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DNA consists of deoxyribonucleotides, RNA consists of ribonucleotides. They differ mainly (apart from the uracil / thymine difference) in the sugar part, the deoxyribose and the ribose. Those two molecules differ in the hydroxy group in the ribose which is only a single proton in the deoxyribose. This part of the sugar molecule is not directly involved in binding reactions, nevertheless it causes the whole difference in RNA and DNA.

I wonder: could a dNTP be used in an RNA strand (or vice versa)? Is it chemically possible that we have a RNA molecule that contains a dNTP next to its NTPs?

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Are you interested in whether this happens naturally, or if we can do it in the lab? And depending on which interactions you mean, it's not really correct to say that the 2'-OH is not involved in binding. –  Mad Scientist Jul 2 '13 at 8:07
    
I'm interested in both -- if we can do it in the lab, it's technically feasible and this would be interesting. But if it is possible, could it even happen naturally? And you are of course right, the 2'-OH is involved in binding, I tried to say that it is not used to form a new bond (therefore not directly involved). –  suvidu Jul 2 '13 at 8:16
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This is rather easy to do if you synthesize oligonucleotides chemically and not enzymatically. This is typically done using phosphoramidite chemistry, and it allows for the synthesis of chimeric RNA/DNA oligos. You can even incorporate modified nucleosides like 2'-O-Me or LNA.

This is typically done if you want to change the properties of an oligo, e.g. if you want to make it resistant to degradation by enzymes.

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That plus the paper Alan Boyd posted below answered my question. Thank you! –  suvidu Jul 17 '13 at 12:59
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All DNA polymerases use an RNA primer during DNA replication - they cannot begin a DNA molecule de novo. Before the primer is removed the newly synthesised strand is an RNA-DNA hybrid. The first deoxynucleotide to be incorporated into the new DNA is added to the 3'-OH of an RNA.

Does this count?

Added later: this looks like a place to start reading

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It counts. But I still wonder if it is possible to find a deoxynucleotide in the middle of an RNA strand. BTW: thank you for correcting the question :-) –  suvidu Jul 2 '13 at 8:36
    
Great, thank you for the paper! –  suvidu Jul 2 '13 at 8:44
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