Selecting DNA, RNA, and PCR Fragment Markers and Ladders for Gel Electrophoresis

Standard DNA Markers
Digested DNA Markers
PCR Markers
RNA Markers

DNA and RNA Markers for size determination

DNA and RNA size markers contain a mixture of DNA (or RNA) fragments of known length, making them suitable for estimating the fragment length of concurrently run samples. Markers and ladders stain well with ethidium bromide and other common nucleic acid stains for visualization after gel electrophoresis.

We offer a variety of markers for nucleic acid size determination of samples separated by various gel electrophoresis methods.

Figure 1.

Standard DNA Markers

Agarose gel electrophoresis requires standard DNA markers. DNA ladders are available in a convenient, ready-to-use versions.

D3812 – DirectLoad™ Step Ladder, 50 bp	S7025 – Step Ladder, 50 bp	D7058 – DirectLoad™ Wide Range DNA Marker	D5042 – 123 bp Ladder	D3937 – DirectLoad™ 1 kb DNA Ladder	D0428 – 1 kb Ladder
50-3,000 bp	50-3,000 bp	50-10,000 bp	123-4,182 bp	500-10,000 bp	500-10,000 bp

Digested DNA Markers

Agarose gel electrophoresis for size determination of DNA digest fragments benefits from markers prepared as fragments of digested DNA. The gel bands for DNA digest markers are illustrated below.

D9655 – pBR322 Hae III Digest	D0672 – φX174 DNA Marker Hae III Digest	D6293 – pUC18 DNA Hae III Digest	D9780 – Lambda DNA Hind III Digest	D9281 – Lambda DNA EcoR I Hind III Digest	D2916 – Lambda DNA Mixed Digest	D5282 – Lambda DNA EcoR I Digest
8-587	72-1,353	80-587	564-23,130	564-21,226	1,053-48,505	3,530-21,226

PCR Markers

Agarose or polyacrylamide gel electrophoresis for size determination of PCR fragments benefits from markers designed for use with PCR fragments.

P1598 – PCR 20 bp Low Ladder	D3687 – DirectLoad™ PCR 100 bp Low Ladder	P1473 – PCR 100 bp Low Ladder	P9577 – PCR Marke

RNA Markers

RNA electrophoresis requires markers prepared from RNA. The Transcript RNA Marker contains nine RNA transcripts. The ladder is diluted in gel loading buffer and then loaded in a single lane on an agarose gel. Markers are suitable for size determination of small RNA using native or denaturing agarose gel electrophoresis. The Transcript RNA Markers 0.2-10 kb has been used as a molecular weight marker for northern blot hybridization. The Transcript RNA Marker is provided in a gel-loading solution with 10 mM Tris-HCl (pH 8.0), with 1.0 mM EDTA and contains nine defined RNA transcripts. For optimal resolution, the recommended agarose gel concentration is 1.0%.

R7020 – Transcript RNA Markers 0.2-10 kb	R7644 – Transcript RNA Markers 0.28-6.6 kb