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

FEBS Letters

Happ, Claudia Scalfi¹  Clore, G.Marius¹  Happ, Erwin¹  Gronenborn, Angela M.¹ 

[1] Max-Planck Institut für Biochemie, D-8033 Martinsried bei München, FRG

关键词: RNA-DNA hybrid;    Solution conformation;    NMR;    Interproton distance;    Restrained molecular dynamics;    NMR;    nuclear magnetic resonance;    NOE;    nuclear Overhauser effect;    NOESY;    two-dimensional NOE spectroscopy;    HOHAHA;    two-dimensional homonuclear Hartmann-Hahn spectroscopy;    rms;    root mean square;    RD;    restrained dynamics;   

DOI  :  10.1016/0014-5793(88)80286-2

学科分类：生物化学/生物物理

来源: John Wiley & Sons Ltd.

【 摘 要 】

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 ¹H-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].

【 授权许可】

Unknown