Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Characterization of Hydrogen Bonds in Double-Helical DNA Using H/D Fractionation Factors

Protium/deuterium fractionation factors have been widely used to study the strength and geometry of hydrogen bonds in proteins. These studies have shown that amide hydrogen bonds in proteins have fractionation factors in the range of 0.28 to 1.47 (1). A fractionation factor less then 1 is indicative of a hydrogen bond stronger then those in water, while a fractionation factor greater then 1 reflects a weaker hydrogen bond compared to water. For nucleic acids, fractionation factors have only recently been used to study double and triple DNA helices (2, 3).

In the present study, we have measured the fractionation factors of Watson-Crick imino hydrogen bonds in DNA double helices of different length and base sequence, namely, the decamer [5'-d(CCAACGTTGG)-3']2, and the dodecamers [5'-d(CGCACATGTGCG)-3']2 and [5'-d(CGCAGATCTGCG)-3']2. The fractionation factors were obtained from the dependence of the intensity of imino proton NMR resonances on the D2O/H2O ratio. The results revealed that the fractionation factors in the three DNA molecules investigated are all in the range of 1.00 ± 0.07. This finding indicates that, for the DNA molecules investigated, the strength of Watson-Crick imino hydrogen bonds is the same as that of hydrogen bonds in water, and is independent of the length and the base sequence of the DNA.


Supported by a grant from the NIH, GM65159.

References and Footnotes
  1. Harris, T. K. and Mildvan, A. S. Proteins: Structure, Function, and Genetics 35, 275-282 (1999).
  2. Vakonakis, I., Salazar, M., Kang, M., Dunbar, K. R., and LiWang, A. C. J. Biomol. NMR 25, 105-112 (2003).
  3. Coman, D. and Russu, I. M. J. Am. Chem. Soc.125, 6626-6627 (2003).

Alicia E. Every1
Daniel Coman2
Irina M. Russu1,*

1Department of Chemistry and Molecular Biophysics Program
Hall-Atwater Laboratories
Wesleyan University
Middletown, CT 06459
2Magnetic Resonance Research Center
TAC N147
Department of Diagnostic Radiology
Yale University School of Medicine
300 Cedar St.
New Haven, CT 06520

*Corresponding author:
Phone: (860)-685-2428
Fax: (860)-685-2211
Email: irussu@wesleyan.edu