Oligodeoxynucleotide folding in solution: loop size and stability of B-hairpins

Abstract

The secondary structures of the synthetic DNA fragments d(CGCGCGTTTTTCGCGCG) (T5), d(CGCGCGAAAAACGCGCG) (A5), d(CGCGCGTACGCGCG) (TA), and d(CGCGCGATCGCGCG) (AT) were investigated in a combined electrophoretic and spectroscopic study. All the oligomers exist, at low temperature and over a wide range of ionic strength (0.5-100 mM salt) and of nucleotide concentration [0.1-2.0 mM (phosphate)], as a mixture of two slowly interconverting species, identified as the dimeric duplex and the monomeric hairpin structure. The thermodynamic parameters for hairpin denaturation of T5, A5, TA, and AT and for duplex denaturation of d(CGCGCG) show that (a) the hairpins are more stable than the reference hexamer duplex at all accessible nucleotide concentrations; (b) the loop contributes favorably to the enthalpy change of hairpin denaturation in the four DNA fragments; (c) the base composition of the loop (A vs T) and the size of the loop (A5/T5 vs TA/AT) do not appreciably influence the enthalpic contents of the hairpins; (d) hairpins TA and AT, with two AT bases intervening in the CG self-complementary part of the molecule, exhibit a markedly higher thermal stability than hairpins T5 and A5, which is entropic in origin. These findings are consistent with the presence of two-residue loops in the tetradecamers TA and AT.

Towards a better understanding of the unusual conformations of the alternating guanine–adenine repeat strands of DNA

“…However, their thermal melting is only slightly cooperative, but this is also the case with hairpins of such short molecules. 26 …”

Hairpins in a DNA site for topoisomerase II studied by1H-and31P-NMR

“…For instance, repeating sequences as (GC) or (AC) (i.e. purine-pyrimidine) have the ability of forming left-handed Z-DNA while purine or pyrimidine runs form triplexes and inverted repeats accomodate hairpin and cruciform conformations (1,(10)(11)(12)(13)(14)(15). They are frequently located near sites playing important roles in cellular processes such as replication, gene expression and regulation (15,16) and could provide preferential binding sites for proteins and drugs and proteins coupled to drugs.…”

Transcription of synthetic DNA containing sequences with dyad symmetry by wheat‐germ RNA polymerase II

“…As the peculiar kinetic behaviour encountered in the enzymatic synthesis of UpApU could be related to such DNA structural features, we investigated the possibility of hairpin formation using the monomeric units which constitute the polymers. Under the low-salt ionic conditions ofXodo et al [17,31,32], wefound that theabsorbance at 270 nm versus temperature profile of d[(GC),GTAT-(GC),G] exhibited biphasic behaviour (Fig. 6A, B).…”

“…Several recent reports [17, have dealt with the influence of DNA sequence on the processes of hairpin and cruciform formation, and several of these studies report stable hairpin formation with sequences similar to those present in the polymers studied here. As the peculiar kinetic behaviour encountered in the enzymatic synthesis of UpApU could be related to such DNA structural features, we investigated the possibility of hairpin formation using the monomeric units which constitute the polymers.…”

“…Melting curves were obtained in the low-salt buffer described by Xodo et al [17], using a Philips PU8700 spectrophotometer fitted with a PU8732 thermostated cuvette programmer and a PU8764 temperature controller. The temperature was increased at the rate of l"C/min.…”