The addition of the trivalent or tetravalent cations spermidine or spermine to a solution of T7 DNA in aqueous solution causes an alteration of the DNA from its extended coil form to a condensed form. If performed at low DNA concentration and at low ionic strengths, this transformation results in a monomolecular collapse to form a particle with a hydrodynamic radius of about 500 A. We have monitored this change using quasielastic and total intensity light scattering. In a solution of 50% methanol in water, the divalent cations Mg2+ and putrescine also can cause the condensation of DNA. Using Manning's (1978) counterion condensation theory, we calculate a striking unity among these disparate ions: the collapse occurs in each case when from 89 to 90% of the DNA phosphate charges are neutralized by condensed counterions.

Counterion-induced condesation of deoxyribonucleic acid. a light-scattering study.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2881%2980642-4

α-lactalbumin: compact state with fluctuating tertiary structure?

RECENT studies have revealed that the packaging of DNA into phage heads is an ordered sequence of structural and biochemical events rather than a simple, spontaneous self-assembly of component molecules. In the assembly of T7 for example1, heads containing the products of genes 8–10 and 14–16 are apparently formed first. Gene 9 protein is removed from the heads before or during the incorporation of DNA. At least two other gene products which play no direct structural role are required for the maturation of the heads. A somewhat similar situation exists for phage λ, which has been shown to require ATP for the in vitro packaging of DNA into preformed heads (petite λ)2.

Compact form of DNA induced by spermidine.

(1981). The Internal Dynamics of Globular Protein. Critical Reviews in Biochemistry: Vol. 9, No. 4, pp. 293-349.

The internal dynamics of globular proteins.

Condensed phases of DNA: Structures and phase transitions

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2872%2980335-1

A compact form of double-stranded DNA in solution

Based on equilibrium binding studies, as well as on kinetic investigations, two types of interactions of Cu2+ ions with native DNA at low ionic strength could be characterized, namely, a nondenaturing and a denaturing complex formation. During a fast nondenaturing complex formation at low relative ligand concentrations and at low temperatures, different binding sites at the DNA bases become occupied by the metal ions. This type of interaction includes chelate formation of Cu2+ ions with atoms N(7) of purine bases and the oxygens of the corresponding phosphate groups, chelation between atoms N(7) and O of C(6) of the guanine bases, as well as the formation of specific intestrand crosslink complexes at adjacent G°C pairs of the sequence dGpC. CD spectra of the resulting nondenatured complex (DNA–Cu2+)nat may be interpreted in terms of a conformational change of DNA from the B-form to a C-like form on ligand binding. A slow cooperative denaturing complex formation occurs at increased copper concentrations and/or at increased temperatures. The uv absorption and CD spectra of the resulting complex, (DNA–Cu2+)denat, indicate DNA denaturation during this type of interaction. Such a conclusion is confirmed by microcalorimetric measurements, which show that the reaction consumes nearly the same amount of heat as acid denaturation of DNA.



From these and the kinetic results, the following mechanism for the denaturing action of the ligands is suggested: binding of Cu2+ ions to atoms N(3) of the cytosine bases takes place when the cytosines come to the outside of the double helix as a result of statistical fluctuations. After the completion of the binding process, the bases cannot return to their initial positions, and thus local denaturation at the G·C pairs is brought about. The probability of the necessary fluctuations occurring is increased by chelation of Cu2+ ions between atoms N(7) and O of C(6) of the guanine bases during nondenaturing complex formation, which loosens one of the hydrogen bonds within the G·C pairs, as well as by raising the temperature. The implications of the new binding model, which comprises both the sequence-specific interstand crosslinks and the described mechanism of denaturing complex formation, are discussed and some predictions are made. The model is also used to explain the different renaturation properties of the denatured complexes of Cu2+, Cd2+, and Zn2+ ions with DNA.



In temperature-jump experiments with the nondenatured complex (DNA–Cu2+)nat, a specific kinetic effect is observed, namely, the appearance of a lag in the response to the perturbation. The resulting sigmoidal shape of the kinetic curves is considered to be a consequence of the necessity of disrupting a certain number of the crosslinks existing in the nondenatured complex before the local unwinding of the binding regions (a main step of denaturing complex formation) may proceed.

Thermodynamics and kinetics of the interaction of copper (II) ions with native DNA.

Comparative CD and X-ray diffraction studies of DNA compact particules which were obtained in PEG-containing water-salt solutions, have been carried out. Compact particles, formed from native DNA, produce a psi CD spectrum (characterized by a negative band at lambda-270 nm) and a small-angle X-ray diffraction pattern, which shows two reflections: I at 34-40 A and II at 80-90 A (together with its second-order reflection). Compact particules, formed from DNA molecules with partially disordered secondary structure, do not produce the psi CD spectrum and the reflection I, while the reflection II remains unchanged. It is suggested that the spacing of 34-40 A is associated with a side-by-side packing of DNA fragments in "microcrystallization' regions in compact particules and that such "microcrystallization' accounts for the generation of the psi CD spectrum.

/pdf/a-comparative-x-ray-diffraction-and-circular-dichroism-study-2i02hf4lq7.pdf

A comparative X-ray diffraction and circular dichroism study of DNA compact particles formed in water-salt solutions, containing poly(ediylene glycol)

Molecules of single-stranded ribosomal RNA and double-stranded replicative form of phage f2 RNA (dsRNA) adopt a compact form in solutions, containing sufficiently high concentrations of salt (NaCl) and polymer (PEG). However, only in the cases of native dsRNA molecules the compact particles are characterized by a regular internal structure, which accounts for the appearance of an intense positive band in CD spectra. Heating or acidification of PEG-containing solutions of dsRNA leads to the disappearance of the intense positive CD band, which results from the "destruction" of the regular internal structure of compact particles. Comparison of properties of DNA and dsRNA compact particles formed in PEG-containing water-salt solutions suggests the existence of similar mechanisms of compactization of double-stranded polynucleotides.

/pdf/a-compact-form-of-double-stranded-rna-in-solutions-1ogzdooff2.pdf

A compact form of double-stranded RNA in solutions containing poly(ethyleneglycol).

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2876%2980741-7

Ya.M. Varshavsky

Papers

A compact form of double-stranded DNA in solution

Thermodynamics and kinetics of the interaction of copper (II) ions with native DNA.

A comparative X-ray diffraction and circular dichroism study of DNA compact particles formed in water-salt solutions, containing poly(ediylene glycol)

A compact form of double-stranded RNA in solutions containing poly(ethyleneglycol).

Effect of inter-subunit contact on intramolecular conformational motility (conformational stability) of hemoglobin as revealed by hydrogen exchange.