New England Biolabs, N0551L, Quick-Load® Purple 100 bp DNA Ladder

Related Categories Quick-Load Purple DNA Ladders,, DNA Markers & Ladders Applications DNA Analysis Specification Bases Fragment Mass (ng) bp 1 45 1517 2 35 1200 3 95 1000 4 27 900 5 24 800 6 21 700 7 18 600 8 97 500/517 9 38 400 10 29 300 11 25 200 12 48 100 Effective Size Range 100bp to 1,517bp Storage Buffer 2.5% Ficoll®-400 10 mM EDTA 3.3 mM Tris-HCl 0.001% Dye 2 0.02% Dye 1 pH 8 @ 25°C FAQ Q: Can I use Midori Green with the DNA Ladders from NEB? A: NEB DNA Ladders, including Quick-Load Purple 1 kb Plus DNA Ladder (NEB #N0550), are compatible with Midori Green dye with no interference observed. Please follow dye manufacturer's recommendations exactly. Due to low dye intensity, you may need to load between 1 and 2 ug of the DNA ladder to achieve good visualization under standard UV illumination conditions. Q: Why are there extra bands visible on polyacrylamide gels? A: To provide increased intensity for the smaller bands and the reference bands, multiple fragments of the same size have been cloned into the plasmids used for many of the DNA ladders. These fragments, identical in size, are indistinguishable on agarose gels, but, on acrylamide gels, even slight differences in DNA sequence can lead to noticeably different migration rates. Fragments of the same size do not always run the same on acrylamide. For the 100bp DNA Ladder, the 500 and 517bp fragments, which run as a close doublet on agarose, separate very clearly on acrylamide, with the 517bp band running around midway between the 500 and 600bp fragments. This “anomalous” migration is an inherent characteristic of acrylamide gel electrophoresis and does not indicate any error in the stated size of the DNA fragments in our ladder. For the 50bp DNA Ladder and the Low Molecular Weight Ladder, two or more of the bands comprising the 200bp reference band tend to run differently, resulting in one or more extra bands detectable around the 200bp range. As with the 100bp DNA Ladder, this is attributed more to the limitations of acrylamide gel technology than to a problem with the ladder composition. As defined in most molecular biology lab manuals (Maniatis’ Cold Springs Harbor Molecular Cloning Manual, 2nd edition) and as acknowledged by the manufacturers of acrylamide gels, applications requiring precise sizing of DNA fragments should be performed using agarose gels whenever possible. Q: Can I use SYBR® and/or GelRed® dyes with the DNA Ladders from NEB? A: Because high affinity nucleic acid binding dyes can affect DNA migration during electrophoresis, post-staining of gels with SYBR and GelRed dyes is highly recommended. Post-electrophoresis staining results in superior sensitivity and eliminates the possibility of dye interference with DNA migration. While agarose gels can be precast with these dyes, the migration and/or resolution of some DNA ladders may be affected. Therefore, some DNA ladders may require optimization/diution when run on gels precast with these dyes. For optimum results, please follow the dye manufacturer’s recommendations and protocols carefully, specifically concerning the loading amounts. We recommend using our 1 kb Plus DNA Ladder for Safe Stains (NEB #N0559) when using SYBR or GelRed as precast dyes, as this DNA ladder was specifically optimized for this application. Additionally, avoid using loading dyes that contain SDS, as SDS might cause an abnormal band pattern in precast gels. We recommend using Gel Loading Dye, Purple (6X), no SDS (NEB #B7025) for this application.” Q: Why is my DNA Ladder floating out the wells? Why are there no bands visible in my DNA ladder gel lane? A: If the ready-to-load DNA Ladder or the 6X Loading Dye supplied with the ladder has been frozen at any time, the Ficoll will form a density gradient in the vial upon thawing. Any volume pipetted from the top of the vial will contain only a small amount of density agent and will float out of the wells. To prevent this, mix well upon receipt and before use. Q: What are the differences in the four versions of the 1 kb Plus (formerly called the 2-Log DNA Ladder), 100 bp and 1 kb DNA Ladders that NEB sells? A: These ladders come in four formats. Choose from the conventional ladder, the Quick-Load® version using either non-flourescing purple dye (NEB #B7024) or bromophenol blue as a tacking dye, or TriDye™ containing three dyes that serve as visual aids to monitor the progress of migration during agarose gel electrophoresis. Quick-load versions also include a vial of loading dye, free of charge.