Background: DNA Melting and Absorbance at 260 nm

• When double-stranded nucleic acids (DNA or RNA) are heated, the strands separate (denature), leading to an increase in absorbance at 260 nm (hyperchromicity).

• This change is typically sharp and sigmoidal, with a well-defined melting temperature (Tm) where 50% of the strands are denatured.

• Melting curves are widely used to analyze nucleic acid stability and sequence characteristics.

Analysis of the Options

1. Double stranded DNA

   • Shows a sharp melting curve with a clear Tm due to cooperative strand separation.

2. Double stranded RNA

   • Also exhibits a typical melting profile with a sharp transition because of stable base pairing.

3. DNA:RNA hybrid

   • Forms stable duplexes with characteristic melting curves similar to double-stranded nucleic acids.

4. Single stranded DNA having imperfect secondary structures

   • Does not show a typical sharp melting transition.

   • Imperfect secondary structures (like hairpins or loops) melt over a broad temperature range, resulting in a gradual, less cooperative increase in absorbance.

   • The melting profile is often noisy or lacks a clear Tm.

Supporting Information from Literature

• Melting curve analysis typically assumes a two-state transition between double-stranded and single-stranded forms.

• Single-stranded DNA with imperfect or transient secondary structures does not undergo a cooperative melting transition, leading to atypical or absent sharp melting curves.

• This is confirmed by UV absorbance and fluorescence melting studies showing broad or multiple transitions for such samples.

Conclusion

The nucleic acid sample not expected to generate a typical melting profile with a sharp transition upon heating is:

(4) Single stranded DNA having imperfect secondary structures

Keywords

DNA melting curve, nucleic acid denaturation, hyperchromicity, melting temperature, single-stranded DNA, secondary structure, DNA:RNA hybrid, double-stranded RNA, UV absorbance at 260 nm, nucleic acid stability

Final answer:
(4) Single stranded DNA having imperfect secondary structures