Structural Biology: Chapter 9 — Nucleic acid structure

9.1 DNA helices #

9.1.1 A, B, and Z #

The 1953 model is two antiparallel strands, bases inside, adenine with thymine and guanine with cytosine. Franklin’s B-form diffraction, Wilkins’s laboratory, and Chargaff’s ratios were the evidence it had to meet. Correct pairs are isosteric, which is why a polymerase or a ribosome can test shape. A–T has two hydrogen bonds, G–C three. Hoogsteen geometry is a special case, not the genomic default.

B-DNA is the cellular form: right-handed, C2′-endo sugars, about 10.5 base pairs per turn in solution, rise about 3.4 Å. Fibre diffraction classically gave 10 base pairs per turn. The major groove is wide, about 12 Å; the minor groove is narrow, about 6 Å. A-tracts narrow it further and bend the axis. A-form is right-handed, C3′-endo, about 11 base pairs per turn, rise near 2.6 Å, with a deep narrow major groove. Duplex RNA and DNA–RNA hybrids adopt it because the 2′-hydroxyl disfavours B-form. Calling RNA “B-form” is a mistake about the sugar. Z-DNA is left-handed, with a zigzag backbone and a dinucleotide repeat, about 12 base pairs per turn, favoured by alternating purine–pyrimidine sequence, especially GC, and by negative supercoiling. It is local. The Zα domain of ADAR1 binds it. It is not a second genome-wide conformation.

9.1.2 Reading a groove #

The edges of the pairs are exposed. The major groove distinguishes all four pairs by its pattern of donors, acceptors, and nonpolar patches. The minor groove does not: A–T resembles T–A. Minor-groove contacts often read shape, including the narrow negative minor groove of an A-tract, which arginine probes. A site can also be chosen because the DNA bends there cheaply. Both the hydrogen-bond inventory and the deformability are part of recognition.

9.2 Three protein strategies #

The study of Three protein strategies provides fundamental principles governing cellular architecture, molecular interactions, and physiological regulation.

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9.2.1 Helix–turn–helix, zinc finger, and leucine zipper #

The usual reading head is an α helix in the major groove. A helix–turn–helix, as in λ CI, braces that helix with a second helix. Specificity is the side-chain pattern, not the mere presence of the motif. Homeodomains add an arm in the minor groove. A classical zinc finger is a ββα module of about thirty residues. Zinc, held by two cysteines and two histidines, builds the module and does not touch the DNA. Each helix reads about three base pairs; the Zif268 structure shows the docking. A strict one-residue-to-one-base code is only a first approximation. A leucine zipper is the coiled coil of Chapter 1, with leucine every seventh residue. Dimerisation is separate from reading: a basic region lies in the major groove and, in Gcn4, folds into a helix only on the DNA. Fos pairs with Jun rather than with itself, so the partner chooses the site. TATA-binding protein is the warning against “always a helix”: a β sheet opens the minor groove and bends TATA DNA by about 80°.

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9.3 RNA as a folded catalyst #

9.3.1 Tertiary motifs, as an idea #

Local RNA duplexes are A-form. Tertiary structure packs them into one fold, using non-Watson–Crick pairs and the 2′-hydroxyl, a hydrogen-bonding group the protein backbone lacks. Magnesium shields phosphates so helices can approach. An A-minor contact packs an adenosine into the minor groove of a helix and is abundant in the ribosome. A tetraloop receptor docks a GNRA loop, often GAAA, onto a distant helix. A pseudoknot pairs a loop with a downstream sequence. The catalogue is long. The point is short: RNA can specify a compact fold, and a fold can contain a chemical site.

9.3.2 Ribozymes, and the lesson of an incomplete structure #

The ribosome is the large proof that the fold can catalyse. The hammerhead is a small one. Its 2′-hydroxyl attacks the adjacent phosphorus in line, leaving a 2′,3′-cyclic phosphate, which is alkaline cleavage made fast and specific by the structure. Crystal structures of a minimal hammerhead lacked that in-line geometry. They were accurate maps of a fragment. Peripheral tertiary contacts, absent from the minimal construct, align the active site. A high-resolution structure can miss the mechanism if the molecule is incomplete. The group I intron, Cech’s self-splicing Tetrahymena example, binds an exogenous guanosine whose 3′-hydroxyl attacks the 5′ splice site; the upstream exon then attacks the 3′ splice site. The fold aligns the phosphate and uses magnesium. Proteins often assist in the cell. The active site in the structures is RNA. Bacterial RNase P is the parallel case. Splicing as gene expression is Molecular Biology. Nothing here is a sequence to build.

9.4 Key terms, summary, and self-check #

Key terms. A-DNA; B-DNA; Z-DNA; major groove; minor groove; helix–turn–helix; zinc finger; leucine zipper; A-minor motif; tetraloop receptor; hammerhead; group I intron.

Summary. B-DNA is the cellular form, about 10.5 base pairs per turn, with a wide major groove. A-form is duplex RNA. Z-DNA is a local left-handed helix. Proteins read base edges in the major groove and shape in the minor groove, using a braced helix, a zinc-stabilised module, or a coiled-coil dimer. A-minor contacts and tetraloop receptors pack RNA into a tertiary fold. The hammerhead, the group I intron, and the ribosome show that the fold can catalyse, and the minimal hammerhead shows that a fragment can miss the chemistry.

Self-check.

1. Which form is left-handed, which is physiological RNA, and which has the wide major groove?

2. Why does the major groove support a four-letter code when the minor groove mostly reports shape?

3. What do the zinc and the leucine heptad each do, as distinct from the recognition helix?

4. What does an A-minor contact add to a lone A-form helix?

5. What was wrong with the minimal hammerhead structures, and what is the exogenous guanosine for in a group I intron?

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