DNA Structure: Alphabet Soup for the Cellular Soul
Department of Biochemistry and Molecular Biology, Colorado State University USA 1. Introduction
The story of DNA structure is as varied as it is interesting, the most famous tale being the “discovery” of B-DNA by Watson and Crick. For many biologists, this simple, but elegant structure is all that is needed for a basic, albeit superficialunderstanding of cellular genetics. A deeper appreciation for how DNA functions comes from the recognition that this is a highly malleable molecule, providing the cell with a plethora of conformations to exploit in replication and transcription. Some of these conformations can give rise to mistakes, while others help to repair those mistakes in the genetic code. In this chapter, we dive into thecellular pot and find a literal alphabet soup of DNA structures. We start our journey by presenting the fundamental principles that serve as the vocabulary to analyze and describe the features of nucleic acid structures. We will explore the conformational variations that lead from double-helices to complexes composed of three or four strands, then consider how conformations interconvert throughvarious intermediates. Although B-DNA is the standard form in the cell, we suggest that this dance away from the norm is essential for cellular function, giving the cell life and, hence, its genetic soul. Replication is the process by which the cell creates an exact copy of the genetic information encoded in DNA—it is thus intuitive that we would be interested in the actual structure of DNA as amolecule. One would think that, for replication, we need only be concerned with the DNA duplex at the beginning, the single-stranded intermediate state, and the final duplex, since these structures generally tell us how the information is stored and read, and what the resulting product is. However, it is becoming clear that although the general structure of DNA is important in the overall mechanism ofreplication (Watson & Crick, 1953a), the conformational details are important for understanding how proteins recognize their cognate DNA sequence, and how mutations may be introduced and are repaired. Thus, we must explore and dissect the details in terms of variations that define the particular sequence dependent shape of DNA. We will not attempt the impossible task of covering every aspect of DNAstructure, only those that may be relevant to replication. Also, as crystallographers, we will have a bias towards studies derived from X-ray diffraction and other physical methods, although we will always attempt to relate these back to the biology of replication. In the process, we will explore the details of DNA structure that help elucidate structural principles that contribute to ourunderstanding of the mechanism and fidelity of the replicative process.
P. Shing Ho and Megan Carter
DNA Replication - Current Advances
2. A brief history of DNA structure
DNA structure has had over 55 years of history and, in that time, has undergone periods of discovery that have pushed the field forward in spurts. The evidence that DNA is the genetic molecule in the cell came from thestudies of Avery, MacLeod, and McCarty (Avery et al., 1944), and confirmed by Hershey and Chase (Hershey and Chase, 1952). The seminal experiments of Meselsen and Stahl (Meselson and Stahl, 1958) using heavy atom labeled DNA demonstrated that replication is semiconservative, with each newly replicated daughter strand being paired with one of the two parental strands. These classic studies from the1940’s and 1950’s set the stage for a race to determine the molecular structure of DNA, a now familiar story that helps to bring perspective to the discussions in this chapter. 2.1 The race for the structure of DNA: X-ray fiber diffraction studies. The key element in the race towards the structure of DNA was the availability of X-ray diffraction photographs of DNA fibers, the best of which came...