Abstract

A single-point substitution of the O4' oxygen by a CH2 group at the sugar residue of (A) under bar (6) (i.e. 2'-deoxyaristeromycin moiety) in a self-complementary DNA duplex, 5'd-(C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)C(9)G(10)C(11)G(12))(2)(-3,), has been shown to steer the fully Watson-Crick basepaired DNA duplex (1A), akin to the native counterpart, to a doubly (A) under bar (6):T-7 Hoogsteen basepaired (1B) B-type DNA duplex, resulting in a dynamic equilibrium of (1A)reversible arrow (1B): K-eq = k(1)/k-(1) = 0.56 +/-0.08. The dynamic conversion of the fully Watson-Crick basepaired (IA) to the partly Hoogsteen basepaired (1B) structure is marginally kinetically and thermodynamically disfavoured [k(1) (298K) = 3.9 0.8 sec(-1); DeltaH degrees (double dagger) = 164 +/- 14 kJ/mol; -T DeltaS degrees (double dagger) (298K) = -92 kJ/mol giving a DeltaG(298)(degrees double dagger) of 72 kJ/mol. Ea (k1) = 167 14 kJ/mol] compared to the reverse conversion of the Hoogsteen (1B) to the Watson-Crick (1A) structure [k-1 (298K) = 7.0 0.6 sec-1, DeltaH degrees (double dagger) = 153 13 kJ/mol; -T DeltaS degrees (double dagger) (298K) = -82 kJ/mol giving a DeltaG(298)degrees (double dagger) of 71 kJ/mol. Ea (k-1) = 155 13 kJ/mol]. A comparison of DeltaG(298)degrees (double dagger) of the forward (k1) and backward (k-1) conversions, (1A)Ff(1B), shows that there is ca 1 kJ/mol preference for the Watson-Crick (1A) over the double Hoogsteen basepaired (1B) DNA duplex, thus giving an equilibrium ratio of almost 2:1 in favour of the fully Watson-Crick basepaired duplex. The chemical environments of the two interconverting DNA duplexes are very different as evident from their widely separated sets of chemical shifts connected by temperature-dependent exchange peaks in the NOESY and ROESY spectra. The fully Watson-Crick basepaired structure (1A) is based on a total of 127 intra, 97 inter and 17 cross-strand distance constraints per strand, whereas the double A(6):T-7 Hoogsteen basepaired (1B) structure is based on 114 intra, 92 inter and 15 cross-strand distance constraints, giving an average of 22 and 20 NOE distance constraints per residue and strand, respectively. In addition, 55 NMR-derived backbone dihedral constraints per strand were used for both structures. The main effect of the Hoogsteen basepairs in (1B) on the overall structure is a narrowing of the minor groove and a corresponding widening of the major groove. The Hoogsteen basepairing at the central A6:T7 basepairs in (1B) has enforced a syn conformation on the glycosyl torsion of the 2'-deoxyaristeromycin moiety, A6, as a result of substitution of the endocyclic 4'-oxygen in the natural sugar with a methylene group in A6. A comparison of the Watson-Crick basepaired duplex (1A) to the Hoogsteen basepaired duplex (1B) shows that only a few changes, mainly in alpha, sigma and gamma torsions, in the sugar-phosphate backbone seem to be necessary to accommodate the Hoogsteen basepair.

Published in

Journal of Biomolecular Structure and Dynamics
2001, Volume: 18, number: 6, pages: 783-806
Publisher: ADENINE PRESS INC

UKÄ Subject classification

Structural Biology


Publication identifier

DOI: https://doi.org/10.1080/07391102.2001.10506707

Permanent link to this page (URI)

https://res.slu.se/id/publ/83901