       Document 0079
 DOCN  M9630079
 TI    Occurrence, solution structure and stability of DNA hairpins stabilized
       by a GA/CG helix unit.
 DT    9603
 AU    Sandusky P; Wooten EW; Kurochkin AV; Kavanaugh T; Mandecki W; Zuiderweg
       ER; Biophysics Research Division, University of Michigan, Ann Arbor;
       48109-1055, USA.
 SO    Nucleic Acids Res. 1995 Nov 25;23(22):4717-25. Unique Identifier :
       AIDSLINE MED/96103605
 AB    The occurrence and NMR solution structure of a class of biloop hairpins
       containing the sequence 5'-CGXYAG are presented. These hairpins, which
       are variations on a sequence found in the reverse transcript of the
       human T-cell leukemia virus 2 (HLV2), show elevated melting points and
       high chemical stability toward denaturation by urea. Hairpins with the
       5'-CGXYAG configuration have melting points 18-20 degrees higher than
       hairpins with 5'-CAXYGG or 5'-GGXYAC configurations. The identities of
       the looping bases, X and Y above, play a negligible role in determining
       the stability of this DNA hairpin stability. This is very different from
       G-A based loops in RNA, where the third base must be a purine for high
       stability [the GNRA loops; V.P. Antao, S.Y. Lai and I. Tinoco, Jr (1991)
       Nucleic Acids Res., 19, 5901-5905]. We show that these properties are
       associated with a four base helix unit that contains both a sheared GA
       base pair and a Watson-Crick CG base pair upon which it is stacked. As
       an understanding of the significance of AG base pairs has become
       increasingly important in the structural biology of nucleic acids, we
       compute an 0.7-0.9 A precision ensemble of NMR solution structures using
       iterative relaxation matrix methods. Calculations performed on
       NMR-derived structures indicate that neither base-base electrostatic
       interactions, nor base-solvent dispersive interactions, are significant
       factors in determining the observed differences in hairpin stability.
       Thus the stability of the 5'-CGXYAG configuration would appear to derive
       from favorable base-base London/van der Waals interactions.
 DE    Base Composition  Base Sequence  Comparative Study  Computer Graphics
       Drug Stability  DNA/*CHEMISTRY  Human  HTLV-II/GENETICS  Models,
       Molecular  Models, Structural  Molecular Sequence Data  Nuclear Magnetic
       Resonance  *Nucleic Acid Conformation  Nucleic Acid Denaturation
       Oligodeoxyribonucleotides/*CHEMISTRY  Support, Non-U.S. Gov't  Support,
       U.S. Gov't, Non-P.H.S.  Support, U.S. Gov't, P.H.S.  Transcription,
       Genetic  Urea  JOURNAL ARTICLE

       SOURCE: National Library of Medicine.  NOTICE: This material may be
       protected by Copyright Law (Title 17, U.S.Code).

