The structures of the three major classes of biopolymers-polynucleotides, polypeptides and polysaccharides-are surveyed in the light of the most recent results from X-ray diffraction, electron microscopy and other studies. The review contains an introductory section setting out the basic features of each class of biopolymer: the natures of the 'building blocks', the linkages between them, conformational principles, types of repeating (secondary) structures and so on. The main section on each class is deliberately selective, because of the large amount of structural information now available. The section on polynucleotides concentrates on DNA, reviewing the classical double-helical models and the evidence provided by X-ray fibre diffraction, but also paying special attention to the rapid growth of new information on such features as the variations in helix geometry and in base-stacking, those data being derived primarily from studies of small self-complementary oligonucleotides. Alternative models and the question of right-handed versus left-handed structures are also considered. Among polypeptide structures, both globular and fibrous proteins are described. Globular proteins are treated as a group, with no detailed description of any one of them; this section concentrates on the organisation of globular proteins via folding units and domains, some general features (protein homology, catalysis, flexibility, interaction with water), membrane proteins, immunoglobulins and viruses.

REVIEW ARTICLE: Biopolymers

Conformation of two-stranded DNA in H2O–methanol, H2O–ethanol, H2O–isopropanol, and H2O–dioxane solutions at different concentrations of alkaline ions has been studied with the aid of circular dichroism. The following conclusions are drawn:

The conformation of DNA in H2O and H2O–methanol belongs to a family of B forms (B, C, T forms are the representatives of the family). The magnitude of the winding angle between adjacent base pairs (θ) is determined by the concentration and type of the cations. In H2O the cation action is nonspecific and leads to an increase in θ value. In 80% methanol the ions act specifically, Cs+ being to stabilize a form with a greater θ value, and Li+ being with a lesser one. The total θ change is likely within the limits of 33° ⩽ θ ⩽ 45°.

At high content of ethanol, isopropanol, or dioxane (∼80%), but not with methanol, and in low ionic strength the conformation of DNA belongs to a family of A forms (A form is one of the members of the family) and is specified by the concentration and type of cation involved. The two-stranded regions of RNA in H2O are also of A type and winds with the rise of cation concentration. The range of θ variation is not narrower than 30° ⩽ θ 33°.

The conformational transitions within the families (induced by ions) are of non-cooperative pattern, wheras the transitions between the families (induced by nonpolar component) are of cooperative pattern. The effect of cations, when specific, is discussed on the basis of steric correspondence between the width of DNA narrow groove and the size of a hydrated cation.

Different conformations of double‐stranded nucleic acid in solution as revealed by circular dichroism

The DNA tetramer d(CpGpCpG) or CGCG crystallizes from high-salt solution as a left-handed double helix, the Z' helix. Its structure differs from that of the other known left-handed helix, Z-DNA, by a Cl'-exo sugar pucker at deoxyguanosines rather than C3'-endo, and these represent two alternative solutions to the same steric constraint arising from the syn glycosyl bond orientation. The apparent molecular basis for the Z to Z' transition in going from intermediate to high salt is substitution of a bound anion for water at guanine amino groups, and consequent charge repulsion of anions and backbone phosphates.

High-salt d(CpGpCpG), a left-handed Z′ DNA double helix

Three chemical reactions can probe the secondary and tertiary interactions of RNA molecules in solution. Dimethyl sulfate monitors the N-7 of guanosines and senses tertiary interactions there, diethyl pyrocarbonate detects stacking of adenosines, and an alternate dimethyl sulfate reaction examines the N-3 of cytidines and thus probes base pairing. The reactions work between 0 degrees C and 90 degrees C and at pH 4.5--8.5 in a variety of buffers. As an example we follow the progressive denaturation of yeast tRNAPhe terminally labeled with 32P as the tertiary and secondary structures sequentially melt out. A single autoradiograph of a terminally labeled molecule locates regions of higher-order structure and identifies the bases involved.

https://www.pnas.org/content/pnas/77/8/4679.full.pdf

Chemical probes for higher-order structure in RNA

Structures for the polynucleotide complexes poly(dA) · poly(dT) and poly(dT) · poly(dA) · poly(dT)

RNA can exist in three distinct forms, all with a similar structure to that of the A form of DNA. The possible biological significance of these structures in protein synthesis and transcription mechanisms is discussed.

Molecular conformations and structure transitions of RNA complementary helices and their possible biological significance.

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Molecular conformations and structure transitions of RNA complementary helices and their possible biological significance.