Stability of DNA Duplexes Containing GG, CC, AA, and TT Mismatches

Abstract

We employed salt-dependent differential scanning calorimetric measurements to characterize the stability of six oligomeric DNA duplexes (5'-GCCGGAXTGCCGG-3'/5'-CCGGCAYTCCGGC-3') that contain in the central XY position the GC, AT, GG, CC, AA, or TT base pair. The heat-induced helix-to-coil transitions of all the duplexes are associated with positive changes in heat capacity, DeltaC(p), ranging from 0.43 to 0.53 kcal/mol. Positive values of DeltaC(p) result in strong temperature dependences of changes in enthalpy, DeltaH degrees, and entropy, DeltaS degrees , accompanying duplex melting and cause melting free energies, DeltaG degrees, to exhibit characteristically curved shapes. These observations suggest that DeltaC(p) needs to be carefully taken into account when the parameters of duplex stability are extrapolated to temperatures distant from the transition temperature, T(M). Comparison of the calorimetric and van't Hoff enthalpies revealed that none of the duplexes studied in this work exhibits two-state melting. Within the context of the central AXT/TYA triplet, the thermal and thermodynamic stabilities of the duplexes in question change in the following order: GC> AT > GG > AA approximately TT > CC. Our estimates revealed that the thermodynamic impact of the GG, AA, and TT mismatches is confined within the central triplet. In contrast, the thermodynamic impact of the CC mismatch propagates into the adjacent helix domains and may involve 7-9 bp. We discuss implications of our results for understanding the origins of initial recognition of mismatched DNA sites by enzymes of the DNA repair machinery.

Mechanisms of Antisense Transcription Initiation from the 3′ End of the GAL10 Coding Sequence In Vivo

“…This is possibly due to hybridization of the P1 primer with the poly(A) tails of mRNAs via matched (A·T) and mismatched (A·G, A·C, and A·A) base pairs at 42°C during cDNA synthesis by AMV reverse transcriptase. In support of this possibility, previous studies have demonstrated and characterized A·G, A·C, and A·A mismatched base pairs (72)(73)(74)(75)(76)(77)(78). Further, the P1 primer may also randomly hybridize to RNAs (including mRNAs, rRNAs, and tRNAs) at 42°C during cDNA synthesis via matched (A·T and G·C) and previously demonstrated mismatched (G·T, G·A, A·C, T·C, G·G, A·A, T·T, and C·C) base pairs (72)(73)(74)(75)(76)(77)(78)(79)(80)(81)(82)(83)(84).…”

Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification

“…Changing the 5′ terminal base from a guanine to a cytosine in the SNP-containing target DNA relative to the fully complementary DNA target is the most destabilizing mismatch in terms of enthalpy42, reducing the T m by ∼2.6 °C. A similar change is observed in Fig.…”

Base Flipping within the α-Hemolysin Latch Allows Single-Molecule Identification of Mismatches in DNA

“…This is consistent with reports that incorporation of a mismatch into dsDNA has only a limited effect on the global conformation of a duplex. 36 …”