Base pair analogs in the gas phase

Abstract

A rotationally resolved electronic spectrum of the gas-phase dimer 2-aminopyridine⅐2-pyridone, an analog of the adenine⅐thymine base pair, has been observed and assigned, leading to precise measurements of its moments of inertia and preliminary determinations of its structure. A Watson-Crick configuration results, with N⅐⅐⅐HON and NOH⅐⅐⅐O hydrogen bond lengths of 2.898 and 2.810 Å, respectively. The two bases are found not to be coplanar; a dihedral angle of 6.1°between the base planes is also estimated from the measured moments of inertia. Possible chemical and biological implications of these results are discussed. F ifty years have elapsed since x-ray diffraction photographs of fibers pulled from concentrated solutions of DNA revealed that its structure is a double-stranded helix held together by hydrogen bonds between the complementary base pairs adenine (A) and thymine (T), and guanine (G) and cytosine (C) (1-3), providing a molecular-level explanation of heredity (4). Despite this passage of time, the structure of an isolated A⅐T or G⅐C base pair in the absence of solvent and͞or a surrounding medium has yet to be determined. Only the average structure of the base pairs in the condensed phase can be determined from fiber-diffraction patterns of DNA. To be sure, we now know that many different kinds of DNA exist and that, although they share many common features, they can differ significantly in detail. These differences include the number of residues per turn, the translation per residue, the angle between the base planes and the helix axis, and the dihedral angle between base planes (5). We also know that these features may be functionally important, both in gene expression and in the construction of the cell (6), but we do not know the extent to which the differences in DNA structures are a consequence of the condensed-phase environment in which they are found. Gas-phase studies are needed not only to provide benchmark structures but also to quantify the relative importance of intra-and intermolecular interactions in molecular biology.Toward this end, we report here a preliminary determination of the structure of the base-pair mimic 2-aminopyridine⅐2-pyridone (2AP⅐2PY) by using the technique of rotationally resolved electronic spectroscopy in the gas phase. 2AP⅐2PY is found to be held together by two N⅐⅐⅐HON and NOH⅐⅐⅐O hydrogen bonds, identical with those found in the A⅐T base pair itself. As will be seen, understanding the nature of these interactions provides insight into the structure, stability, and electronic properties of the bonds that hold DNA together. MethodsOur experiments were performed in the collision-free environment of a molecular beam (7). Approximately 1 g of 2AP was placed in a quartz sample container at nearly 200°C and entrained in 41 kPa (6 psig) of He. After equilibrium was established, Ϸ2 g of 2PY was added to the sample container, and the spectrum of the 2AP⅐2PY dimer appeared shortly thereafter. During this time, the mixture was expanded through a 280-m quartz nozzle held at 150...

Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical DNA

“…For example, the angle between the planes of paired adenine and thymine, which can be extracted from the buckle and propeller angles, is remarkably similar to the dihedral angle estimated from the measured moments of inertia of 2-aminopyridine·2-pyridone, an analog of the A·T base pair, in the gas phase, i.e ., 6.7° predicted vs . 6.1° found experimentally (Roscioli and Pratt 2003). The predicted length of the A(N1)···T(H3)–T(N3) hydrogen bond also closely matches the value found in the same experiment, i.e ., 2.87 Å computed vs .…”

Direct Measurements of Electric Fields in Weak OH···π Hydrogen Bonds

“…1–6 In conventional hydrogen bonds, X – H · · · A , a hydrogen atom bridges the proton donor X and proton acceptor A. The donor is usually very electronegative, e.g.…”

Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences

“…Among them, 2-aminopyridine ͑AP͒ dimer, see Scheme 1, is probably the most widely used model for investigating basic photochemical reaction mechanisms. [5][6][7][8][9] This dimer consists of the N-H donor and the aromatic N acceptor group of the single base and is also of doubly hydrogen-bonded structure. Earlier theoretical studies on one-dimensional potential-energy surfaces of excited-states in the 2-AP dimer 7 have shown that a conical intersection between a local excited-state ͑LE͒ and a charge transfer ͑CT͒ state along a proton-transfer coordinate was responsible for the deactivation of the 2-AP dimer in vacuum.…”