Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges

Abstract

Ultraviolet absorption techniques were used to study the thermodynamics of duplex formation for a DNA decamer, d(GCGAAAAGCG).d(CGCTTTTCGC), and a series of related duplexes, each of which contains a bulged base centered in the A.T tract. Thermodynamic parameters were obtained from nonlinear least-squares fits of the melting curves and the concentration dependences of the melting temperatures. Duplexes containing a localized single-base bulge were found to be 3.5-4.6 kcal/mol less stable than the decamer at 37 degrees C. These results indicate that both the identity of the bulged base and the strand in which it is located may influence the amount by which the duplex is destabilized. Bulged bases located in the T-strand, d(CGCTTYTTCGC), in position Y, were observed to be slightly more destabilizing than those located in the A-strand, d(GCGAAXAAGCG), in position X. Bulged purines may be more destabilizing than bulged pyrimidines.

Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs

“…Single-nucleotide bulge loops have been studied in DNA (LeBlanc and Morden 1991;Zhu and Wartell 1999;Minetti et al 2010) loop parameters are underestimated in current models for DNA structure prediction due to a lack of systematic experimental data on bulge loops.…”

Role of the Structure of the Top Half of HIV-1 cTAR DNA on the Nucleic Acid Destabilizing Activity of the Nucleocapsid Protein NCp7

“…A min ðTÞ and A max ðTÞ are the absorbances in the pre and post-transition regions, respectively 48,69 and are fitted according to a linear equation: A max;min ðTÞ ¼ A 0 max;min þ TA 1 max;min . 25 Moreover, assuming that DH8 is independent of temperature, we can further deduce the entropy change, DS8 by: DS8 ¼ DH8=t m : Finally, the free energy change, DG8 37 ; at 37 8C is calculated by: DG8 37 ¼ DH8 2 TDS8: Noticeably, significant heat capacity changes DC p have been recently associated with DNA melting.…”

HIV-1 Nucleocapsid Protein Binds to the Viral DNA Initiation Sequences and Chaperones their Kissing Interactions

“…A min (T) and A max (T) are the absorbances in the pre-transition and post-transition regions, respectively, 61 …”