Chemistry Reference
In-Depth Information
NMR spectroscopy
70
and molecular dynamics (MD)
71
studies have shown that
A
n
T
n
and T
n
A
n
duplexes have unusual structures and dynamics. Anomalous broad-
ening of the TpA adenine H2 resonance indicative of large amplitude base motion,
has been observed for a series of nine unique four-nucleotide sequences.
70
In A
n
T
n
sequences, the DNA assumes a unique structure characterized by a gradual and
increasingly compressed minor groove, which reaches a minimum at the ApT step.
In conclusion, this type of sequences does not exhibit a regular B-form conformation
and thus minor groove cation binding may be unique to A-tract sequences.
1.5.4 Conclusion on Groove Binding
The general trend is that ions bind in the minor groove of DNA A-tracts and in the
major groove of DNA G-tracts. NMR spectroscopic studies indicate that sequence-
specifi c binding of alkali and alkali earth ions appears to have only minor infl uence
on the heterogeneity of DNA structures.
67
. The relative lack of hydration of alkali
cations makes their interactions with base atoms largely electrostatic and relatively
nonspecifi c. Divalent alkali earth cations tend to be fully hydrated and their interac-
tions with duplex DNA are more sequence-specifi c through formation of hydrogen
bonds to base atoms.
55,67
Abbreviations
MEP
Molecular electrostatic potential
HOMO
Highest occupied molecular orbital
LUMO
Lowest occupied molecular orbital
ODN
Oxidation oligodeoxynucleotides
MD
Molecular dynamics
EDTA
Ethylene diamine tetraacetic acid
XANES
X - ray absorption near edge structure
NOESY
Nuclear overhauser effect spectroscopy
MRD
Magnetic relaxation dispersion
References
1.
Flessel , C.P. ; Furst , A. ; Radding , S.B. ; A comparison of carcinogenic metals. In: Metal Ions
in
Biological Systems
. Vol. 10 , H. Sigel , Ed., Marcel Dekker , New York , 1980 .
Frieden , E. ; Alles , J. ; Subtle interactions of cupric ions with nucleic acid components ;
J. Biol. Chem.
, 1958 ,
230
, 797 - 804 .
Eichhorn , G.L. ; Shin , Y.A. ; Interaction of metal ions with polynucleotides and related
compounds. XII. The relative effect of various metal ions on DNA helicity;
J. Am. Chem.
Soc.
, 1968 ,
90
, 7323 - 7328 .
Sletten , E. ; Lie , B.; Copper complex of guanosine- 5
2.
3.
4.
′
- monophosphate ;
Acta. Cryst.
, 1976 ,
B32
, 3301 - 3304 .
