50bp DNA Ladders for Precise Sizing of Small DNA Fragments
50bp DNA Ladders covers the 50-base-pair-increment size standard for gel electrophoresis applications where small DNA fragments in the 50–1000 bp range need to be precisely sized, including microsatellite and STR marker analysis, short restriction digest products, small amplicons from nested or multiplex PCR, and other applications where a 100 bp ladder's reference bands are spaced too far apart for reliable size discrimination. These ladders are typically run on high-percentage agarose (2–4%) or polyacrylamide gels. Academic and core laboratories can benefit from guidance when selecting the appropriate ladder and gel format for high-resolution analysis of small DNA fragments.
Explore available 50 bp DNA ladders or request a quotation by contacting customerservice@mbpinc.net. Our team can help identify the appropriate size standard and electrophoresis conditions for your DNA fragment analysis workflow.
50bp DNA Ladders
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What is a 50 bp DNA ladder?
A 50 bp DNA ladder provides reference bands spaced at 50-base-pair intervals, most commonly covering 50 bp to 1000 bp (or up to 1500 bp in some extended formats), making it suitable for gel electrophoresis experiments where samples are very small DNA fragments that a 100 bp ladder cannot resolve accurately because 100 bp band spacing is too coarse. Common applications include microsatellite and STR genotyping, analysis of small restriction digest products, multiplex or nested PCR amplicons, and other short-fragment applications in the 50–500 bp range where precise size discrimination is needed.
What you will find:
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ZR 50 bp DNA Marker for precise analysis of smaller DNA fragments
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Azura PureView™ 50 bp DNA Ladder for high-resolution gel results in electrophoresis
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Accuris SmartCheck™ 50bp DNA Ladder for size determination of PCR products
How to choose and use a 50 bp DNA ladder
Use a 50 bp ladder when your fragments differ by less than 100 bp and are below 500 bp
The primary reason to use a 50 bp ladder over a 100 bp ladder is when your samples include fragments with size differences of less than 100 bp that need to be resolved, such as microsatellite alleles or closely-sized PCR amplicons from multiplex reactions.
Run small-fragment gels on 2–4% agarose or polyacrylamide for adequate resolution
High-percentage agarose (2–4%) or polyacrylamide gels are needed to resolve very small DNA fragments as distinct bands rather than all migrating together near the gel front, since standard 1% agarose does not provide sufficient resolution for fragments below approximately 200 bp.
Use a reference band at a convenient size for quick orientation
Many 50 bp ladders include a brighter reference band at a convenient, easy-to-remember size such as 250 bp or 500 bp, which serves as an anchor for identifying surrounding bands without counting from the well each time.
Confirm the 50 bp ladder's smallest band is detectable with your staining system
Very small DNA fragments, especially below 100 bp, can be difficult to detect or may run off the gel front quickly, and confirming that the ladder's smallest defined bands are visible under your staining and imaging setup helps ensure the full ladder range is usable.
Consider polyacrylamide gels for the highest resolution of fragments below 200 bp
Polyacrylamide gel electrophoresis provides substantially higher resolution than high-percentage agarose for fragments below 100–200 bp, making it the preferred format when single-base or very fine size discrimination is needed in this range, such as for SSR or STR genotyping.
Specifications context
Standard 50 bp DNA ladders typically cover from 50 bp to 1000 bp with bands at 50 bp intervals, and many include a brighter reference band at 250 bp or 500 bp for quick orientation. As of 2026, the 50 bp ladder remains the standard small-fragment size reference for microsatellite and STR genotyping workflows, whether on standard agarose or capillary electrophoresis platforms where defined size standards are loaded alongside samples.
Contact the expert team of Molecular Biology Products Inc. (MBP) and get premium-quality 50bp DNA ladders for your next experiment.
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