The main focus is to further our understanding of the physico-chemical properties of unusual DNA structures. We designed a set of stem-loop DNA molecules to mimic a common motif of mRNA i.e., a hairpin with internal loops. We used a combination of UV spectroscopy and differential scanning calorimetry (DSC) techniques to determine the unfolding thermodynamics of a set of hairpins with sequence: d(GCGCTnGTAACT5GTTACTnGCGC), where "Tn" corresponds to internal loops with n = 1, 3 or 5 and "T5" is an end loop of 5 thymines. UV melts of each hairpin show monophasic transitions with TMs that are independent of strand concentration i.e., all hairpins formed intramolecularly. DSC profiles indicate hairpin unfolding results from the typical compensation of an unfavorable enthalpy with a favorable entropy. The increase in the size of the internal loop yielded: a) lower TMs and similar enthalpy contributions; b) lower heat capacity values that correlated with the lower releases of structural water; and c) higher ion releases. Therefore, hairpin loops with large internal loops are less stable and amenable for their targeting with complementary oligonucleotides. © 2011 American Chemical Society.