&#160;of diluted template and 20 &#181;l&#160;of mastermix. 
		Note: The final template concentrations in the PCR reactions shown were 50 pg, 5 pg, 500 fg, 50 fg, 5 fg, 500 ag, and 0 g Lambda DNA per microliter, and were performed in triplicate.</li>
		<li>Thermocycle PCR reaction in qPCR machine with the following program. Run 40 cycles of 95 &#176;C for 30 sec, 57 &#176;C for 20 sec, 72 &#176;C for 30 sec before 2 min at 72 &#176;C for 2 min and holding at 4 &#176;C.</li>
		<li>Normalize dsDNA binding dye fluorescence using reference dye fluorescence prior to further analysis.</li>
	</ol>
	</li>
	<li>Prepare MDA reaction.
	<ol>
		<li>Dilute samples as described in step 8.1.1.</li>
		<li>Prepare 11 &#181;l&#160;of master mixture per sample on ice. The 2x MDA reaction master mixture consists of 2x dsDNA-binding dye, 2x reference dye, 50 &#181;M randomized oligo, 2 mg/ml&#160;BSA, 2x phi29 DNA Polymerase Reaction Buffer, 4.8 mM dNTPs, nuclease-free water, and 40 &#181;g/ml&#160;Phi29 DNA Polymerase.</li>
		<li>Add the Phi29 DNA polymerase to 40 &#181;g/ml&#160;last to ensure the polymerase does not encounter pH levels much higher or lower than 7.5. Mix well.</li>
		<li>Denature 3.3 &#181;L of diluted template with 3.3 &#181;l&#160;of Denaturation Buffer in a qPCR tube. Incubate at RT for 3 min. Add 3.3 &#181;l&#160;of Neutralization Buffer.</li>
		<li>Combine 10 &#181;L of denatured template and 10 &#181;l&#160;of master mixture. Mix well.</li>
		<li>Run MDA reaction in qPCR machine with the following program.</li>
		<li>Hold at 30 &#176;C for 4 hr, measure fluorescence every 7.5 min.</li>
		<li>Inactivate at 75 &#176;C for 1 min.</li>
		<li>Normalize dsDNA binding dye fluorescence using reference dye fluorescence. Further normalize by the maximum fluorescence for each sample.</li>
	</ol>
	</li>
</ol>

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S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monodisperse+double+emulsions+generated+from+a+microcapillary+device.">Monodisperse double emulsions generated from a microcapillary device.</a> Science. 308 (5721), 537-541 (2005).</li><li>Eastburn, D. J., Sciambi, A., Abate, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Picoinjection+enables+digital+detection+of+RNA+with+droplet+rt-PCR.">Picoinjection enables digital detection of RNA with droplet rt-PCR.</a> PLoS One. 8 (4), e62961 (2013).</li><li>Dube, S., Qin, J., Ramakrishnan, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mathematical+analysis+of+copy+number+variation+in+a+DNA+sample+using+digital+PCR+on+a+nanofluidic+device.">Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device.</a> PLoS One. 3 (8), e2876 (2008).</li><li>Shen, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiplexed+quantification+of+nucleic+acids+with+large+dynamic+range+using+multivolume+digital+RT-PCR+on+a+rotational+SlipChip+tested+with+HIV+and+hepatitis+C+viral+load.">Multiplexed quantification of nucleic acids with large dynamic range using multivolume digital RT-PCR on a rotational SlipChip tested with HIV and hepatitis C viral load.</a> J Am. Chem. Soc. 133 (44), 17705-17712 (2011).</li><li>Link, D. R., Anna, S. L., Weitz, D. A., Stone, H. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Geometrically+mediated+breakup+of+drops+in+microfluidic+devices.">Geometrically mediated breakup of drops in microfluidic devices.</a> Phys. Rev. Lett. 92 (5), 054503 (2004).</li><li>Nisisako, T., Torii, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microfluidic+large-scale+integration+on+a+chip+for+mass+production+of+monodisperse+droplets+and+particles.">Microfluidic large-scale integration on a chip for mass production of monodisperse droplets and particles.</a> Lab Chip. 8 (2), 287-293 (2008).</li><li>Romanowsky, M. B., Abate, A. R., Rotem, A., Holtze, C., Weitz, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High+throughput+production+of+single+core+double+emulsions+in+a+parallelized+microfluidic+device.">High throughput production of single core double emulsions in a parallelized microfluidic device.</a> Lab Chip. 12 (4), 802-807 (2012).</li></ol>

