J. Phys. Chem. B 2001, 105, 11859-11865
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On the Non-Uniform Distribution of Guanine in Introns of Human Genes: Possible Protection of Exons against Oxidation by Proximal Intron Poly-G Sequences† Keith A. Friedman and Adam Heller* Department of Chemical Engineering and Texas Materials Institute, The UniVersity of Texas at Austin, Austin, Texas 78712-1062 ReceiVed: May 30, 2001; In Final Form: August 24, 2001
Earlier studies of oligonucleotides have shown that the rate of oxidation of the 5′-G in GGG sequences is faster than that of other nucleotides in other sequences. Recent studies have shown that nondissolved, doublestranded DNA is a one-dimensional conductor of holes or electrons. GGG and longer poly-G sequences could, therefore, act as sacrificially oxidizable sinks for holes injected remotely into the DNA strand by oxidizing agents. This could cathodically protect the most essential parts of genes: their protein-coding exons. The protection of exons would be optimal if GGG sequences were concentrated near the termini of introns, flanking exons. We find, indeed, that GGG sequences are nonuniformly distributed in introns, and that they are much more frequent near 5′ intron termini, which flank the 3′ ends of exons. We conclude that introns contain sacrificially oxidizable GGG sequences that are optimally positioned both to absorb holes injected directly into exons, and to intercept holes that could diffuse to exons from introns, which are much larger targets for oxidizing agents.
Introduction Essential parts of metallic structures commonly are protected against corrosion. An expendable, sacrificially oxidized conductor protects an essential, preserved conductor, when the two are electrically connected and reside in the same pool of electrolyte. For example, zinc coating (galvanizing) protects fuel storage tanks, steel roofs, and even nails (Figure 1a). This longrange protection, termed by electrochemists and materials scientists as “cathodic protection”, was introduced in 1824, when Sir Humphrey Dave attached zinc plates to the steel hulls of British warships to prevent their corrosion in seawater.1,2 In the zinc/aerated seawater/steel electrochemical cell, the zinc plate is the anode and the steel hull is the (inert) cathode. When oxygen in the seawater captures electrons from the steel cathode, the electron vacancies (“holes”) in the steel drift to the zinc anode. There the holes oxidize the zinc metal to Zn2+, while the steel remains intact. There are three requirements for cathodic protection. First, the anode and the cathode must be electrically connected, so that electrons or holes freely diffuse between them. (Insertion of an insulator between the anode and the cathode precludes cathodic protection.) Second, the anode and the cathode must be in electrolytic contact through an ion-transporting electrolyte. Third, the rate of oxidation of the sacrificial electrode (anode) by holes must exceed that of the protected electrode (cathode). The electrode with the fastest oxidation rate usually is the one with the lowest (most reducing) half-cell potential, because the (thermodynamic) redox potential and the (kinetic) corrosion rate usually are related through the Tafel and Butler-Volmer equations.3 According to these equations, the rate of a corrosion reaction increases exponentially with its overpotential, which is the excess potential driving it. When the anode is more reducing, the corrosion reaction is driven by a larger potential. Earlier studies have shown that DNA has both rapidly oxidized domains and difficult to oxidize domains. Several recent papers have shown that nondissolved double-stranded †
Part of the special issue “Howard Reiss Festschrift”. * To whom correspondence should be addressed. E-mail: heller@ che.utexas.edu.
Figure 1. Cathodic protection of (a) steel by zinc coating (shaded) and (b) exon by flanking intron domains (shaded).
DNA is an electronic conductor, conducting holes or electrons.4-6 It is, therefore, plausible that some genome domains could be protected microcathodes, whereas others could be protective microanodes. If the protective microanodes were in introns, whereas the protected microcathodes were exons (Figure 1b), there would be almost obvious advantages. Genes are alternating sequences of protein-coding exons and noncoding introns. In the nucleus, genes are transcribed into segments of pre-mRNA, and the introns between the exons are spliced out.7,8 Thus, mRNA production differs from DNA replicated prior to cell division which incorporates exons and introns and everything else. Mature mRNA segments are transported from the nucleus to be translated into proteins in the cytoplasm. Protein-coding exons comprise ∼5% of the nucleotides of genes, with noncoding introns comprising the remaining ∼95%.9 Because introns comprise 95% of gene-nucleotides, it is likely that they, not exons, comprise most of the sites at which oxidizing agents inject holes. If chromosomal DNA conducts holes over hundreds or thousands of base pairs, then the main culprit in exon oxidation could be holes diffusing or drifting from introns to exons. This attack could be mitigated if there were sacrificially oxidizable domains at the termini of introns, proximal to exons. Then, many of the holes injected into introns could be intercepted and trapped by the protective domains (which would be oxidized) before they reached exons (Figure 2). A double
10.1021/jp012043n CCC: $20.00 © 2001 American Chemical Society Published on Web 10/11/2001
11860 J. Phys. Chem. B, Vol. 105, No. 47, 2001
Friedman and Heller TABLE 1: Average Number of Triplet Gs, Doublet Gs and Total Gs in 100 bps of Intron (Long, >500 bp; Short 200 bp; Short
