Document 0042
 DOCN  M95A0042
 TI    The bend in RNA created by the trans-activation response element bulge
       of human immunodeficiency virus is straightened by arginine and by
       Tat-derived peptide.
 DT    9510
 AU    Zacharias M; Hagerman PJ; Department of Biochemistry, Biophysics, and
       Genetics, University; of Colorado Health Sciences Center, Denver 80262,
       USA.
 SO    Proc Natl Acad Sci U S A. 1995 Jun 20;92(13):6052-6. Unique Identifier :
       AIDSLINE MED/95320213
 AB    The trans-activation response element (TAR) found near the 5' end of the
       viral RNA of the human immunodeficiency virus contains a 3-nt bulge that
       is recognized by the virally encoded trans-activator protein (Tat), an
       important mediator of transcriptional activation. Insertion of the TAR
       bulge into double-stranded RNA is known to result in reduced
       electrophoretic mobility, suggestive of a bulge-induced bend.
       Furthermore, NMR studies indicate that Arg causes a change in the
       structure of the TAR bulge, possibly reducing the bulge angle. However,
       neither of these effects has been quantified, nor have they been
       compared with the effects of the TAR-Tat interaction. Recently, an
       approach for the quantification of bulge-induced bends has been
       described in which hydrodynamic measurements, employing the method of
       transient electric birefringence, have yielded precise estimates for the
       angles of a series of RNA bulges, with the angles ranging from 7 degrees
       to 93 degrees. In the current study, transient electric birefringence
       measurements indicate that the TAR bulge introduces a bend of 50 degrees
       +/- 5 degrees in the absence of Mg2+. Addition of Arg leads to
       essentially complete straightening of the helix (to < 10 degrees) with a
       transition midpoint in the 1 mM range. This transition demonstrates
       specificity for the TAR bulge: no comparable transition was observed for
       U3 or A3 (control) bulges with differing flanking sequences. An
       essentially identical structural transition is observed for the
       Tat-derived peptide, although the transition midpoint for the latter is
       near 1 microM. Finally, low concentrations of Mg2+ alone reduce the bend
       angle by approximately 50%, consistent with the effects of Mg2+ on other
       pyrimidine bulges. This last observation is important in view of the
       fact that most previous structural/binding studies were performed in the
       absence of Mg2+.
 DE    Amino Acid Sequence  Arginine/*PHARMACOLOGY  Base Sequence  Binding
       Sites  Birefringence  Comparative Study  Dose-Response Relationship,
       Drug  Gene Products, tat/*PHARMACOLOGY  HIV/*GENETICS  Kinetics
       Magnesium/PHARMACOLOGY  Molecular Sequence Data  Mutagenesis,
       Site-Directed  *Nucleic Acid Conformation/DRUG EFFECTS
       Oligodeoxyribonucleotides  Peptide Fragments/*PHARMACOLOGY  Restriction
       Mapping  RNA, Viral/*CHEMISTRY/DRUG EFFECTS  Support, U.S. Gov't, P.H.S.
       *Trans-Activation (Genetics)  JOURNAL ARTICLE

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