The Broad Institute may move to file a patent application that includes aspects of this work.

Digital assays are powerful methods that enable detection of rare cells and counting of individual of nucleic acid molecules. However, digital assays are still not routinely applied in analytical laboratories, due in part to the cost of specialized equipment associated with commercially available methods. Here we describe an endpoint digital assay for quantifying nucleic acids with a simplified analog readout using a standard real-time quantitative PCR machine. This method is quick to set-up, and readout is much simpler ...

Digital assays for nucleic acid quantification (digital PCR)1-4 and base order (sequencing) are strongly impacting the life sciences and medicine. Digital assays provide quantification of molecular counts on an absolute scale (not relative to a control), providing high sensitivity, enabling facile comparisons across experiments, and crucially, enabling the construction of large databases containing comparable data5 (Table 1).
Over the last 15 years, whole genome amplification (WGA) emerged alongside PCR as a general tool for nucleic acid amplification. Like PCR, WGA is useful for analytical and preparative applications by amplifying minute sample elements up to a level that can be easily detected or used for subsequent analyses like base sequencing. Unlike PCR, WGA is not specific to a particular DNA locus, rather allowing amplification of all sequences in the sample, including unknown sequences. This fundamental difference between PCR and WGA makes the methods complementary to one another and gives rise to different challenges in their application.
The high yield of WGA reactions6 enables routine amplification of genomic DNA from single molecules7, single cells8 and other low-biomass samples9 for quantification or further analysis. The major challenges associated with WGA chemistry are its extreme sensitivity to contaminants and the uneven amplification across individual template molecules6. However, WGA is gaining popularity as single-cell sequencing has emerged as the &#8220;killer application&#8221; of WGA technology10, and template quantification by WGA is important in&#160;many fields of application7.
Instrumentation for digital nucleic acid quantification has been previously described in a variety of valved and valveless microfluidic formats11-14, including droplet-based assays15,16 (Table 2). However, commercial microfluidic systems for digital analysis require specialized equipment for reaction setup and product detection17. Custom valved microfluidics are flexible, but require precision microfabrication and pneumatic control systems18. While it is relatively simple to make monodisperse micro-droplets for emulsion-based digital assays19,20, digital readout is technically burdensome, requiring either large-scale wide-field imaging (similar to popular next-generation sequencing technologies)21,22 or high-speed flow-based droplet detection23-25. Ideally, a digital assay would be simple from set-up to readout, reducing the need for complex instrumentation and allowing large numbers of samples to be read out quickly. Here we describe a simplified method for readout of digital droplet assays that uses a conventional real-time PCR instrument to measure bulk fluorescence of droplet-based digital assays.
While the new approach can be applied to digital PCR assays, it is particularly advantageous for digital WGA assays for which analog real-time amplification assays (that give excellent results for PCR) are problematic. WGA is commonly applied to samples with template molecules that are heterogeneous in sequence, length, and base content. These different template molecules are amplified at different rates6, necessitating the use of a reference (&#8220;standard&#8221;) sample with matching characteristics. Often, no such standard is available, or the characteristics of the incoming samples are unknown. The heterogeneity of the input material and length-dependent property of WGA chemistries26 also complicate the interpretation of results by creating ambiguity in what is being quantified--the input mass, input number of molecules, a combination of the two, or neither. Finally, the sequence-non-specificity renders quantitative multiple displacement amplification (MDA) more sensitive to contamination than quantitative PCR since contaminant molecules of any sequence have a potential to interfere. Microfluidic digital assays address contamination by segregating template molecules and reducing reaction volumes such that fewer contaminants are sampled.
Here we use a popular isothermal WGA method, MDA27. Of note, several other WGA chemistries including PicoPlex and MALBAC28 depend crucially on initial isothermal strand displacement steps. Isothermal steps exacerbate the challenge of applying analog real-time assays for quantitative WGA. WGA can neither be entirely prevented during setup, leading to unwanted variable pre-amplification, nor discretized (&#8220;cycled&#8221;) in a way where replication of heterogeneous molecules can be driven to completion and stopped prior to the next cycle like PCR11 (Figure 1). A digital assay format for WGA accomodates typical&#160;reaction setup procedures due to the segregation of each molecule&#160;for enumeration at the assay endpoint (so pre-amplification does not affect the results) original readout&#160;means accuracy would be largely independent of variation in amplification efficiency.
The assay depends on droplets produced in oil with uniform volumes, as the signal level per droplet at the assay endpoint will depend on the droplet volume, and we do not want the consistency of results to depend on averaging across a distribution of droplet sizes. Making monodisperse droplets is now a standard procedure (about 3,500 monodisperse droplet papers have been published since 2013), but requires microfluidic instrumentation25. In fact, more than six companies have developed independent commercial products that rely on production of such droplets, and droplet-making microfluidic chips are commercially available23,29. For this study, we used custom microfluidic devices produced in-house (see Protocol). Syringe pumps to drive flow through the devices are also commercially available, but alternatively, can be substituted with a single disposable syringe for vacuum-driven flow to reduce costs30.

