Nuclear magnetic resonance studies of the helix-coil transition of poly (dA-dT) in aqueous solution.

Abstract

The well-resolved base and sugar proton resonances in the high resolution proton nuclear magnetic resonance (NMR) spectra of poly (dA-dT) Arnott and coworkers (1) have recently extended the early studies of Davies and Baldwin (2) on the x-ray diffraction patterns from oriented, crystalline fibers of poly(dA-dT). They propose a novel, 8-fold helical structure, with an axial rise per residue of 3.03 A and a C3 exo sugar pucker conformation. Baldwin and coworkers (3-6) have investigated the helix-coil transition of poly(dA-dT) and circular oligo(dAdT). They have characterized the role of hairpin and straight chain helices by monitoring absorbance melting curves as a function of salt, temperature, and pH. The thermodynamic parameters for the helix-coil transition of poly(dA-dT) have been elucidated from differential heat calorimetry (7,8).High resolution nuclear magnetic resonance (NMR) spectroscopy is capable of monitoring many aspects of the helixcoil transition of alternating deoxypurine-deoxypyrimidine oligonucleotides in aqueous solution. These studies include investigations of the exchangeable and nonexchangeable protons in the duplex of the self-complementary hexanucleotide d(A-T-G-C-A-T) (9-12) and the d[C-G(-C-G)n], n = 1,2 duplexes (13) in aqueous solution.The Watson-Crick thymine imino protons in the oligomer duplexes d(pT-A)n, n = 3,4,5, were monitored in our laboratory as a function of temperature by high resolution proton NMR spectroscopy in H20 solution (14). The chemical shifts and line widths of these exchangeable resonances were obAbbreviation: NMR, nuclear magnetic resonance. servable when the double helix was predominantly intact but broadened with increasing coil concentration. An alternate NMR approach monitors the entire helix-coil transition as followed by the nonexchangeable protons and the, phosphates in D20 solution (11)(12)(13)(15)(16)(17).Nuclear magnetic resonance spectral line widths yield kinetic information about the helix-coil transition when the exchange rate is on the order of the chemical shift difference between the helix and coil states. It will be demonstrated that the adenine H2 proton in poly(dA-dT) exhibits an about 1 ppm chemical shift difference between the two states and provides a handle for monitoring the kinetic aspects of the helix-coil transition. EXPERIMENTAL Sample preparationThe alternating copolymer poly(dA-dT) samples for proton NMR studies were purchased from Long Island Biochemical Corp. and were shipped in Tris buffer (chain length: about 300 nucleotides).270 MHz Proton NMR Studies. The purchased sample in Tris buffer was lyophilized and the spectra were recorded on 18.8 mM (with respect to phosphorus) poly (dA-dT)

Conformational transitions of poly(dA-dT).poly(dA-dT) in ethanolic solutions

“…If the measurements were performed at low temperatures the resonances broadened beyond detection (24). Addition of CsCl neccessary to preserve double-strandedness of the polynucleotide at higher temperatures, however, resulted in its aggregation.…”

1H NMR investigation of the conformational states of DNA in nucleosome core particles

“…1H NMR has also been used to investigate the conformational properties of DNA and RNA in solution, but most previous studies have been limited to low molecular weight material (generally less than 5000 and rarely over 30,000 daltons) (22)(23)(24)(25)(26)(27)(28). However, recent studies in our laboratory (Early and Kearns, submitted) indicate that DNA is sufficiently flexible that partially resolved spectra can be observed from DNA helices that are 500 base pairs long.…”

Effect of Bridging Units on Photophysical and DNA Binding Properties of a Few Cyclophanes

“…To determine the DNA binding modes of the cyclophanes, we have carried out circular CD and LD (46–49), viscosity (36,50,51) and DNA thermal denaturation (52,53) measurements as well as studied the effect of ionic strength. The CD spectrum of CT DNA in buffer consisted of a positive peak at 290 nm and a negative band at 260 nm (Fig.…”