What is a DNA ladder? What does the DNA ladder do in PCR?

Polymerase chain reaction (PCR) has revolutionized molecular biology research and diagnostics. This versatile technique allows exponential amplification of target DNA sequences in just a few hours. But how do you know if your PCR worked? And if you generated the expected product, how can you determine its precise size? This is where DNA ladders come in.

What is a DNA Ladder?

A DNA ladder contains DNA fragments of known, specific sizes. Just like a ruler with markings in inches or centimeters, a DNA ladder acts as a size reference when running gel electrophoresis. By comparing your PCR sample bands to the ladder fragments, you can estimate the size of your unknown DNA fragments.

DNA ladders are composed of DNA molecules ranging from 100 base pairs to over 10,000 base pairs. The fragments are often multiples of 100 or 1,000 base pairs. Ladders with intervals of 100 bp are best for determining the size of small PCR products, while 1 kb ladders work better for larger amplicons.

How is a DNA Ladder Made?

While ready-made ladders can be purchased, you can also create your DNA ladder in the lab. Here are some common preparation methods:

• Restriction enzyme digestion of plasmid DNA– Plasmids are cut with enzymes like HindIII or EcoRI to liberate specific-sized fragments.
• Amplification by PCR– Target sequences of varying lengths are amplified individually and then combined into a ladder.
• Partial digestion of concatamers– Tandem repeats of a DNA sequence are cleaved to produce multimers.
• Synthetic oligonucleotide hybridization– Short single-stranded DNA fragments are annealed into double-stranded multimers.

No matter the production method, the key is generating a set of discrete bands covering the desired size range.

How is a DNA Ladder Used?

Now that you understand what a DNA ladder is, how is it used? DNA ladders serve two essential purposes:

1. Size Estimation

By running a DNA ladder alongside your PCR samples on an agarose or polyacrylamide gel, you can estimate the size of your unknown DNA fragments.

During electrophoresis, the ladder and samples migrate through the gel matrix at rates dependent on their size. Smaller fragments travel farther down the gel, while larger fragments lag.

When the DNA is stained and visualized, the ladder fragments appear as sharp, discrete bands. By lining up your sample bands with ladder bands of matching size, you can determine the approximate length of your PCR products.

2. Quality Control

The inclusion of a DNA ladder also serves as a visual control that your PCR amplification worked. When you observe distinct sample bands migrating at the expected positions relative to the ladder, this provides quick confirmation that your PCR was successful.

If you fail to see any bands, the ladder indicates that the electrophoresis itself was performed properly. This suggests your PCR reaction may have failed and troubleshooting is needed.

What Size DNA Ladder Should I Use?

With the variety of DNA ladders available, how do you choose the right one for your experiment? Here are the key factors to consider:

• Size range– The ladder range must encompass your expected PCR product sizes. For amplicons under 1 kb, a 100 bp or 1 kb ladder is suitable. For larger products, choose a higher ladder like 5 kb or 10 kb.
• Band spacing– Ladders with more reference bands in a given size range allow greater sizing precision. However, closely spaced bands take longer to fully resolve. If time is limited or you only need approximate sizes, use a ladder with fewer fragments.
• Ready-to-load– Premade, ready-to-load ladders guarantee accurate band intensities. Avoid diluting or mixing ladders yourself.
• Sample number– For multiple samples, choose a larger ladder lane size to allow side-by-side comparison.
• Budget – Consider the cost if producing large volumes of gels. Some ladders are more economical.

How Do I Read a DNA Ladder?

Once your gel is visualized after electrophoresis, how do you read the ladder to determine PCR product sizes? Follow these steps:

1. Identify the lanes containing the DNA ladder fragments. This is typically loaded in the first and/or last lane.
2. Note the size of the base pair DNA bands based on the ladder manufacturer’s reference chart. Ladders are color-coded for easy reading.
3. Compare your unknown sample bands to the ladder, identifying the closest band in the ladder lane. The size of your band is approximate to that ladder fragment.
4. For greater precision, interpolate band size between two ladder fragments. For example, if your band runs between the 500 and 600 bp ladder bands, estimate its size as 550 bp.
5. To increase sizing accuracy, run gels longer to maximize separation between ladder bands. Loading smaller amounts of ladder can also improve band resolution.

