Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG.C+ triplets

Three's a crowd - stabilisation, structure, and applications of DNA triplexes

DNA is a strikingly flexible molecule and can form a variety of secondary structures, including the triple helix, which is the subject of this review. The DNA triplex may be formed naturally, during homologous recombination, or can be formed by the introduction of a synthetic triplex forming oligonucleotide (TFO) to a DNA duplex. As the TFO will bind to the duplex with sequence specificity, there is significant interest in developing TFOs with potential therapeutic applications, including using TFOs as a delivery mechanism for compounds able to modify or damage DNA. However, to combine triplexes with functionalised compounds, a full understanding of triplex structure and chemical modification strategies, which may increase triplex stability or in vivo degradation, is essential - these areas will be discussed in this review. Ruthenium polypyridyl complexes, which are able to photooxidise DNA and act as luminescent DNA probes, may serve as a suitable photophysical payload for a TFO system and the developments in this area in the context of DNA triplexes will also be reviewed.

Oligonucleotides Containing Phenoxazine Artificial Nucleobases: Triplex-Forming Abilities and Fluorescence Properties

1,3-Diaza-2-oxophenoxazine ("phenoxazine"), a tricyclic cytosine analogue, can strongly bind to guanine moieties and improve π-π stacking effects with adjacent bases in a duplex. Phenoxazine has been widely used for improving duplex-forming abilities. In this study, we have investigated whether phenoxazine and its analogue, 1,3,9-triaza-2-oxophenoxazine (9-TAP), could improve triplex-forming abilities. A triplex-forming oligonucleotide (TFO) incorporating a phenoxazine component was found to show considerably decreased binding affinity with homopurine/homopyrimidine double-stranded DNA, so the phenoxazine system was considered not to function as either a protonated cytosine or thymine analogue. Alternatively, a 9-TAP-containing artificial nucleobase developed by us earlier as a new phenoxazine analogue functioned as a thymine analogue with respect to AT base pairs in a parallel triplex DNA motif. The fluorescence of the 9-TAP moiety was maintained even in triplex (9-TAP:AT) formation, so 9-TAP might be useful as an imaging tool for various oligonucleotide nanotechnologies requiring triplex formation.

Stabilization of RNA hairpins using non-nucleotide linkers and circularization

An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs are impeded by their thermodynamic instability, as they tend to unfold to form duplexes, especially at high concentrations required for crystallography or nuclear magnetic resonance spectroscopy. We have elaborated techniques to stabilize the RNA hairpins by linking the free ends of the RNA strand at the base of the hairpin stem. One method involves stilbene diether or hexaethylene glycol linkers and circularization by T4 RNA ligase. Another method uses click chemistry to stitch the RNA ends with a triazole linker. Both techniques are efficient and easy to perform. They should be useful in making stable, biologically relevant RNA constructs for structural studies.

Designed nucleotide binding motifs

Gaps in the central strand of oligonucleotide triplexes bind nucleoside phosphates tightly. Watson-Crick and Hoogsteen base pairing as design principle yield motifs with high affinity for nucleoside phosphates with A or G as nucleobase, including ATP. The second messenger 3',5'-cAMP is bound with nanomolar affinity. A designed DNA motif accommodates seven nucleotides at a time. The design was implemented for both DNA and RNA.

The stability of triplex DNA is affected by the stability of the underlying duplex

We have studied the formation of DNA triple helices in different sequence contexts and show that, for the most stable triplexes, their apparent stability is affected by the stability of the underlying duplex. For a 14-mer parallel triplex-forming oligonucleotide (generating C(+).GC and T.AT triplets) at pH 5.0 the T(m) is more than 10 degrees C lower with an intermolecular 14-mer duplex target, than it is with an intramolecular duplex, or one which is flanked by 6 GC base pairs at either end. A similar effect is seen with triplex-forming oligonucleotides that contain stabilising analogues, for which the T(m) is higher for an intramolecular than an intermolecular duplex target. These results suggest that the use of simple intermolecular duplex targets may underestimate the triplex stabilisation that is produced by some nucleotide analogues.

The dynamic properties of an intramolecular transition from DNA duplex to cytosine-thymine motif triplex

We here report that the formation and breakdown of an intramolecular cytosine-thymine (CT) motif DNA triple-helix can be performed repeatedly, quickly and independently of its local concentration without performance reduction over successive cycles; as a consequence, we propose that this set of characteristics makes the DNA duplex-triplex transition an ideal candidate to power simple nanometer-scale devices capable of maintaining effective performance regardless of their local concentration.

Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives

The structural, dynamical, and recognition properties of antiparallel DNA triplexes formed by the antiparallel d(G#G.C), d(A#A.T), and d(T#A.T) motifs (the pound sign and dot mean reverse-Hoogsteen and Watson-Crick hydrogen bonds, respectively) are studied by means of "state of the art" molecular dynamics simulations. Once the characteristics of the helix are defined, molecular dynamics and thermodynamic integration calculations are used to determine the expected stabilization of the antiparallel triplex caused by the introduction of 8-aminopurines. Finally, oligonucleotides containing 8-aminopurine derivatives are synthesized and tested experimentally using several approaches in a variety of systems. A very large stabilization of the triplex is found experimentally, as predicted by simulations. These results open the possibility for the use of oligonucleotides carrying 8-aminopurines to bind single-stranded nucleic acids by formation of antiparallel triplexes.

Beyond nucleic acid base pairs: from triads to heptads

Hydrogen-bonded base pairs are an important determinant of nucleic acid structure and function. However, other interactions such as base-base stacking, base-backbone, and backbone-backbone interactions as well as effects exerted by the solvent and by metal or NH(4)(+) ions also have to be taken into account. In addition, hydrogen-bonded base complexes involving more than two bases can occur. With the rapidly increasing number and structural diversity of nucleic acid structures known at atomic detail higher-order hydrogen-bonded base complexes, base polyads, have attracted much interest. This review provides an overview on the occurrence of base polyads in nucleic acid structures and describes computational studies on these nucleic acid building blocks.

Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives

The structure of parallel-stranded duplexes of DNA-containing a mixture of guanines (G) and adenines (A) is studied by means of molecular dynamics (MD) simulation, as well as NMR and circular dichroism (CD) spectroscopy. Results demonstrate that the structure is based on the Hoogsteen motif rather than on the reverse Watson-Crick one. Molecular dynamics coupled to thermodynamic integration (MD/TI) calculations and melting experiments allowed us to determine the effect of 8-amino derivatives of A and G and of 8-amino-2'-deoxyinosine on the stability of parallel-stranded duplexes. The large stabilization of the parallel-stranded helix upon 8-amino substitution agrees with a Hoogsteen pairing, confirming MD, NMR, and CD data, and suggests new methods to obtain DNA triplexes for antigene and antisense purposes.

The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine

The effect of amino groups attached at positions 2 and 8 of the hypoxanthine moiety in the structure, reactivity and stability of DNA duplexes and triplexes is studied by means of quantum mechanical calculations, as well as extended molecular dynamics (MD) and thermodynamic integration (MD/TI) simulations. Theoretical estimates of the change in stability related to 2'-deoxyguanosine (G) --> 2'-deoxyinosine (I) --> 8-amino-2'-deoxyinosine (8AI) mutations have been experimentally verified, after synthesis of the corresponding compounds. An amino group placed at position 2 stabilizes the duplex, as expected, and surprisingly also the triplex. The presence of an amino group at position 8 of the hypoxanthine moiety stabilizes the triplex but, surprisingly, destabilizes the duplex. The subtle electronic redistribution occurring upon the introduction of an amino group on the purine seems to be responsible for this surprising behavior. Interesting 'universal base' properties are found for 8AI.

A two B-Z junction containing DNA resolves into an all right-handed double-helix

Natural and artificial oligonucleotides are capable of assuming many different conformations and functions. Here we present results of an NMR restrained molecular modelling study on the conformational preferences of the modified decanucleotide d((m)C1G2(m)C3G4C5(L)G6(L)(m)C7G8(m)C9G10) .d((m)C11G12(m)C13G14C15(L)G (L)16(m)C17-G18(m)C19G20 ) which contains L deoxynucleotides in its centre. This chimeric DNA was expected to form a right-left-right-handed B-type double-helix (BB*B) at low salt concentration. Actually, it matured into a fully right-handed double helix with its central C(L)pG(L) core forming a right-handed Z-DNA helix embedded in a B-DNA matrix (BZ*B). The interplay between base-base and base-sugar stackings within the core and its immediately adjacent residues was found to be critical in ensuring the stabilisation of the right-handed helix. The structure could serve as a model for the design of antisense oligonucleotides resistant to nucleases and capable of hybridising to natural DNAs and RNAs.

