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Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Stereoselectivelly deuterated nucleosides for NMR studies of DNA

In nucleic acids, 5'-protons of desoxyribose moiety form numerous inter- and intranucloetide nOe contacts that carry valuable information about the sugar pucker, glycosidic and sugar-phosphate torsion angles. However, impossibility to unambiguously assign 5' and 5" protons makes the extraction of these important structural parameters problematic. A stereoselective substitution of one nucleotide 5?-proton with deuterium has been proposed as the most straightforward solution of the assignment problem [1-3]. Using Alpine-Borane chemistry [4] we introduced deuterium at 5?-position of ribonucleosides with stereoselectivity of ca 20:1 [1]. Recently we applied the same approach to the synthesis of deuterated 2?-deoxynucleoside phosphoramidites suitable for chemical incorporation of the deuterated moieties into DNA. We utilized selective deuteration to establish the structure of the DNA adduct formed by one of the most powerful naturally occurring mutagens and carcinogens ? aristolochic acid (AA). The AA lesion disrupts the normal Watson-Crick structure of the damaged base pair and causes extrusion of the complementary thymidine out of the helix, so canonical internucleotide nOe contacts are insufficient for structure refinement. In that case the information extracted from stereospecifically assigned 5' and 5? resonances appeared to be extremely helpful in obtaining the precise structure of the lesion site.

Mark Lukin*
Tanya Zaliznyak
Carlos de los Santos

Department of Pharmacological Sciences
SUNY at Stony Brook
Stony Brook NY 11794-8651

ph: 631 444-3842
fx: 631 444-3218
email Mark Lukin



Left: Fragments of 300 ms NOESY spectra of 5?-deuterated (Ia, IIa) and non-deuterated (Ib, IIb) DNA duplex with single AA-dA damage site. Resonances corresponding to H5? are absent on the panels Ia and IIa.
Right: 3D structure of the lesion site (only the aristolochic acid residue and opposing thymidine are shown). Interproton distances corresponding to T17H5? cross-peaks are shown as dashed lines.
References and Footnotes
  1. Lukin MA., Bushuev VN. Nucleosides & Nucleotides 18, 1255-1256 (1999).
  2. Oogo Yu., Ono A.(M)., Ono A., Kainosho M. Tetr. Lett. 38, 395-398 (1997).
  3. Cromsigt J., Schleucher J., Gustafsson T., Kihlberg J., Wijmenga S. Nucl. Acids Res. 30, 1639-1645 (2002).
  4. Midland MM., Asirwatham G., Cheng JC., Miller JA., Morell L. J. Org. Chem. 59, 4438-4442 (1994).