Structural characteristics of 2'-O-(2-methoxyethyl)-modified nucleic acids from molecular dynamics simulations

Kenneth E. Lind, Venkatraman Mohan, Muthiah Manoharan, David M. Ferguson

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The structure and physical properties of 2'-sugar substituted O-(2-methoxyethyl) (MOE) nucleic acids have been studied using molecular dynamics simulations. Nanosecond simulations on the duplex MOE[CCAACGTTGG]-r[CCAACGUUGG] in aqueous solution have been carried out using the particle mesh Ewald method. Parameters for the simulation have been developed from ab initio calculations on dimethoxyethyl fragments in a manner consistent with the AMBER 4.1 force field database. The simulated duplex is compared with the crystal structure of the self-complementary duplex d[GCGTAT(MOE)ACGC]2, which contains a single modification in each strand. Structural details from each sequence have been analyzed to rationalize the stability imparted by substitution with 2'-O-(2-methoxyethyl) side chains. Both duplexes have an A-form structure, as indicated by several parameters, most notably a C3' endo sugar pucker in all residues. The simulated structure maintains a stable A-form geometry throughout the duration of the simulation with an average RMS deviation of 2.0 Å from the starting A-form structure. The presence of the 2' substitution appears to lock the sugars in the C3' endo conformation, causing the duplex to adopt a stable A-form geometry. The side chains themselves have a fairly rigid geometry with trans, trans, gauche+/- and trans rotations about the C2'-O2', O2'-CA', CA'-CB' and CB'-OC' bonds respectively.

Original languageEnglish (US)
Pages (from-to)3694-3699
Number of pages6
JournalNucleic acids research
Issue number16
StatePublished - Aug 15 1998

Bibliographical note

Funding Information:
We would like to thank Professor Martin Egli for providing a preprint of his paper detailing the crystal structure of a MOE-substituted duplex. K.E.L. would like to acknowledge support from NIH Training Grant GM07994. We would also like to thank the National Cancer Institute for allocation of computing time and staff support at the Frederick Biomedical Supercomputing Center.


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