A solution structure for poly(rA).poly(dT) with different furanose pucker and backbone geometry in rA and dT strands and intrastrand hydrogen bonding of adenine 8CH.
Equilibrium Raman spectra show that A- and B-form phosphodiester backbone geometries are both present in the solution structure of the RNA.DNA hybrid poly(rA).poly(dT) and that these arise from C3'-endo-rA and C2'-endo-dT nucleosides, respectively. Raman dynamic measurement of deuterium exchange of adenine 8CH groups reveals (i) a single kinetic class of rA conformers and (ii) extraordinary retardation of 8CH exchange in this class--more than 100-fold slower than in canonical DNA structures. The equilibrium and kinetic results, in conjunction with model building, indicate an unusual intrastrand hydrogen bond involving adenosine donor (8C-H) and acceptor (5'O) groups and a double-helical conformation in solution similar to that proposed for fibers at high relative humidity [Zimmerman, S. B., & Pheiffer, B. H. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 78-82]. In fibers of poly(rA).poly(dT) at low relative humidity, the Raman spectra indicate a conventional A-helix structure.
Benevides
J M
JM
Division of Cell Biology and Biophysics, School of Basic Life Sciences, University of Missouri, Kansas City 64110.
Thomas
G J
GJ
D000225:Adenine; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011061:Poly A; D011071:Poly T; D011089:Polydeoxyribonucleotides; D012996:Solutions; D013059:Spectrum Analysis, Raman / Q000379:methods
D011089:Polydeoxyribonucleotides; D012996:Solutions; D011061:Poly A; D011071:Poly T; C008950:poly A-T; D000225:Adenine