<table><tbody><tr><td>Evagreen Dye</td><td>Biotium</td><td>31000</td><td></td></tr><tr><td>Bovine serum albumin</td><td>New England Biotechnologies</td><td>B9000S</td><td></td></tr><tr><td>Phi29 DNA Polymerase Reaction Buffer</td><td>New England Biotechnologies</td><td>B0269S</td><td>Vortex periodically until aggregate dissolves</td></tr><tr><td>Lambda DNA</td><td>New England Biotechnologies</td><td>N3011S</td><td>Heated to 50 &lt;sup&gt;o&lt;/sup&gt;C and quenched on ice prior to dilution</td></tr><tr><td>Randomized MDA oligos</td><td>Integrated DNA Technologies</td><td></td><td>5&#039;-NNNNN*N-3&#039;</td></tr><tr><td>PCR primers</td><td>Integrated DNA Technologies</td><td></td><td>5&amp;rsquo;-CGGCAAACGGGAATGAAACGCC-3&amp;rsquo; and 5&amp;rsquo;-TGCGGCAAAGACAGCAACGG-3&amp;rsquo;</td></tr><tr><td>UltraPure Nuclease-free water</td><td>Life Technologies</td><td>10977-015</td><td>UV-treated for 30 min in Stratalinker 2400 before use (optional)</td></tr><tr><td>ROX reference dye</td><td>Life Technologies</td><td>12223-012</td><td></td></tr><tr><td>PCR optical strip caps</td><td>Life Technologies</td><td>4323032</td><td></td></tr><tr><td>PCR tubes</td><td>Agilent Technologies</td><td>401428</td><td></td></tr><tr><td>dNTP (25 micromolar each)</td><td>Agilent Technologies</td><td>200415</td><td></td></tr><tr><td>Thermocycler - Mx3000P qPCR system</td><td>Agilent Technologies</td><td>401403</td><td></td></tr><tr><td>Barrier pipette tips</td><td>VWR</td><td>89003-046</td><td></td></tr><tr><td>Bio-rad oil for evagreen</td><td>Bio-rad</td><td>186-4005</td><td></td></tr><tr><td>JumpStart Taq ReadyMix</td><td>Sigma-Aldrich</td><td>P2893-100RXN</td><td></td></tr></tbody></table>

