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Abstract
Nucleic acids are the fundamental building blocks of the genetic systems of all living organisms. The structural conformation and function of nucleic acids are determined by the balance among a lot of factors. This work examines two of the key factors: electrostatics and hydration. Because electrostatic interactions are strong and long-ranged in nature, they play an important role in many aspects of the structural and functional properties of polyelectrolytes, including nucleic acids. Currently, the most popular approach for analyzing electrostatics of nucleic acids is the continuum model based on the Poisson-Boltzmann equation (PBE), which is typically solved numerically using the finite difference algorithm. In the first part of this work, the electrostatic features of the most common and basic structural form of nucleic acids, the Watson-Crick (WC) DNA double helices in A- and B-conformations, are examined using a newly developed hybrid boundary element and finite difference PBE algorithm (Boschitsch, A.H. and Fenley, M.O., J. Comput. Chem., 2004, 25:935-55). The hybrid PBE algorithm is an improvement of the current finite difference algorithm and can produce accurate surface electrostatic potentials of nucleic acids in a simulated aqueous salt environment.
The high resolution surface electrostatic potential maps and the numerical results obtained by the hybrid PBE solver illustrated many fine and distinct electrostatic features of A- and B-DNA. It shows that the major groove of A-DNA is much more electronegative than the minor groove. The closely packed backbone atoms are mainly responsible for creating the enhanced negativity. The minor groove of B-DNA is more negative than the major groove, and the base atoms contribute to the sequence specific features in both the major and minor groove. DNA with A/B junction has both profoundly negative major and minor grooves. Next, the electrostatic characteristics of the most common non-WC base pair in RNA, the G·U wobble base pairs are studied in details. Results show that the major groove of an isolated G·U wobble base pair has a region of broad and pronounced electronegativity, compared with WC base pairs. However, when incorporated in RNA helices, the presence of the enhanced electronegativity depends on the stacking pattern and groove geometry of the G·U wobble base pairs.
Finally, the hydration patterns of the pseudouridine dependent spliceosomal branch site helix are examined using molecular dynamics simulations with explicit solvent representation. The branch site helix, formed by the base pairing between the pre-mRNA intron and U2 snRNA, is part of the critical RNA:RNA interaction network in the spliceosome. The branch site helix positions the branch site adenosine, the nucleophile in the first step of splicing, for reaction. NMR structures illustrated that the highly conserved pseudouridine in U2 snRNA induces the extrahelical position of the branch site adenosine (Newby, M.I. and Greenbaum N.L., Nat Struct Biol., 2002, 9:958-65). The hydration analysis obtained in this work located two tightly bound water molecules in the pseudouridine dependent branch site helix. One is near the backbone of the conserved pseudouridine, forming water mediated hydrogen bonding between pseudouridine NH1 and the backbone. This bridging interaction presumably will enhance the conformational stability of the helix, and has been identified for pseudouridine in tRNA. The other hydration site is near the branch site adenosine, contributing to the formation of the base tripe, which stabilize the extrahelical position of the branch site adenosine. In comparison, the unmodified counterpart of the branch site helix, where the pseudouridine is replaced with uridine, shows only one hydration site. It is located between the stacked branch site adenosine and its neighboring base, stabilizing the stacked conformation of the branch site adenosine.
