RESUMO
We have correlated the structural perturbations caused by DNA mismatches with the enzymatic data of the interaction of the restriction endonuclease EcoRI with DNA. Oligonucleotides d(CGAGAATTCTCA5GAXAATTCT) (X = G, A, T) and d(CGCGAATTYGCGT4CGCXAATTCGCG) (Y = C, X = G, T and Y = A, X = T) containing single mismatches within the EcoRI recognition site were characterized by NMR spectroscopy and by their EcoRI substrate properties. UV melting and gel electrophoresis studies confirm that the oligonucleotides form hairpin structures. The presence of either a CT or a CA mismatch results in markedly lower Tm and van't Hoff enthalpies compared with the fully base paired control. NMR imino proton spectra of these hairpins demonstrate that the perturbation caused by the two mispairs or a noncanonical AT pair is localized and limited to one or two base pairs on either side of the perturbation. The DNA hairpin structures containing single mismatches, and to a lesser extent also sequences with a single noncanonical base pair, are substrates for the restriction endonuclease. In addition to the strand scission at the nonperturbed GpA phosphodiester bond some cleavage is observed at the mismatched position. The interactions of the CA and CT mismatched hairpin with the enzyme are characterized by binding constants that are only 33 and 57 times lower, respectively, than that for the canonical sequence, corresponding to 8-10 kJ x mol(-1) less favorable free binding energy. This, taken together with the NMR data, indicates that the CA and CT mismatches have only small effects on the EcoRI recognition of the DNA substrate. We conclude that two out of the three hydrogen bonds that characterize the interaction of EcoRI with the CG base pair in the canonical sequence can still be formed for either the CT or CA mismatched recognition site.
Assuntos
Pareamento de Bases , Sequência de Bases , Dano ao DNA , Desoxirribonuclease EcoRI/metabolismo , Espectroscopia de Ressonância Magnética , Conformação de Ácido Nucleico , Reparo do DNA , Eletroforese em Gel de Poliacrilamida , Hidrólise , Cinética , Desnaturação de Ácido Nucleico , Oligodesoxirribonucleotídeos/química , Espectrofotometria Ultravioleta , Especificidade por Substrato , TermodinâmicaRESUMO
The solution conformations of RC-160, cyclic D-Phe1-Cys2-Tyr3-D-Trp4-Lys5-Val6-Cys7+ ++-Trp8-NH2, an analog of the tumor antiproliferatory neuropeptide somatostatin, and RC-160 labeled with rhenium (Re-RC-160), have been determined by using two-dimensional 1H NMR spectroscopy (600 MHz) and restrained molecular dynamics simulations. Re-RC-160 yields the same average solution conformation as does the apo form with an antiparallel beta-sheet fold and a type II' beta-turn centered at D-Trp4-Lys5. These results indicate that the spatial topography of the side chains essential for somatostatin receptor binding is maintained in Re-RC-160.
Assuntos
Antineoplásicos/química , Rênio/química , Somatostatina/análogos & derivados , Sequência de Aminoácidos , Simulação por Computador , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Dados de Sequência Molecular , Somatostatina/químicaRESUMO
Fructose 1,6-bisphosphate (fru-1,6-P2), but not other glycolytic intermediates, activates highly purified 2',5' A synthetases from rabbit reticulocyte lysates and from 2',5'-ADP-agarose purified extracts of interferon-treated HeLa cells without the addition of dsRNA. The 2',5' A was structurally and biologically identical to authentic 2',5' A. Micrococcal nuclease inhibited the activation of 2',5' A synthetase by poly(I)-poly(C), but did not affect activation by fru-1,6-P2. Addition of fru-1,6-P2 aldolase prevented the activation of 2',5' A synthetase by fru-1,6-P2.