simple bulk readout of digital nucleic acid quantification assays

Digital assays are powerful methods that enable detection of rare cells and counting of individual nucleic acid molecules. However, digital assays are still not routinely applied, due to the cost and specific equipment associated with commercially available methods. Here we present a simplified method for readout of digital droplet assays using a conventional real-time PCR instrument to measure bulk fluorescence of droplet-based digital assays.
We characterize the performance of the bulk readout assay using synthetic droplet mixtures and a droplet digital multiple displacement amplification (MDA) assay. Quantitative MDA particularly benefits from a digital reaction format, but our new method&#160;applies to any digital assay. For established digital assay protocols such as digital PCR, this method serves to speed up and simplify assay readout.
Our bulk readout methodology brings the advantages of partitioned assays without the need for specialized readout instrumentation. The principal limitations of the bulk readout methodology are reduced dynamic range compared with droplet-counting platforms and the need for a standard sample, although the requirements for this standard are less demanding than for a conventional real-time experiment. Quantitative whole genome amplification (WGA) is used to test for contaminants in WGA reactions and is the most sensitive way to detect the presence of DNA fragments with unknown sequences, giving the method great promise in diverse application areas including pharmaceutical quality control and astrobiology.

While conventional bulk/real-time readouts can be used for both quantitative PCR and quantitative WGA assays (Figure 1), digital quantitative assays provide advantages (Table 1). In the method described, we read out digital assays in micro-droplet format with a simple bulk endpoint measurement (Figure 2). While this method is broadly applicable, we focus on quantitative WGA (MDA) because this method presents special challenges for conventional real-time assays.
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Watch this Scientific Journal Video about Simple Bulk Readout of Digital Nucleic Acid Quantification Assays at JoVE.com

Simple Bulk Readout of Digital Nucleic Acid Quantification Assays

We describe an endpoint digital assay for quantifying nucleic acids with a simplified (analog) readout. We measure bulk fluorescence of droplet-based digital assays using a standard qPCR machine rather than specialized instrumentation and confirm our results by microscopy.

Digital assays are powerful methods that enable detection of rare cells and counting of individual nucleic acid molecules. However, digital assays are ...

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Biology

8.3K Views.  Broad Institute. We describe an endpoint digital assay for quantifying nucleic acids with a simplified (analog) readout. We measure bulk fluorescence of droplet-based digital assays using a standard qPCR machine rather than specialized instrumentation and confirm our results by microscopy. 

Video: Simple Bulk Readout of Digital Nucleic Acid Quantification Assays

Rapid Colorimetric Assays to Qualitatively Distinguish RNA and DNA in Biomolecular Samples

Biochemical experimentation generally requires accurate knowledge, at an early stage, of the nucleic acid, protein, and other biomolecular components in potentially heterogeneous specimens. Nucleic acids can be detected via several established approaches, including analytical methods that are spectrophotometric (e.g., A260), fluorometric (e.g., binding of fluorescent dyes), or colorimetric (nucleoside-specific chromogenic chemical reactions).1 Though it cannot readily distinguish RNA from DNA, the A260/A280 ratio is commonly employed, as it offers a simple and rapid2 assessment of the relative content of nucleic acid, which absorbs predominantly near 260 nm and protein, which absorbs primarily near 280 nm. Ratios &lt; 0.8 are taken as indicative of 'pure' protein specimens, while pure nucleic acid (NA) is characterized by ratios &gt; 1.53.
However, there are scenarios in which the protein/NA content cannot be as clearly or reliably inferred from simple uv-vis spectrophotometric measurements. For instance, (i) samples may contain one or more proteins which are relatively devoid of the aromatic amino acids responsible for absorption at &asymp;280 nm (Trp, Tyr, Phe), as is the case with some small RNA-binding proteins, and (ii) samples can exhibit intermediate A260/A280 ratios (~0.8 &lt; ~1.5), where the protein/NA content is far less clear and may even reflect some high-affinity association between the protein and NA components. For such scenarios, we describe herein a suite of colorimetric assays to rapidly distinguish RNA, DNA, and reducing sugars in a potentially mixed sample of biomolecules. The methods rely on the differential sensitivity of pentoses and other carbohydrates to Benedict's, Bial's (orcinol), and Dische's (diphenylamine) reagents; the streamlined protocols can be completed in a matter of minutes, without any additional steps of having to isolate the components. The assays can be performed in parallel to differentiate between RNA and DNA, as well as indicate the presence of free reducing sugars such as glucose, fructose, and ribose (Figure 1).

