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Refinement of the solution structure of the RNA‐DNA hybrid 5′‐[r(GCA)d(TGC)] 2 Combined use of nuclear magnetic resonance and restrained molecular dynamics
Author(s) -
Happ Claudia Scalfi,
Happ Erwin,
Clore G.Marius,
Gronenborn Angela M.
Publication year - 1988
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(88)80286-2
Subject(s) - molecular dynamics , nuclear magnetic resonance , dynamics (music) , dna , rna , physics , chemistry , gene , quantum mechanics , biochemistry , acoustics
The solution conformation of the self‐complementary RNA‐DNA hybrid hexamer 5′‐[r(GCA)d(TGC)] 2 is investigated by NMR spectroscopy and restrained molecular dynamics. The 1 H‐NMR spectrum is assigned in a sequential manner using two‐dimensional homonuclear Hartmann‐Hahn and nuclear Overhauser enhancement spectroscopy. From the latter a set of 178 approximate interproton distance restraints are determined and used as the basis of a structure refinement by restrained molecular dynamics. Eight independent calculations are carried out, four from a classical A‐type geometry and four from a classical B‐type one. Convergence is achieved to very similar A‐type structures with an average atomic root mean square difference between them of 1.0±0.2 Å. The converged structures exhibit variations in helical parameters similar to those found previously for the analogue RNA hexamer 5′‐r(GCAUGC) 2 [(1988) Biochemistry 27, 1735–1743].