Question

We normally think that single-stranded nucleic acids should not melt, but many, in fact, do have a Tm. How can this be explained?

Answer 1

The melting temperature (Tm) is defined as the temperature at which 50% of the double stranded nucleic acids have changed into single stranded nucliec acids.

In case of single stranded DNA and RNA, the single strands often fold onto themselves to form complimentarity with sequences internal to them, as shown in the image attached below. This causes the single stranded nucliec acid to develop partial characteristics of double-strandedness. Hence, when it is subjected to increasing temperatures, the secondary structures thus formed start to melt away. Hence, there exists a Tm at which half of the total single-stranded nucleic acids have lost their secondary structures formed due to self-complimentarity.

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