Parallel-Stranded DNA with Mixed AT/GC Composition:  Role of trans G·C Base Pairs in Sequence Dependent Helical Stability

Abstract

Parallel-stranded (ps) DNAs with mixed AT/GC content comprising G.C pairs in a varying sequence context have been investigated. Oligonucleotides were devised consisting of two 10-nt strands complementary either in a parallel or in an antiparallel orientation and joined via nonnucleotide linkers so as to form 10-bp ps or aps hairpins. A predominance of intramolecular hairpins over intermolecular duplexes was achieved by choice of experimental conditions and verified by fluorescence determinations yielding estimations of rotational relaxation times and fractional base pairing. A multistate mode of ps hairpin melting was revealed by temperature gradient gel electrophoresis (TGGE). The thermal stability of the ps hairpins with mixed AT/GC content depends strongly on the specific sequence in a manner peculiar to the ps double helix. The thermodynamic effects of incorporating trans G.C base pairs into an AT sequence are context-dependent: an isolated G. C base pair destabilizes the duplex whereas a block of > or =2 consecutive G.C base pairs exerts a stabilizing effect. A multistate heterogeneous zipper model for the thermal denaturation of the hairpins was derived and used in a global minimization procedure to compute the thermodynamic parameters of the ps hairpins from experimental melting data. In 0.1 M LiCl at 3 degrees C, the formation of a trans G.C pair in a GG/CC sequence context is approximately 3 kJ mol(-)(1) more favorable than the formation of a trans A.T pair in an AT/TA sequence context. However, GC/AT contacts contribute a substantial unfavorable free energy difference of approximately 2 kJ mol(-)(1). As a consequence, the base composition and fractional distribution of isolated and clustered G.C base pairs determine the overall stability of ps-DNA with mixed AT/GC sequences. Thus, the stability of ps-DNA comprising successive > or =2 G.C base pairs is greater than that of ps-DNA with an alternating AT sequence, whereas increasing the number of AT/GC contacts by isolating G.C base pairs exerts a destabilizing effect on the ps duplex. Molecular modeling of the various helices by force field techniques provides insight into the structural basis for these distinctions.

Synthesis and Pairing Properties of α‐Tricyclo‐DNA

“…All duplexes show similar hyperchromicities, indicating similar extents of base pairing and base stacking. While Watson-Crick-paired structures are expected with parallel complements, the matter of the pairing mode in the antiparallel duplex was open; pH variation did not result in T m differences, ruling out Hoogsteen and reversed-Hoogsteen structures, so the most likely interaction of the bases is the reversed-Watson-Crick mode ( Figure 5), as is also observed in parallel b-DNA duplexes [28,29] and in antiparallel b-DNA/a-DNA duplexes exhibiting noncanonical G-A base pairs. [30] In this mixed sequence context, a-tc-DNA/RNA duplex stability is approximately the same as DNA/DNA duplex stability, lying between DNA/RNA and RNA/RNA duplex stability (Table 2).…”

“…This is not unusual and is also observed for parallel reversed-WatsonCrick and antiparallel Watson-Crick paired DNA. [28] In the cases of pDNA or apDNA as the complement, the two positive ellipticity maxima at 220 and 275 nm are inverted in their relative amplitude. As can be seen from the curves at high temperatures, at which the CD reflects the sum of the CD traces of the single strands, this inversion of maxima is to a large extent due to the spectral properties of the single strands and so is not a specific property of the ordered structure.…”

Anomeric DNA quadruplexes

“…37 The free dye contribution was taken into account as described elsewhere. 38 The concentration of EtBr was 4 μM, and the oligonucleotide concentration was in the range of 4-6 μM. The fluorescence lifetime (τ) of EtBr:TBA complexes was evaluated using the Easy Life V fluorometer.…”

Stability of DNA upon interaction with dimethyltin dichloride

“…In addition, biologically important agents that modify DNA may also affect its thermal and thermodynamic stability, which may be associated with the mechanism underlying biological activity of such agents. Thus, the studies of thermal and thermodynamic stability of DNA modified by various agents are of great interest (Shchyolkina et al, 2000). The interaction of organometallic derivatives with DNA is of great interest for therapeutic treatment, since these compounds can recognize specific DNA sequences, alter the local DNA structure, and affect the gene-expression process.…”