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Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Perturbations in Structures of Backbone Modified DNA to Probe Cation-DNA Interactions

Computational and NMR structural studies of backbone modified duplex DNA fragments have supported the suggestion that cation binding to phosphates plays an important role in DNA structure and in binding of nucleic acids to proteins. The NMR solution structures for several unmodified and dithioate backbone modified 14-base paired duplex aptamers targeting NF-κB have been determined by a hybrid, complete matrix (MORASS)/restrained molecular dynamics method. Structural perturbations of the dithioate substitutions support our suggestion that the dithioate binds cations less tightly than phosphoryl groups. This increases the electrostatic repulsion across the B-form narrow minor groove and enlarges the minor groove, similar to that found in A-form duplexes. Structural analysis of modeled aptamer complexes with NF-κB homo and heterodimers suggests that the dithioate backbone substitution can increase the aptamer?s relative affinity to basic groups in proteins such as NF-κB by helping to ?strip? the cations from the aptamer backbone. Similarly, structural perturbations in DNA methylphosphonates support the role of cation binding in stabilizing duplex structures. High resolution proton and phosphorus NMR experiments were performed on two duplexes, formed by diastereomerically pure methylphosphonates with complementary DNA. The NMR structures of two hybrid duplexes, d(TGTTTGGC):d(CRCRARARARCRA) and d(TGTTTGGC):d(CRCRARASARCRA), were determined.

David Volk1
XianBin Yang1
David Power1
Ekaterina V. Viazovkina1,2
Elena V. Bichenkova
V. Thiviyanathan1
Bruce A. Luxon1
Elliot K.Gozansky1
Alexander V. Lebedev2
David G. Gorenstein1,*

1Department of Human Biological Chemistry & Genetics
Sealy Center for Structural Biology
University of Texas Medical Branch
Galveston, TX, USA
2Institute of Bioorganic Chemistry
Novosibirsk, Russia
*david@nmr.utmb.edu