100bp DNA Ladders for PCR Amplicon and Small Fragment Sizing
100bp DNA Ladders covers the 100-base-pair-increment size standard, the most commonly used ladder for sizing small DNA fragments and PCR amplicons in the 100 bp to 2000 bp range. A 100 bp ladder provides closely spaced reference bands at 100 bp intervals, well suited to verifying PCR products from routine amplifications, checking small restriction digest products, and sizing DNA where expected fragments fall below 2 kb. Academic and core laboratories sourcing or restocking DNA size standards can benefit from guidance when selecting ladder formats and matching them to expected fragment size distributions.
Explore available 100 bp DNA ladders or request a quotation by contacting customerservice@mbpinc.net. Our team can help identify the appropriate size standard for PCR validation and small-fragment DNA analysis workflows.
100bp DNA Ladders
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What is a 100 bp DNA ladder?
A 100 bp DNA ladder provides reference bands at 100-base-pair intervals, typically covering 100 bp to 1000 bp or 100 bp to 2000 bp depending on the variant, making it the most commonly used size standard for routine sizing of small PCR amplicons and restriction digest products. Most commercially available 100 bp ladders include a brighter reference band at 500 bp or 600 bp for quick orientation, and many are available in ready-to-load formats pre-mixed with loading dye and glycerol for direct pipetting into gel wells.
What you will find:
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ZR 100 bp DNA Marker (M5002-200) for high-resolution sizing of DNA fragments in routine electrophoresis workflows
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PureView 100bp DNA Ladder for precise sizing and enhanced band visualization of small DNA fragments
How to choose and use a 100 bp DNA ladder
Use a 100 bp ladder when your samples are mostly below 2 kb
A 100 bp ladder provides more resolution than a 1 kb ladder in the small-fragment range, since 100 bp spacing gives reference bands every 100 bp rather than every 1000 bp. If samples span a broader size range, the 1 kb Plus ladder extending down to 100 bp may be a more versatile single-ladder choice.
Run small-fragment gels on 1.5–2% agarose for best resolution
Fragments in the 100–500 bp range benefit from 1.5–2% agarose, which gives tighter, better-defined bands in this small-fragment window and reduces the risk of small bands reaching the gel front before larger fragments are adequately separated.
Look for a 500 bp or 600 bp reference band for easy orientation
Most 100 bp ladders include a brighter band at a convenient midpoint like 500 bp or 600 bp, which serves as a visual anchor for counting up or down in 100 bp intervals to identify the nearest ladder band.
Choose between upper ranges (1000 bp vs 2000 bp) based on sample sizes
Some 100 bp ladders cover only to 1000 bp (10 bands), while extended versions cover up to 2000 bp. If samples occasionally include products above 1000 bp, the extended range provides coverage without switching to a separate 1 kb ladder.
Pair with a 1 kb ladder when samples span both large and small size ranges
If an experiment includes both small PCR amplicons around 100–500 bp and larger restriction fragments above 2 kb, loading both a 100 bp and a 1 kb ladder in adjacent lanes provides accurate reference coverage across the full size range.
Specifications context
The 100 bp DNA ladder is one of the two most commonly used DNA size standards in routine molecular biology labs, alongside the 1 kb ladder, and most labs running small PCR products routinely keep a 100 bp ladder on hand. As of 2026, ready-to-load 100 bp ladder formats with a 500 bp or 600 bp bright reference band remain the default choice for routine agarose gel electrophoresis of small PCR products and restriction digest fragments.
Contact the expert team at MBP for assistance in selecting the right 100bp DNA ladder for your lab.
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