What Are Some Examples of Commonly Used DNA Ladders?

Many types of DNA ladders are available from manufacturers like New England Biolabs, ThermoFisher, and Invitrogen. Some commonly used options include:

• 100 bp DNA Ladder – Contains 12 fragments from 100 bp to 1,500 bp. Ideal for PCR products under 1,000 bp.
• 1 kb DNA Ladder– Composed of 13 bands from 250 bp to 10,000 bp. Well-suited for amplicons up to 10 kb.
• 1 kb Plus DNA Ladder– Expanded version of 1 kb ladder with additional high and low molecular weight fragments.
• FastDigest DNA Ladder– Pre-digested ladder ready for direct loading onto gels. Fewer bands allow rapid run times.
• High Molecular Weight DNA Ladder – Contains larger DNA fragments up to 48,500 bp for sizing high molecular weight genomic DNA.

How Do I Prepare and Load a DNA Ladder?

To harness the full benefits of your DNA ladder, proper preparation and loading techniques are key:

• Check ladder integrity before use – Inspect for any band smearing or degradation.
• Mix gently – Avoid vigorous vortexing to prevent shearing DNA.
• Use manufacturer-recommended amounts – Underloading gives weak band intensity. Overloading causes saturation.
• Load ladder in first and/or last lane – Provides a size reference on both sides of your samples.
• Include a lane with no ladder – Serves as a contamination control.

Following these best practices will give you optimal ladder performance every time.

How Do I Create My DNA Ladder?

While buying pre-made ladders is the easiest route, you can also make your DNA ladder using PCR and restriction digestion. Here is an overview of the process:

1. Design PCR primers to amplify specific target sequences of varying lengths, such as 500, 750, 1,000, and 1,500 bp.
2. Run individual PCRs using each primer pair to generate DNA fragments of a defined size.
3. Purify the PCR products and quantify DNA concentration for each fragment.
4. Digest the fragments with the same restriction enzyme to generate compatible sticky ends.
5. Mix the fragments in specific molar ratios to achieve the desired band intensities.
6. Ligate the fragments to form multimers separated by restriction sites.
7. Amplify using universal primers to generate concatamers.
8. Partially digest concatamers with an original restriction enzyme to cut at internal sites.
9. Purify and mix the digests into your final DNA ladder.

Why Are DNA Ladders So Important for PCR?

DNA ladders are essential for Polymerase Chain Reaction (PCR) applications for several key reasons:

Accuracy and Reproducibility

DNA ladders enable accurate sizing and consistent reproducibility of PCR results. By comparing your bands to the molecular weight standards of the ladder, you can precisely determine amplicon size and confirm successful target amplification. This allows results to be reproduced reliably across different users, equipment, and laboratories.

Standardization

Including a DNA ladder standardizes comparisons between multiple PCR samples. Whether you are analyzing different conditions of one sample or screening numerous patient specimens, the ladder provides a constant reference to evaluate results. Standardization is critical for consistency in research and clinical diagnostics.

Optimization

Ladders facilitate PCR optimization by indicating if amplification is occurring as expected. Unexpected band sizes or weak intensity reveal suboptimal conditions. The ladder assists in troubleshooting protocols to derive the best primers, cycling conditions, and sample purity.

Sensitivity

With a broad range ladder, even faint PCR bands can be visualized and sized. This allows the detection of low template copies critical for applications like viral load monitoring. The sensitivity provided by a ladder supports PCR’s use in single-molecule detection.

Multiplexing

For multiplex PCR with several primer sets, ladders verify the identity of each target band. This enables efficient amplification of multiple sequences in one reaction.

Automation

DNA ladders enable automatic software analysis of PCR gels. Computer algorithms rely on the ladder to normalize band migration differences between gels. This allows high-throughput, rapid analysis of large sample numbers.

In short, DNA ladders empower PCR with accuracy, reproducibility, standardization, optimization, sensitivity, multiplexing capability, and automation. Whether you are perfecting a new protocol or analyzing clinical samples, this essential tool will amplify your success and support excellent research outcomes.