Structure of d(GT)_n·d(GA)_n Sequences:  Formation of Parallel Stranded Duplex DNA

Abstract

Alternating polypurine sequences exhibit remarkable polymorphism. In this study, we report that dGA.dGT sequences form parallel stranded duplex DNA at neutral pH. Using two model hairpins, 3'-d(GT)3-5'5'-T4(AG)3-3' (I) and 3'-d(GT)4-5'5'-T4(AG)4-3' (II), containing 5'5' linkages which direct parallel strand formation, we systematically explored the spectroscopic and thermodynamic properties of parallel stranded d(GA)n.d(GT)n. The parallel stranded hairpins are remarkably stable structures with TM's of 41.5 and 47.5 degreesC (in 0.4 M NaCl) for the shorter and longer hairpins, respectively. The van't Hoff enthalpies of 80.7 and 114 kJ mol-1 are relatively low but are comparable to a parallel stranded d(GA)n duplex. On the basis of the spectroscopic and electrophoretic characteristics, we conclude that parallel strand formation is not restricted to hairpin systems, but also readily occurs in unconstrained dimeric duplexes with the appropriate sequence homologies. Both melting curves and electrophoretic analyses of parallel stranded heteroduplexes in which the sequence enforces specific base pairing demonstrate that G-G and A-T base pairs are formed in d(GA)n.d(GT)n segments.

Structural Properties of G,T‐Parallel Duplexes

“…Melting temperature ( Tm ) was 51.8°C with a free energy change associated with the transition of −1.3 kcal/mol. This is consistent with previous data on hairpins of this type [24]. …”

“…The CD spectra of duplexes 4 – 6 consisted of a positive maximum at around 260 nm, zero-crossover at around 250 nm, and a negative band at around 240 nm (Figure 4). These spectra agree with previously described CD spectra for G,T-parallel duplexes [24]. The intensity of the bands was proportional to the number of 8-aminoadenine residues (Figure 4).…”

“…The circular dichroism (CD) spectrum of clamp 1 (Figure 2) was also consistent with reported spectra of G,T-parallel duplexes [24]. The CD spectrum consisted of a positive maximum at 260 nm, zero-crossover at 252 nm, and a negative band at 241 nm.…”

“…In this study, we have prepared several G,T-duplexes and examined the stability of G,T-parallel duplexes and triplexes formed by using G,T-parallel duplexes carrying 8-aminoadenine and 8-aminoguanine. G,T-Parallel duplexes have been studied [24] but there is little information on G,T-parallel triplexes [25]. …”

Unusual DNA Structure and DNA Damage Recognition: Structure and Dynamic Markers

“…Using the appropriate sequence design we could show that GG and AT parallel base pairs form. [19] A parallel strand disposition is also obtained in duplexes formed between complementary α− and β-anomeric sequences [20] (Fig. 3).…”