New detection techniques for microarray analysis - new ideas (Aug/18/2005 )
hi all microarray experts
We can use Radiolabelling which is not a great way of detection due to the handling problems
Most of us use flourescence to detect and quantify their microarray studies. But it has some serious draw backs.
1. Quenching
2. POL effect in end labelling
3. Random labellin ginterferes with hybridisation and cannot be quantified as it depends on the sequence
I was thinking on new ways of detecting the hybridised DNA. One of my collegues was thinking on using stable Isotope labelled DNA like ones of Oxygen which is not radioactive.
But the problem is that is their any way of detecting these stable isotopes in microarray chip based on their difference on their difference in Atomic number
I am really looking forward for some suggesetions
have a nice day
prajwal
For microarry band detection, I use the program from immunokin corp to detect the bands. The program gives me a color value. I use it for array membranes from Superarray, etc.. Immunokin Corp has a color analysis program for digital images that can be used to quantify bands on blots. The program determines color values, such as gray values, of regions of interest. The program is called RGBG Analyzer 1.0.018. The website link is http://www.immunokin.com There is a free demo for download. The full version cost about $25.
We can use Radiolabelling which is not a great way of detection due to the handling problems
Most of us use flourescence to detect and quantify their microarray studies. But it has some serious draw backs.
1. Quenching
2. POL effect in end labelling
3. Random labellin ginterferes with hybridisation and cannot be quantified as it depends on the sequence
I was thinking on new ways of detecting the hybridised DNA. One of my collegues was thinking on using stable Isotope labelled DNA like ones of Oxygen which is not radioactive.
But the problem is that is their any way of detecting these stable isotopes in microarray chip based on their difference on their difference in Atomic number
I am really looking forward for some suggesetions
have a nice day
prajwal
Hello prajwal,
We have also thought about using stable isotopes on arrays (in fact we tried it on a small scale) but using 13C rather than stable isotopes of oxygen. As you say, the problem is detecting the labelled hybrids. You need to use isotope-ratio mass spectrometry (IR-MS) to do this - these instruments are normally used to measure 13C-12C ratios in CO2. One option is to 'burn' the carbon off every spot on a hybridised array with a scanning laser, collect the resulting CO2, and measure the isotope ratio. However, the quantity of DNA on a single microarray spot is so small it gives an inadequate quantity of CO2 after such a 'burn'. We tried this using a nylon membrane macroarray, as the nylon itself is burned, along with the bound DNA (both the probe and the target, if present). We did obtain a detectable amount of CO2, but the 13CO2 derived from the stable isotope label was so dilute that we couldn't detect it...
Overall, I think fluorescence methods are strongest, despite the drawbacks.
Del.