The time-saving evolution of PCR technology

The difference between using an automated thermal cycler with and without a liquid handler platform is the recovery time. What would you do if you had six extra hours in the lab?

Like life itself, modern biotechnology is based on the ability to precisely copy DNA. Biologists hijacked the nucleic acid replication machinery built into cells to create the polymerase chain reaction (PCR), a cornerstone method of modern molecular biology, allowing them to copy DNA on their own. In 1983, Nobel Prize winner Kary Mullis showed that you could manipulate the replication of a target DNA sequence by coordinating the sample with a precise sequence of temperatures. At the time, conducting PCR experiments meant scientists spent hours manually moving test tubes in and out of water baths at different temperatures to achieve these temperature cycles. In 1988, Celtis and Perkin-Elmer introduced a device called a thermal cycler to automate the precise temperature changes required for PCR experiments. It is faster and more efficient than the water bath method, but costs more than $100,000—far beyond the reach of most biologists. Most labs didn't start using thermal cyclers until the mid-1990s, when companies like ML Laboratories began making more affordable machines with heated lids.

Time-saving evolution of PCR technology

Today, time-saving innovations in PCR appear to be stalling. Although new PCRs (such as quantitative and digital PCR) have been created, no significant progress in time savings has been made since the mid-1990s. Most biologists still use thermal cyclers that are technically similar to those invented 20 years ago, and still spend hours each week manually preparing reactions. Opentrons thermal cyclers represent the next major leap in time savings for PCR users.

Why saving time is so important

Robots allow you to work in parallel to get more done faster—especially robots equipped with thermal cyclers, which can handle longer workflows.

The first way to save time is through the benefits of basic one-on-one task completion. If a person can prepare 100 samples in one hour and respond to 10 emails in one hour, it will take them 2 hours to complete both tasks. But if they let a robot do the sample preparation, they could do both tasks in under an hour—a fairly simple way to increase productivity.

However, when you consider longer time periods, the time savings increase exponentially. Let's say you have 600 samples to prepare, running the robot at the same rate of 100 samples per hour. There is also a six-hour session that you have the opportunity to attend.

Can you automatically prepare samples and attend meetings?

In theory, of course: 6 hours x 100 samples/hour = 600 samples. But who will load and unload the robot? Who will set up the automation between runs? You can automate all 6 hours of sample preparation, but you can only do it in six one-hour windows. So, even if you could save yourself six hours of productivity, you can't go to the meeting. What you need (in this case) is a robot that can do all 600 samples in one run. That way, you can hit "start," come back six hours later after presenting at the conference, and have all your lab work done. The difference between one six-hour block and six one-hour blocks can be the difference between meaningful work and busy work. Additionally, some jobs simply require long periods of uninterrupted time to complete. In "The Maker's Timeline, the Manager's Timeline," Paul Graham points out that some creative tasks, such as writing an article or programming an algorithm, are best done this way: an hour is not enough , not enough to focus and make meaningful progress. With only two hours to complete these complex tasks, you barely have enough time to get into the flow—and worse, once you get into flow, you have to give up.

How a benchtop thermal cycler can save you tons of time

If your lab already automates workflows from genotyping and sequencing to cloning and gene editing, adding a benchtop thermal cycler to a liquid handling robot can increase your free time by 3x. The protocol to fully utilize an integrated thermal cycler is complex, involving multiple subprotocols before and after the incubation or PCR step. Let’s take a next-generation sequencing (NGS) library preparation protocol as an example. By automating only the pipetting and bead handling steps of your workflow, you can reduce your workload by approximately 2/3. This is where the enzymatic preparation (fragmentation + a-tailing, etc.), cleaning, indexing and pooling steps can be accomplished by an OT-2 robot with a magnetic module. If the robot does not have a thermal cycler on deck, then a human (or another more expensive robot) must physically move the prepared reagents into the thermal cycler. After amplification is complete, they also need to retrieve the samples themselves—taking them off the thermal cycler and placing them back on the robot for the final magnetic and pipetting steps.

Original address:How to save time in the lab with an automated benchtop thermal cycler