A series of G-rich oligonucleotides able to form tetraplexes has been studied by FTIR spectroscopy. Characteristic markers of the formation of guanine tetrads are given. Moreover we propose a new marker discriminating between parallel and antiparallel tetraplexes: the position of the C6=O6 guanine carbonyl stretching vibration. In intermolecular parallel tetrameric structures formed by four separate strands this absorption is observed at 1693 cm
The site and role of the binding of the 1-53 N-terminal part of H4 on DNA have been studied by optical spectroscopy. The structure of the 1-53 H4 fragment determined by vacuum ultraviolet circular dichroism and infrared spectroscopy is essentially aperiodic. The site of the interacion between the fragment and free DNA is localized by Raman laser spectroscopy in the small groove of the DNA, similar to the interaction site of the whole histone with DNA in nucleosomes. Infrared linear dichroism measurements show that the two 1-53 and 54-102 H4 fragments play a very important role in the histone-DNA interactions, but the roles are extremely different: the N-terminal part of the histone remains effectless on the DNA conformational flexibility and it is proposed that the structurally important interaction occurs between the globular part of the histone and the DNA. The N-terminal fragment appears to be responsible for finding the correct place on the DNA of the nucleosomal core particles.
Present results provide direct evidence of the nature of a conformational change in DNA when nucleosomes are formed from core histones and poly fd(A-T)]. First, we have found some features which have characteristic aspects of the A like conformation of DNA. Thus, an increased contribution due to a sugar conformation close to C3'-endo puckering is detected in the Raman spectra. In addition, the circular dichroism (C.D.) spectra of reconstituted chromatin with poly PI(A-T)j exhibits an increased intensity at about 262 nm.A second feature acquired by poly rd(A-T)l in nucleosome formation from core histones is related to the presence of a negative band at about 280 nm in the C.D. spectra. The nature of this change is correlated with a DNA conformation characterized by a decreased number of base pairs per turn (28,29). This indicates that these two features of reconstituted nucleosomes reflect the presence of two types of DNA conformations, which overall form is of the B type (22,36).
Interaction of the DNA binding nonintercalators Netropsin, Distamycin and the mPD derivative with Z-DNA has been studied. It has been found that environmental factors like the solvent and added cations significantly modulate the interaction of these ligands with Z-DNA. However no definite Z to B transition in presence of these ligands was found in any case, in contrast to previously reported results (Ch. Zimmer, C. Marck and W. Guschlbauer, FEBS Lett. 154, 156-160 (1983)).
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