NanoDrop Nd-1000 UV/Vis 1µl Spectrophotometer
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ND-1000 Frequently Asked Questions NANODROP ND-1000 FAQ1. OPERATION |
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1. OPERATION
A: Continuous spectrum from 220-750 nm. Q: What samples can I measure? A: We currently have modules specifically for DNA, RNA, Oligos, Proteins (A280), Bradford, Lowry and BCA Assays, Labelled protein, and cell cultures. We also provide a module for general UV/Vis measurements so we can measure any sample within the 220nm to 750nm window. For protein A280 we supply the option to input your proteins molar or mass extinction coefficient, use standards of BSA, Lysozyme or IgG or use a measurement of one absorbance unit = 1mg/ml. These options are available from the "sample type" drop down menu on the A280 module. The software will calculate concentration in mg/ml. For Bradford, BCA, Lowry assays - prepare the assay according to the manufacturers normal method. The respective modules associated with the assay require you to add standards and references and will calculate the standard curve for you. For more information please consult the user manual. Please contact us if you have any special requirements not addressed here Q: What sort of accuracy should I expect with the ND-1000? A: Typically within 2% Q: What sort of reproducibility should I expect with the ND-1000? A: Typically +/- 0.003 A at low concentrations. For reference, this corresponds to +/- 1.5 ng/ul for dsDNA. For higher concentrations (>100 ng/ul), standard deviations are typically <2%. However, the reproducibility does depend on how homogeneous the sample is, this can be more difficult to achieve for some samples than others (i.e genomic DNA). If the sample is heterogeneous then it may be necessary to run duplicate or triplicate measurements. Q: What concentration ranges does the NanoDrop ND-1000 measure? A: Typically, the linear ranges are: DNA - 2 ng/ul -> 3700 ng/ul Q: How often does the NanoDrop ND-1000 need calibrating? A: It is recommended that the NanoDrop ND-1000 be checked for calibration every six months. The calibration fluid can be purchased from the Labtech International service team, and the calibration check software can be downloaded from http://nanodrop.com/support-downloads.html Q: I want to measure the incorporation of a dye to my DNA/Protein, but it is not in the dye list. A: In the latest version of the NanoDrop ND-1000 Software (v 3.1.x) there is a dye/chromophore editor. This can be accessed from the main start up screen. In order to add custom dyes the molar extinction coefficient and the peak absorbance (excitation wavelength) must be known. Q: What other information can I get from the spectra? A: One of the key advantages of the NanoDrop ND-1000 is that every measurement is a spectral scan. Whilst interpretation of spectra can be tricky, everyday users of the NanoDrop ND-1000 get used to seeing Nucleic acid and Protein spectra. Obviously for DNA/RNA/Protein, peaks at 260 and 280 are expected. However, if DNA/RNA samples have been prepared with phenol or trizol then it is possible to see carryover. This is usually seen in a peak at 270 nm (although this is pH dependant). If significant carryover is present, the peak absorbance can be shifted to 270nm with the nucleic acid peak appearing as a shoulder at 260nm making the ND-1000 a useful diagnostic tool for sample purity |
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2. SOLVENT USE
A: The sample surfaces of the ND-1000 are resistant to many of the common solvents used in life science laboratory: Methanol
* Solvent must be wiped away immediately and the sample surfaces must be cleaned. Q: Can samples that are in high vapour pressure solvents (such as acetone) be analyzed? A: Yes, but due to the high vapour pressure, the sample should be measured using the short path to reduce evaporation. |
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3. CLEANING
A: This depends on the type of sample that is being measured; both surfaces are actually polished ends of a fibre optic cable. There are no holes or crevices for sample to stay in. Typically, DNA / RNA samples can be simply wiped from the surface with a lint-free tissue before applying the next sample. * Tip - if you are unsure if your sample is being removed from the sample surfaces, simply re-apply your blank and measure it as you would a normal sample. The concentration should be negligible and the resulting spectra should have no-significant peaks. Q: I want to retrieve my sample from the sample surface. What precautions can I take? A: If you are retrieving a DNA or RNA sample, the sample surface can be pre-treated with DNAase or RNAase zap to ensure the sample surface is nuclease free before taking the measurement. |
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4. COLUMN FORMATION