A suite of colorimetric assays is described for rapidly distinguishing protein, RNA, DNA, and reducing sugars in potentially heterogeneous biomolecular samples.

Biochemical experimentation generally requires accurate knowledge, at an early stage, of the nucleic acid, protein, and other biomolecular components in ...

Chemistry

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

The Full-Length Individual Proviral Sequencing (FLIPS) assay is an efficient and high-throughput method designed to amplify and sequence single, near full-length (intact and defective), HIV-1 proviruses. FLIPS allows determination of the genetic composition of integrated HIV-1 within a cell population. Through identifying defects within HIV-1 proviral sequences that arise during reverse transcription, such as large internal deletions, deleterious stop codons/hypermutation, frameshift mutations, and mutations/deletions in cis acting elements required for virion maturation, FLIPS can identify integrated proviruses incapable of replication. The FLIPS assay can be utilized to identify HIV-1 proviruses that lack these defects and are&#160;therefore potentially replication-competent. The FLIPS protocol involves: lysis of HIV-1 infected cells, nested PCR of near full-length HIV-1 proviruses (using primers targeted to the HIV-1 5&#39; and 3&#39; LTR), DNA purification and quantification, library preparation for Next-generation Sequencing (NGS), NGS, de novo assembly of proviral contigs, and a simple process of elimination for identifying replication-competent proviruses. FLIPS provides advantages over traditional methods designed to sequence integrated HIV-1 proviruses, such as single-proviral sequencing. FLIPS amplifies and sequences near full-length proviruses enabling replication competency to be determined, and also uses fewer amplification primers, preventing the consequences of primer mismatches. FLIPS is a useful tool for understanding the genetic landscape of integrated HIV-1 proviruses, especially within the latent reservoir, however, its utilization can extend to any application in which the genetic composition of integrated HIV-1 is required.

Full-length individual proviral sequencing (FLIPS) provides an efficient and high-throughput method for the amplification and sequencing of single, near full-length (intact and defective) HIV-1 proviruses and allows for determination of their potential replication-competency. FLIPS overcomes limitations of previous assays designed to sequence the latent HIV-1 reservoir.

The Full-Length Individual Proviral Sequencing (FLIPS) assay is an efficient and high-throughput method designed to amplify and sequence single, near ...

Genetics

Circulating MicroRNA Quantification Using DNA-binding Dye Chemistry and Droplet Digital PCR

Circulating (of cell-free) microRNAs (miRNAs) are released from cells into the blood stream. The amount of specific microRNAs in the circulation has been linked to a disease state and has the potential to be used as disease biomarker. A sensitive and accurate method for circulating microRNA quantification using a dye-based chemistry and droplet digital PCR technology has been recently developed. Specifically, using Locked Nucleic Acid (LNA)-based miRNA-specific primers with a green fluorescent DNA-binding dye in a compatible droplet digital PCR system it is possible to obtain the absolute quantification of specific miRNAs. Here, we describe how performing this technique to assess miRNA amount in biological fluids, such as plasma and serum, is both feasible and effective.

