Energetic signatures of single base bulges: thermodynamic consequences and biological implications

Abstract

DNA bulges are biologically consequential defects that can arise from template-primer misalignments during replication and pose challenges to the cellular DNA repair machinery. Calorimetric and spectroscopic characterizations of defect-containing duplexes reveal systematic patterns of sequence-context dependent bulge-induced destabilizations. These distinguishing energetic signatures are manifest in three coupled characteristics, namely: the magnitude of the bulge-induced duplex destabilization (ΔΔGBulge); the thermodynamic origins of ΔΔGBulge (i.e. enthalpic versus entropic); and, the cooperativity of the duplex melting transition (i.e. two-state versus non-two state). We find moderately destabilized duplexes undergo two-state dissociation and exhibit ΔΔGBulge values consistent with localized, nearest neighbor perturbations arising from unfavorable entropic contributions. Conversely, strongly destabilized duplexes melt in a non-two-state manner and exhibit ΔΔGBulge values consistent with perturbations exceeding nearest-neighbor expectations that are enthalpic in origin. Significantly, our data reveal an intriguing correlation in which the energetic impact of a single bulge base centered in one strand portends the impact of the corresponding complementary bulge base embedded in the opposite strand. We discuss potential correlations between these bulge-specific differential energetic profiles and their overall biological implications in terms of DNA recognition, repair and replication.

Non-Nucleosidic Analogues of Polyaminonucleosides and Their Influence on Thermodynamic Properties of Derived Oligonucleotides

“…Yet, even three positive charges of a spermine residue do not neutralize the bulge effect as such. The observed changes of ΔG for the studied duplexes (ON7-ON9) are in the range observed for duplexes with a single bulge (ΔΔG, 2-6 kcal/mol) [46,47].…”

“…Next, we investigated the influence of polyamine derivatives X0, X1 and X2 on duplex stability, inserted as bulges in the middle of the sequence (Table 1, entry ON7-ON9). The changes of duplex stability caused by single nucleotide bulges differ and depend on the type of flanking bases [46,47]. Incorporation of X0-X2 resulted in a lowering of melting temperature independently of polyamine residue.…”

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

“…Single-base bulge loops have been extensively studied in DNA and RNA in 1 M NaCl (Tanaka et al 2004;Blose et al 2007;Minetti et al 2010). Temperature-gradient gel electrophoresis has been performed on DNA and RNA single bulge loop constructs in one study where adenine and guanine 1-nt bulge loops had similar mobility for RNA and DNA constructs, implying similar structural conformations form in these constructs (Zhu and Wartell 1999 loop of 3.8 kcal/mol, similar to our proposed value.…”

“…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.…”

“…Single-nucleotide bulge loops have been studied in both RNA and DNA constructs (Zhu and Wartell 1999;Tanaka et al 2004;Blose et al 2007;Minetti et al 2010). A recent study examined the thermodynamic stability of the trinucleotide bulge loops in RNA (Murray et al 2014).…”