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Frequently Asked Questions: RiboRuler™ RNA Ladders (1)
1. Why were RNA Ladders were replaced with RiboRuler™ RNA Ladders and what are the differences?The new RiboRuler™ RNA ladders were designed to meet our customers' requirements for the highest quality RNA ladders suitable for both RNA sizing and quantification on gels, as well as for capillary electrophoresis. RiboRuler™ RNA ladders have the same banding pattern and cover the same range as our previous RNA ladders.
RiboRuler™ Low Range RNA Ladder, #SM1831/3 replaced the former Low Range RNA Ladder, #SM0411/3
RiboRuler™ High Range RNA Ladder, #SM1821/3 replaced the former High Range RNA Ladder, #SM0421/3Using a novel production process, RiboRuler™ RNA ladders have acquired a list of new features:
- Composed of chromatography-purified RNA transcripts
- Suitable both for RNA sizing and quantification on gels
- Free of NTPs
- Concentration of each RNA transcript is precisely measured by spectrophotometry
- New storage buffer composition ensures greater stability
- Suitable for RNA sizing during capillary electrophoresis
- For greater convenience, the package size is now calculated in number of applications
2. Which RiboRuler™ RNA ladder is best suited for my application?
- For analysis of RNA molecules of ~100-1000 bases in length, use RiboRuler™ Low Range RNA Ladder.
- For analysis of RNA molecules of ~200-6000 bases in length, use RiboRuler™ High Range RNA Ladder.
- For RNA quantification, use the ladder which contains a band of similar size to the one you want to quantify.
- For labeling the RNA ladder with T4 Polynucleotide Kinase, use conventional format RiboRuler™ Low Range RNA Ladder (#SM1831) and RiboRuler™ High Range RNA Ladder (#SM1821). Conventional versions of the ladders are prepared in 1 mM EDTA (pH 6.0), and supplied with a vial of 2X RNA Loading Dye for the ladder and the sample RNA.
- For standard applications and for more convenience, use ready-to-use RNA ladders (#SM1833, #SM1823). They are premixed with RNA loading dye for direct loading on gels (after heating), and are also supplied with a vial of 2X RNA Loading Dye for sample RNA.
3. How many applications is one pack of the ladder sufficient for?Each pack of RiboRuler™ RNA ladder is sufficient for 50 applications when using 8 mm wide gel lanes.
Conventional ladders: RiboRuler™ Low Range RNA Ladder, #SM1831 and RiboRuler™ High Range RNA Ladder, #SM1821 are provided as 5x20 µl aliquots (100μl in total), which is sufficient for 50 applications (0.25 µl of RNA ladder applied per 1 mm gel lane width).
Ready-to-use ladders: RiboRuler™ Low Range RNA Ladder, ready-to-use, #SM1833 and RiboRuler™ High Range RNA Ladder, ready-to-use, #SM1823, are provided as 5x40 µl aliquots (200μl in total), which is sufficient for 50 applications (0.5 µl of RNA ladder applied per 1 mm gel lane width).
4. Can RiboRuler™ RNA ladders be used for capillary electrophoresis?RiboRuler™ RNA ladders are suitable for use as size standards in capillary electrophoresis. They have been tested on the Agilent 2100 Bioanalyzer and give sharp peaks in capillary electrophoresis.
5. What quality control tests are performed on the RiboRuler™ RNA ladders?
- Low range RiboRuler™ RNA ladders are tested for band clarity and intensity on native agarose and polyacrylamide gels.
- High range RiboRuler™ RNA ladders are tested on native agarose gels.
- RNA concentration of each band is determined spectrophotometrically.
- The absence of ribonucleases is confirmed by appropriate tests
6. What other products does Fermentas carry for RNA electrophoresis and Northern blots?
- 2X RNA Loading Dye is used for RNA sample preparation prior to electrophoresis. The solution contains an optimal concentration of formamide, which allows for efficient separation of RNA molecules according to their true size even under non-denaturing conditions. The presence of ethidium bromide in the solution allows for RNA visualization without additional staining of denaturing formaldehyde agarose gels.
- 50X TAE and 10X TBE electrophoresis buffers are RNase-free and are ideal for RNA gel electrophoresis. TAE buffer is recommended for analysis of larger RNA; TBE buffer is recommended for RNA smaller than 1500 b as well as for denaturing polyacrylamide gel electrophoresis.
- TopVision™ LE GQ Agarose and TopVision™ LM GQ Agarose are RNase-free and are ideal for analytical and preparative RNA gel electrophoresis.
- DEPC-treated Water is recommended for preparation of RNA samples.
- T4 Polynucleotide Kinase is RNase-free and can be used for radioactive 5'-end labeling of RNA probes.
- FastAP™ Thermosensitive Alkaline Phosphatase and Shrimp Alkaline Phosphatase (SAP) are RNase-free and can be used for dephosphorylation of 5' RNA fragments, resulting in more efficient labeling by T4 Polynucleotide Kinase.
- RiboLock™ RNase Inhibitor is used to protect RNA during labeling or other enzymatic reactions.
- 0.5 M EDTA, a chelator of metal ions, is RNase-free and can be used to stop metal dependant enzymatic reactions such as labeling with T4 Polynucleotide Kinase.
- Glycogen, RNA grade is RNase-free and recommended for precipitation of RNA from diluted solutions.
- SensiBlot™ Plus Nylon Membrane, is a positively charged membrane ideal for Northern blots.
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Updated birželio 30, 2008 12:59
