FTIR and UV spectroscopy of parallel-stranded DNAs with mixed A*T/G*C sequences and their A*T/I*C analogues.
The infrared spectra of parallel-stranded (ps) hairpin duplexes with mixed A*T/G*C composition and either isolated or sequential G*C pairs were studied in comparison with antiparallel-stranded (aps) duplexes and a corresponding set of molecules with hypoxanthine as a G base analogue lacking the exocyclic amino group. The ps duplexes showed the characteristic bands for the C2=O2 and C4=O4 stretching vibrations of thymine residues in trans-Watson-Crick A*T pairing at 1683 and 1668 cm-1. The latter band was superimposed on the stretching vibration of the free C6=O6 group of guanine. Substitution of guanine by hypoxanthine inhibited the formation of ps hairpin duplexes whatever the sequence, demonstrating that in the H-bonding between G and C the 2-NH2 group is necessary for stabilizing all of the investigated ps duplexes. This result is in agreement with a model of trans-Watson-Crick G*C base pairs with two H-bonds [N2H2(G)-N3(C) and N1H(G)-O2(C)]. However, trans-Watson-Crick A*T and G*C base pairs with two H-bonds are not isomorphous, which may explain the decreased stability of the ps, but not the aps, duplexes upon increasing the number of A*T/G*C steps. Molecular modeling studies performed on two of the ps duplexes reveal the existence of propeller twist for avoiding a clash between the N2(G) and N4(C) amino groups, and favorable stacking of sequential G*C base pairs. The optimized hairpin ps duplexes invariably incorporated G*C base pairs with two H-bonds, regardless of the initial structures adopted for the force field calculations.
Mohammadi
S
S
URA CNRS 1430, University of Paris XIII, Bobigny, France.
Klement
R
R
Shchyolkina
A K
AK
Liquier
J
J
Jovin
T M
TM
Taillandier
E
E
D000225:Adenine / Q000031:analogs & derivatives / Q000737:chemistry*; D001482:Base Composition; D001483:Base Sequence; D003596:Cytosine / Q000031:analogs & derivatives / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry*; D006358:Hot Temperature; D006860:Hydrogen Bonding; D019271:Hypoxanthine / Q000737:chemistry; D007288:Inosine / Q000031:analogs & derivatives / Q000737:chemistry*; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet; D017550:Spectroscopy, Fourier Transform Infrared; D013941:Thymine / Q000031:analogs & derivatives / Q000737:chemistry*
D009692:Nucleic Acid Heteroduplexes; D019271:Hypoxanthine; D007288:Inosine; D006147:Guanine; D003596:Cytosine; D004247:DNA; D000225:Adenine; D013941:Thymine