Solution Structure of an Intramolecular DNA Triplex Linked by Hexakis(ethylene glycol) Units:  d(AGAGAGAA-(EG)₆-TTCTCTCT-(EG)₆-TCTCTCTT)^,

Abstract

A DNA molecule was designed and synthesized with three octanucleotide stretches linked by two hexakis(ethylene glycol) chains to form an intramolecular triplex in solution. The structural data obtained from a series of NMR NOESY spectra yielded interproton distances, and COSY experiments provided dihedral angle information for analysis of deoxyribose ring pucker. Using distance geometry followed by simulated annealing with restrained molecular dynamics and relaxation matrix refinement, a well-refined ensemble of conformations was calculated. Although some NOE cross-peaks involving protons of the hexakis(ethylene glycol) linker could be identified, most could not be assigned and the conformations of the linkers were not determined. The deoxyribose conformations are predominantly of the S type, except for the protonated cytosine residues in the third strand which show hybrid N and S character. Overall, the duplex part of the molecule resembles a B-DNA double helix with the third strand bound in its major groove by Hoogsteen hydrogen bonds. This structure provides a basis for comparison with triplexes containing noncanonical or nonnatural nucleotides.

Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices

“…The ligands were built and optimized in MacroModel and the RESP charges were derived using ab initio calculations with 6–31G* basis set in Jaguar program [57]. The structure of the dA 10 .2dT 10 triplex was built starting from the experimental (NMR) solution structure of related DNA triplex [62,63]. Twenty seven sodium ions were added to neutralize the initial structure.…”

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“…1c), so that the structural elements most essential in H-DNA formation are represented. Based on the present H-y5 structure and the structural data from H-y3 systems [14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29] , a mechanism is proposed for H-DNA formation consistent with the collective biochemical and biophysical data 2,3,9-13 . Fig.…”

“…None of these theories could rely on direct conformational evidence, because all three-dimensional structures available were obtained for H-y3 type intramolecular triple helices [14][15][16][17][18][19][20][21][22][23] , containing limited data for their (triplex) loops and no data for the interaction of the latter with the purine strand extension. We present the complete solution structure of a DNA fragment that forms an intramolecular triple helix of the H-y5 type.…”

Stabilization of RNA hairpins using non-nucleotide linkers and circularization

“…In the literature there are few examples where EG6 was used in structural studies. To date, the spacer was used only in NMR studies showing a stabilization effect on the DNA duplexes and a triplex structure (30–34). The NMR models revealed that EG6 did not interfere with the native DNA structure and showed conformational flexibility.…”

“…The non-nucleotide spacers has been shown to increase the thermal stability of the structure of duplexes, triplexes or tetraplexes (23–29). They were also implemented in nuclear magnetic resonance (NMR) (30–34) and crystallographic studies (29,35,36) but so far such linkers has not been used to stabilize the native structure of RNA hairpins.…”