A sensitive and accurate method for cell-free microRNAs quantification using a dye-based chemistry and droplet digital PCR technology is described.

Circulating (of cell-free) microRNAs (miRNAs) are released from cells into the blood stream. The amount of specific microRNAs in the circulation has been ...

Bioengineering

Quantification of dsDNA using the Hitachi F-7000 Fluorescence Spectrophotometer and PicoGreen Dye

Quantification of DNA, especially in small concentrations, is an important task with a wide range of biological applications including standard molecular biology assays such as synthesis and purification of DNA, diagnostic applications such as quantification of DNA amplification products, and detection of DNA molecules in drug preparations. During this video we will demonstrate the capability of the Hitachi F-7000 Fluorescence Spectrophotometer equipped with a Micro Plate Reader accessory to perform dsDNA quantification using Molecular Probes Quant-it PicoGreen dye reagent kit.
The F-7000 Fluorescence Spectrophotometer offers high sensitivity and high speed measurements. It is a highly flexible system capable of measuring fluorescence, luminescence, and phosphorescence. Several measuring modes are available, including wavelength scan, time scan, photometry and 3-D scan measurement. The spectrophotometer has sensitivity in the range of 50 picomoles of fluorescein when using a 300 &#956;L sample volume in the microplate, and is capable of measuring scan speeds of 60,000 nm/minute. It also has a wide dynamic range of up to 5 orders of magnitude which allows for the use of calibration curves over a wide range of concentrations. The optical system uses all reflective optics for maximum energy and sensitivity. The standard wavelength range is 200 to 750 nm, and can be extended to 900 nm when using one of the optional near infrared photomultipliers. The system allows optional temperature control for the plate reader from 5 to 60 degrees Celsius using an optional external temperature controlled liquid circulator. The microplate reader allows for the use of 96 well microplates, and the measuring speed for 96 wells is less than 60 seconds when using the kinetics mode.
Software controls for the F-7000 and Microplate Reader are also highly flexible. Samples may be set in either column or row formats, and any combination of wells may be chosen for sample measurements. This allows for optimal utilization of the microplate. Additionally, the software allows importing micro plate sample configurations created in Excel and saved in comma separated values, or "csv" format. Microplate measuring configurations can be saved and recalled by the software for convenience and increased productivity. Data results can be output to a standard report, to Excel, or to an optional Report Generator Program.

Demonstration of quantification of dsDNA using Molecular Probes PicoGreen dye and Hitachi F-7000 Fluorescence Spectrophotometer equipped with a microplate reader accessory.

Quantification of DNA, especially in small concentrations, is an important task with a wide range of biological applications including standard molecular ...

NanoDrop Microvolume Quantitation of Nucleic Acids

Biomolecular assays are continually being developed that use progressively smaller amounts of material, often precluding the use of conventional cuvette-based instruments for nucleic acid quantitation for those that can perform microvolume quantitation.
The NanoDrop microvolume sample retention system (Thermo Scientific NanoDrop Products) functions by combining fiber optic technology and natural surface tension properties to capture and retain minute amounts of sample independent of traditional containment apparatus such as cuvettes or capillaries. Furthermore, the system employs shorter path lengths, which result in a broad range of nucleic acid concentration measurements, essentially eliminating the need to perform dilutions. Reducing the volume of sample required for spectroscopic analysis also facilitates the inclusion of additional quality control steps throughout many molecular workflows, increasing efficiency and ultimately leading to greater confidence in downstream results.
The need for high-sensitivity fluorescent analysis of limited mass has also emerged with recent experimental advances. Using the same microvolume sample retention technology, fluorescent measurements may be performed with 2 &mu;L of material, allowing fluorescent assays volume requirements to be significantly reduced. Such microreactions of 10 &mu;L or less are now possible using a dedicated microvolume fluorospectrometer.
Two microvolume nucleic acid quantitation protocols will be demonstrated that use integrated sample retention systems as practical alternatives to traditional cuvette-based protocols. First, a direct A260 absorbance method using a microvolume spectrophotometer is described. This is followed by a demonstration of a fluorescence-based method that enables reduced-volume fluorescence reactions with a microvolume fluorospectrometer. These novel techniques enable the assessment of nucleic acid concentrations ranging from 1 pg/ &mu;L to 15,000 ng/ &mu;L with minimal consumption of sample.

