Nature of conformational changes in poly[d(A-T)-d(A-T)] in the premelting region.

Abstract

The conformation of the synthetic DNA, poly-[d(A-T)d(A T)J, has been investigated both in the solid state and in dilute aqueous solutions at different temr ratures below its melting point The change of the circular dichroism (CD) spectra of poly[d(A-T)d(A-T)J solutions with decreasing temperatures from just below the melting point to 00 involves a specific de-crease of the intensity of the 262 nm CD band. This conformational change has been assigned to a gradual and partial transition from the B to C form, on the basis of the following results:(i) By the use of infrared dichroism measurements on oriented films we have defined humidity and salt conditions under which One of the unexplained phenomena in molecular biology is the exact nature of premelting changes in DNAs. Many observations indicate the occurrence of significant changes in DNA structure at temperatures below the helix-coil transition. Such changes were initially detected by optical rotation at the sodium D line (1) and by viscosity measurements (2). They have since been confirmed by the more sensitive method of UV circular dichroism (3). That these occur in a temperature region below the helix-coil transition is indicated by the constant absorbance at 260 nm. The positive circular dichroism (CD) band of DNA becomes more intense as the temperature increases toward the melting temperature (tm). Explanations proposed for the premelting phenomenon postulate the existence of some conformational alterations of DNA before the transition to the random coil (3). More recently these CD observations have been confirmed and extended to different DNAs of various origins and base compositions (4). All DNAs exhibit the CD premelting phenomenon. Oligomers of d(AT)n with n = 10-21 yielded results similar to those found for the polymer, without showing chain length dependence. This indicates that the cooperative unit in this transition is very small (4).Although the premelting phenomenon in DNA can be detected by several methods, it is not observable by changes in hypochromicity (3, 4) or by Raman scattering (5, 6). In fact, investigation of poly[d(A-T)-d(A-T)] by laser Raman scattering indicates the absence of any premelting spectral changes (7), whereas in DNA the changes before melting are observed only at temperature higher than about 50°C (5).Since the premelting changes of DNA are observed by CD at temperatures of biological reactions, they may be important in biological processes. For example, they may be relevant for the understanding of interactions of DNA with proteins as diverse as histones, polymerases, or repressors. In order to make precise structural determinations we have chosen to investigate poly[d(A-T)-d(A-T)] for which different A, B, and C forms, as well as a particular D form, have been well characterized by x-ray diffraction (8, 9) and by infrared linear dichroism (10). We have used CD to investigate both films and solutions in order to establish structural correlations between the two states. MATERIALS AND METHODS Samples of poly[d(A-...

Physical properties of inner histone-DNA complexes

“…Inner histone complexes with poly(dA-dT)-poly(dA-dT) and with poly(dI-dC)-poly(dI-dC) exhibited a similar "suppression" of DNA ellipticities. A recent study (24) on the effects of temperature on the circular dichroic spectrum of poly(dA-dT) poly(dA-dT) revealed similar "suppression" within the "pre-melting zone," which was interpreted as a possible B-+C transition.…”

DNA coiled coils

“…In particular, it has been known for a long time that poly[d(AT)], under certain conditions, forms a duplex with eight base pairs per turn, the D form of DNA (12). The polymorphism of AT-rich DNA is also apparent from melting (13) and NMR studies (14), which suggest additional conformational transitions. In view of this situation, we have studied the crystallization of a longer sequence, the dodecamer d(ATATATATATAT).…”

Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

“…At low temperatures (0-25°C), it appears that AT-rich oligonucleotides may have several conformational forms (9)(10)(11). In the case of poly[d(A-T)], it has been suggested that the C form of DNA is stabilized at low temperature (12). The polymorphism of AT regions suggested by all these studies prompted us to determine the structure of an oligonucleotide with 100% A⅐T base pairs.…”