DNA-triplex stabilizing properties of 8-aminoguanine

A DNA-triplex stabilizing purine (8-aminoguanine) is designed based on molecular modeling and synthesized. The substitution of guanine by 8-aminoguanine largely stabilizes the triplex both at neutral and acidic pH, as suggested by molecular dynamics and thermodynamic integration calculations, and demonstrated by melting experiments. NMR experiments confirm the triplex-stabilizing properties of 8-aminoguanine and demonstrate that few changes are found in the structure of the triplex due to the presence of this modified base.

Sequence-dependent stability of intramolecular DNA triple helices

A set of 21 oligodeoxynucleotides were designed to fold into intramolecular triple helices of the pyrimidine motif under appropriate conditions. UV melting experiments on the triplexes which only differ in the number and distribution of third strand cytosines reveal the influence of sequence and pH on triplex stability and can be summarized as follows: (1) increasing the cytosine content in the third strand results in a higher thermal stability of the triplex at acidic pH but lowers the triplex to duplex melting temperature at neutral pH; (2) cytosines at terminal positions destabilize the triple helical structure as compared to non-terminal positions; (3) contiguous cytosines lead to a pH dependent destabilization of the triplex, the destabilizing effect being more pronounced at higher pH. Analysis of these effects in terms of the various interactions within a triple helical complex indicate that the sequence-dependent stabilities are largely determined by the extent of protonation for individual third strand cytosines.

Multistranded DNA structures

DNA oligonucleotides can form multistranded helices through either the folding of a single strand or the association of two, three or four strands of DNA. Structures of several new DNA triplexes, G-quartet DNA quadruplexes and I-motif DNA quadruplexes have been reported recently. These structures provide new insights into helix stability and folding, loop conformations and cation interactions.

Can G-C Hoogsteen-wobble pairs contribute to the stability of d(G. C-C) triplexes?

Quantum mechanics, molecular dynamics and statistical mechanics methods are used to analyze the importance of neutral Hoogsteen-wobble G.C pairing in the stabilization of triple helices based on the poly-(G.C-C) trio at neutral pH and low ionic strength. In spite of the existence of a single hydrogen bond, the Hoogsteen-wobble G.C pair is found to be quite stable both in gas phase and solvated DNA. Molecular dynamics simulations of different triplexes based on the d(G.C-C) trio leads to stable structures if the neutral d(G.C-C) steps stabilized by Hoogsteen-wobble pairs are mixed with d(G.C-C+) steps. Finally, high level ab initio calculations and thermodynamic integration techniques are used to determine the relative stability of G.C wobble and G.C imino pairings. It is found that triplexes containing the imino pairing are slightly more stable structures than those with the wobble one, due mainly to a better stacking.

Solution conformation of a parallel DNA triple helix with 5' and 3' triplex-duplex junctions

BACKGROUND

Polypurine x polypyrimidine sequences of DNA can form parallel triple helices via Hoogsteen hydrogen bonds with a third DNA strand that is complementary to the purine strand. The triplex prevents transcription and could therefore potentially be used to regulate specific genes. The determination of the structures of triplex-duplex junctions can help us to understand the structural basis of specificity, and aid in the design of optimal antigene oligonucleotides.

RESULTS

The solution structures of the junction triplexes d(GAGAGACGTA)-X-(TACGTCTCTC)-X-(CTCTCT) and d(CTCTCT)-X-(TCTCTCAGTC)-X-(GACTGAGAGA) (where X is bis(octylphosphate) and nucleotides in the triplex regions are underlined) have been solved using nuclear magnetic resonance (NMR) spectroscopy. The structure is characterised by significant changes in the conformation of the purine residues, asymmetry of the 5' and 3' junctions, and variations in groove widths associated with the positive charge of the protonated cytosine residues in the third strand. The thermodynamic stability of triplexes with either a 5' or a 3'CH+ is higher than those with a terminal thymidine.

CONCLUSIONS

The observed sequence dependence of the triplex structure, and the distortions of the DNA at the 5' and 3' termini has implications for the design of optimal triplex-forming sequences, both in terms of the terminal bases and the importance of including positive charges in the third strand. Thus, triplex-stabilising ligands might be designed that can discriminate between TA x T-rich and CG x C+-rich sequences that depend not only on charge, but also on local groove widths. This could improve the stabilisation and specificity of antigene triplex formation.