I would like to capture guanosine, a nucleoside, from a sample. Based on the specific H-bonding interaction between nucleobases cytosine and guanine, I would like to design a sequence of nucleobases comprising mostly of cytosine. Later I can attach that sequence to nanoparticle and use that composite to capture gaunosine. I would like to know what should be my sequence of nucleobases for ideal effecient capturing of guanosine. It should be all cytosine ? or cytosines spaced by other bases or spacers ? Anyone who has experience in oligonucleotide interactions can help me out in finding out the right sequence for efficient interaction. Thanks a lot.
It is possible to capture oligonucleotides containing guanosine by hydrogen bonding with complementary nucleic acid strand (preferentially RNA than DNA). You won't obtain a sufficiently strong interaction with guanosine as a monomer nucleoside by hydrogen bonding with cytosine alone, regardless of the chain length.
Thank you so much Andriy for your response. But, I am interested in capturing only guanosine nucleoside. So, you feel it may not work so effeciently ? Also, will hydrogen bonding interactions take place in water ? Do you have any suggestions ?
Thank you very much
The chain length and composition should not be much of an issue- the problem would be with such complex stability/energy. Hydrogen bonding of guanosine with solvent will compete quite effectively with that of guanosine with cytidine base, so it wil "fall off" easily. With oligo to oligo binding there is "zipper" interaction with multiple bases "holding each other back". With single base, it won't work as easily.
So the main issue with cytidine oligonucleotide should be economic- price vs amount vs needed excess.
You may want to tweak the solvent (add some solvent where guanosine is less soluble) to shift equilibrium of such binding.
Thank you so much Mikhail. The information you have given is very helpful. Will try to work on this based on the information you have given. Thanks again
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