A: Reproducibility problems are very rare but when they occur they are commonly associated with the inability of the NanoDrop ND-1000 to make a column. Substances in the buffer reducing the surface tension, or dirty sample surfaces can cause this and so decrease reproducibility. Thoroughly clean both surfaces of the sample pedestal and repeat. If you are still unsure contact us Q: The NanoDrop ND-1000 does not make a column with some of my samples. A: This may be because of compounds in the buffer lowering the surface tension of the sample. Also, contaminants such as phenol or trizol can also cause this to happen. As a general 'rule of thumb' if the NanoDrop ND-1000 has difficultly making a column with some samples then use a 2 ul sample volume. Version 3.2.x of the NanoDrop control software has an inbuilt routine to detect that the sample column has formed corectly. Please ensure you are using the latest version of the software by visiting the download page Q: The NanoDrop ND-1000 does not make a column anymore, why is that? A: See above. Q: Are there any special concerns when analyzing proteins? A: Yes. Proteins have a lower surface tension than DNA, typically, a 2 ul sample is required. |
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5. LAMP ISSUES
A: A pulsed xenon flash lamp. Q: Is the flash lamp continuously on, or is it on only when performing a measurement? A: The lamp is only on during measurements. Q: Should the ND-1000 be unplugged when not in use? A: No, this is not necessary. Q: Does ND-1000 need warm-up time? A: No. The instrument is ready for measurements as soon as it is plugged in and the software is started. Q: How long before I need to replace the flash lamp? A: The lamp will last for 30000-50000 measurements before it will need to be replaced. For the price of a replacement lamp please contact the Labtech International service department. Q: I keep getting error messages when the NanoDrop ND-1000 tries to measure a sample. A: The most common error message that is seen when the NanoDrop ND-1000 tries to measure the sample is the signal error and connection error warnings. This can occur for a number of reasons. Firstly, the sample surfaces are dirty. Secondly, lack of power to the NanoDrop ND-1000. The PSU to the NanoDrop ND-1000 is used to supply power for the bulb. The power for the communication to the PC is supplied by the USB cable to the computer. Check that the power connector to the NanoDrop ND-1000 is seated correctly, also, check that the 'kettle lead' type connector from the mains plug to the NanoDrop ND-1000 power supply is firmly seated (sometimes it may look as if it is but it may need to be clicked into place) Lastly, if the NanoDrop ND-1000 is connected to a laptop computer, this error message can appear if the laptop has been put into hibernation or standby. Simply, shut down the NanoDrop ND-1000 software pull out the USB cable from the computer and replace it, re-open the NanoDrop ND-1000 Software and the error message should disappear. To stop this error message re-appearing, ensure the laptop is connected to the mains power and disable standby / hibernation features and ensure the laptop is correctly shut down after use. |
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6. DATA
A: The NanoDrop Nd-1000 will make a spectral scan from 220nm to 750nm. From this, it will automatically calculate (depending on application) concentration, 260/280, 260/230, standard curves, pMol per ul dye incorporation Q: Is there any way of saving the spectral data? A: There are several ways of saving the spectral data. A screen shot of the spectra can be saved in jpeg format, this includes the spectra and all the concentration information associated with it. This can be manipulated as a normal picture (i.e. the spectra can be cropped out and saved independently). This feature is particularly useful for placing spectral images into MS PowerPoint presentations or MS Word documents. One of the most powerful features of the NanoDrop ND-1000 software is its ability to automatically archive all the spectral data points. The archive will store sample ID / time and date information, in addition it will log all the concentration information, Abs values, ND-1000 firmware version / serial number, software version and all the spectral information for each sample. The archive files have an .ndj extension and can be opened via the inbuilt data viewer or in Excel. Q: Where does the NanoDrop ND-1000 archive all the data? A: The software archive is usually located in the 'C:\NanoDrop Data' folder; If the software has been installed on a different drive (e.g D:\ drive) then the archive will be located in a 'D:\NanoDrop Data' folder Q: How do I save my data? A: All data is automatically archived to c:/nanodrop data and is accessible through the data viewer or can be opened with a spreadsheet application Q: How do I back up my data? A: The data can be backed up manually by copying the contents of the NanoDrop Data folder to a CD or a network drive. However, the current release of the NanoDrop ND-1000 software (v 3.2.x) contains a feature to allow the archive data to be automatically duplicated across to a Network drive. This is located under the user preferences. Q: How can I search the archive data for a specific sample? A: Version 3.2.1 of the NanoDrop software now includes a data viewer. Using this, reports can be generated from any stored data and the spectral traces overlayed. It also contains a search utility. Q: Is there any way of saving / loading standard curves when in Bradford/BCA/Lowry modules? A: Yes, the latest version of the NanoDrop ND-1000 software does have the ability to save and load standard curves for the protein assay modules, these options can be found under the standard curve menu within each module. The standard curve can only be saved when enough standards have been entered (i.e. when the indicator turns from red to green). |
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