Molecular Dynamics Investigations of DNA Triple Helical Models: Unique Features of the Watson-Crick Duplex

Abstract

We have built computer models of triple helical structures with a third poly(dT) strand Hoogsteen base paired to the major groove of a poly(dA).poly(dT) Watson-Crick (WC) base-paired duplex in the canonical A-DNA as well as B-DNA. For the A-DNA form, the sugar-phosphate backbone of the third strand intertwines and clashes with the poly(dA) strand requiring a radical alteration of the duplex to access the hydrogen bonding sites in the major groove. In contrast, when the duplex was in the canonical B-DNA form, the third strand was readily accommodated in the major groove without perturbing the duplex. The triple helical model, with the duplex in the B-DNA form, was equilibrated for 400ps using molecular dynamics simulations including water molecules and counter-ions. During the entire simulations, the deoxyriboses of the adenine strand oscillate between the S-type and E-type conformations. However, 30% of the sugars of the thymine strands-II & III switch to the N-type conformation early in the simulations but return to the S-type conformation after 200ps. In the equilibrium structure, the WC duplex portion of the triplex is unique and its geometry differs from both the A- or B-DNA. the deoxyriboses of the three strands predominantly exhibit S-type conformation. Besides the sugar pucker, the major groove width and the base-tilt are analogous to B-DNA, while the X-displacement and helical twist resemble A-DNA, giving a unique structure to the triplex and the Watson & Crick and Hoogsteen duplexes.

Targeting neighbouring poly(purine·pyrimidine) sequences located in the human bcr promoter by triplex‐forming oligonucleotides

“…Molecular modeling was carried out to visualize the nature and extent of stacking interactions at base inversion sites in the case of 24‐mer triplex, as well as between the 5′‐ and 3′‐terminal bases of the two split triplexes formed by different 13‐mer and 14‐mer TFOs. Earlier modeling studies [21,22] have shown that DNA duplex in a triplex is similar to DNA except for the displacement of base pairs by about −2 to −2.5 Å from the centre of the line joining the long axis of Watson‐Crick pairs. This is consistent with the recent crystal structure [23] and NMR studies [24,25].…”

“…The bases corresponding to 24‐mer, 13‐mer and 14‐mer TFOs are positioned against the corresponding purine‐rich strand of the duplex to form reverse Hoogsteen hydrogen bonds of either G·GC or A·AT type so as to generate antiparallel triplexes. Stereochemistry of the third strand was regularized to overcome steric interactions, especially at steps formed by mixed triplets of nonisosteric types, utilizing the constrained–restrained molecular geometry optimization and energy minimization using only the van der Waal’s interactions as reported earlier [22] by using x plor [26]. Subsequently, these were subjected to complete minimization to include water and ions as well as long‐range electrostatic interactions using amber 5.0 [27].…”

A Kinetic Study of Triple‐Helix Formation at a Critical R · Y Sequence of the Murine c‐Ki‐ras Promoter by (A,G)‐ and (G,T) Oligonucleotides

“…To understand why triplex formation occurs at a slower rate, in particular when the third strand is a G-rich sequence, it is helpful to analyse the structural changes accompanying the interaction between a TFO and a duplex. The factors that are expected to influence negatively the rate of triplex formation are, duplex rigidity, a triple helix formation requires that a third strand wraps around the duplex, so it is possible that the lower flexibility of the duplex with respect to a single strand makes triplex formation more difficult than duplex recombination; local structural changes, a duplex to host a third strand may undergo some local structural changes such as major groove widening, as suggested by Sekharudu et al (1993); electrostatic repulsion, the phosphate repulsion between a duplex and a single strand is expected to be stronger than the repulsion between two single strands; TFO hyperstructures, the formation by G-rich oligonucleotides of unusual structures, which subtracts free TFO from its interaction with the target duplex, may be relevant under physiological conditions. This self-association phenomenon may represent a serious problem to triplex formation.…”

Base triplet nonisomorphism strongly influences DNA triplex conformation: Effect of nonisomorphic G∗︁ GC and A∗︁ AT triplets and bending of DNA triplexes

“…Nearly uniform values of $À2.5 A is found in the isomorphic T * AT and C þ * GC triplex for both C Á Á Á G and A Á Á Á T pairs to maintain the optimum geometry for the Hoogsteen hydrogen bonds. [47][48][49] Average values of major groove width in the average structure of the polypurine and polypyrimidine d(AG) 7 …”

“…Of the prominent structural changes seen are the widening of the major groove and X-displacement, indicating that the duplex in a DNA triplex exhibits features intermediate between the canonical A-and B-DNA. 47 In the average structure of a GA triplex (last 2.4 ns), mean values of X-displacement for the C Á Á Á G and T Á Á Á A pairs correspond to À4.1(5) and À2.2(4) A , respectively. This is in contrast to the nearly similar values ($À3 A ) found in the nonisomorphic GT triplex.…”