The use of NanoDrop microvolume systems as practical and efficient alternatives to traditional nucleic acid quantitation methodology is described through the demonstration of two microvolume nucleic acid quantitation protocols.

Biomolecular assays are continually being developed that use progressively smaller amounts of material, often precluding the use of conventional ...

Standardized Protocol for Viral Genome Quantification Using Digital Droplet PCR

Quantification of Adeno-Associated Viral Genomes in Purified Vector Samples by Digital Droplet Polymerase Chain Reaction

Adeno-associated virus (AAV) is a non-pathogenic virus used as a delivery vehicle to transfer therapeutic genes into patients. Accurate quantification of AAV genome copy number in vector preparations is essential for bioprocess optimization and dosage calculation in both preclinical and clinical studies of AAV-based gene therapy products. Currently, a consensus protocol for AAV viral genome titration is lacking. Here, we present a digital droplet PCR (dd_PCR) protocol for the quantification of viral genomes in purified vector samples. Samples are treated with DNase I to eliminate unpackaged contaminant DNA. DNase-treated samples are then mixed with an appropriate primer-probe set (designed according to the target AAV genome) and PCR reagents, and then loaded into a droplet generator. The prepared droplets are transferred into a PCR plate, where PCR amplification is performed and analyzed. The viral genome titer is calculated based on the concentration (copies/&#181;L), accounting for sample dilutions. A successful measurement shows a clear separation of the positive and negative droplet clouds, has at least 10,000 accepted droplets, shows a value between 10 copies/&#181;L and 10,000 copies/&#181;L, and has a coefficient of variation (CV) between repeats lower than 20%. Reliable viral genome titration will aid in the development of safe and effective AAV-based gene therapy products.

Author Spotlight: Optimizing Digital Droplet PCR Method for Accurate Adeno-Associated Viral Genome Quantification

Precise quantification of adeno-associated virus (AAV) vector genome copies is critical, but a standardized protocol has yet to be established. This protocol describes a validated method for preparing purified AAV samples and conducting digital droplet polymerase chain reaction (dd_PCR) to reliably quantify the viral genome titer.

Adeno-associated virus (AAV) is a non-pathogenic virus used as a delivery vehicle to transfer therapeutic genes into patients. Accurate quantification of ...

Two-Step Reverse Transcription Droplet Digital PCR Protocols for SARS-CoV-2 Detection and Quantification

Diagnosis of the ongoing SARS-CoV-2 pandemic is a priority for all countries across the globe. Currently, reverse transcription quantitative PCR (RT-qPCR) is the gold standard for SARS-CoV-2 diagnosis as no permanent solution is available. However effective this technique may be, research has emerged showing its limitations in detection and diagnosis especially when it comes to low abundant targets. In contrast, droplet digital PCR (ddPCR), a recent emerging technology with superior advantages over qPCR, has been shown to overcome the challenges of RT-qPCR in diagnosis of SARS-CoV-2 from low abundant target samples. Prospectively, in this article, the capabilities of RT-ddPCR are further expanded by showing steps on how to develop simplex, duplex, triplex probe mix, and quadruplex assays using a two-color detection system. Using primers and probes targeting specific sites of the SARS-CoV-2 genome (N, ORF1ab, RPP30, and RBD2), the development of these assays is shown to be possible. Additionally, step by step detailed protocols, notes, and suggestions on how to improve the assays workflow and analyze data are provided. Adapting this workflow in future works will ensure that the maximum number of targets can be sensitively detected in a small sample significantly improving on cost and sample throughput.

This work summarizes steps on developing different assays for SARS-CoV-2 detection using a two color ddPCR system. The steps are elaborate and notes have been included on how to improve the assays and experiment performance. These assays may be used for multiple SARS-CoV-2 RT-ddPCR applications.

Diagnosis of the ongoing SARS-CoV-2 pandemic is a priority for all countries across the globe. Currently, reverse transcription quantitative PCR (RT-qPCR) ...

Quantification of Circular RNAs Using Digital Droplet PCR

Digital droplet polymerase chain reaction (dd-PCR) is one of the most sensitive quantification methods; it fractionates the reaction into nearly 20,000 water-in-oil droplets, and the PCR occurs in the individual droplets. The dd-PCR has several advantages over conventional real-time qPCR, including increased accuracy in detecting low-abundance targets, omitting reference genes for quantification, eliminating technical replicates for samples, and showing high resilience to inhibitors in the samples. Recently, dd-PCR has become one of the most popular methods for accurately quantifying target DNA or RNA for gene expression analysis and diagnostics. Circular RNAs (circRNAs) are a large family of recently discovered covalently closed RNA molecules lacking 5' and 3' ends. They have been shown to regulate gene expression by acting as sponges for RNA-binding proteins and microRNAs. Furthermore, circRNAs are secreted into body fluids, and their resistance to exonucleases makes them serve as biomarkers for disease diagnosis. This article aims to show how to perform divergent primer design, RNA extraction, cDNA synthesis, and dd-PCR analysis to accurately quantify specific circular RNA (circRNA) levels in cells. In conclusion, we demonstrate the precise quantification of circRNAs using dd-PCR.

This protocol describes the detailed method of digital droplet PCR (dd-PCR) for precise quantification of circular RNA (circRNA) levels in cells using divergent primers.

Digital droplet polymerase chain reaction (dd-PCR) is one of the most sensitive quantification methods; it fractionates the reaction into nearly 20,000 ...

Chip-Based Digital PCR to Detect Rare Transcript Variants Using a Nanofluidic Chip

Source: Molinari, C., et al. <a href="https://app.jove.com/v/57066">Detection of a CDH1 Rare Transcript Variant in Fresh-frozen Gastric Cancer Tissues by Chip-based Digital PCR.</a> J. Vis. Exp. (2018).
This video demonstrates chip-based digital PCR &#8212; a variation of the digital PCR technique that is useful in detecting rare transcript variants. The PCR reaction is partitioned into the chambers of a nanofluidic chip, each of which acts as an independent reaction. The detection of fluorescence signals from the chambers with amplified targets confirms the presence of rare transcript variants in the sample.

Source: Molinari, C., et al. Detection of a CDH1 Rare Transcript Variant in Fresh-frozen Gastric Cancer Tissues by Chip-based Digital PCR. J. Vis. Exp. ...

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Biological Techniques

PCR Techniques

Chip-in-a-Tube-Based Digital PCR for Quantification of Single Nucleotide Variants

Source: Kahyo, T., et al. <a href="https://app.jove.com/v/58199">Digital Polymerase Chain Reaction Assay for the Genetic Variation in a Sporadic Familial Adenomatous Polyposis Patient Using the Chip-in-a-tube Format.</a> J. Vis. Exp. (2018).
This video demonstrates the utility of digital PCR in a chip-in-a-tube format for the detection of single nucleotide variations in DNA samples. A single PCR reaction is partitioned into chambers that act as independent PCR reactions, and the detection of fluorescence signals from the amplified targets in the chambers is used to compute the frequency of the variant allele in the sample.

Source: Kahyo, T., et al. Digital Polymerase Chain Reaction Assay for the Genetic Variation in a Sporadic Familial Adenomatous Polyposis Patient Using the ...