Studies on conformational changes in the DNA structure induced by protonation: Reversible and irreversible acid titrations and sedimentation measurements

Zimmer, Ch.; Triebel, Hans

doi:10.1002/bip.1969.360080503

Cited by 30 publications

(13 citation statements)

References 48 publications

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“…4) exhibits a binding effect with positive CD band as previously reported for the complex of GC-rich DNA at 0.1 M NaCl and pH 6.5 (12). Presumably protonation of GC pairs is reduced on progressive binding of highly positive charged polyhistidine molecules, which is similar to the already known suppression of protonation of GC pairs at increased ionic strength (15,22) or by divalent cations (23). Binding of protonated polyhistidine to extremely AT-rich DNA at the same low ionic strength is very different in the CD binding effect; in contrast to GO-rich DNA a decrease of the CD occurs in the region from 260 to 270 nm and a CD maximum appears around 293 nm, characteristic for AT-dependent polyhistidine binding.…”

Section: Resultssupporting

confidence: 64%

Conformation and reactivity of DNA in the complex with protein. IV.Circular dichroism of poly-L-histidine model complexes with DNA polymers and specificity of the interaction

Burckhardt¹,

Zimmer²,

Luck³

1976

Nucleic Acids Research

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The CD study of the DNA-poly-L-histidine complex at high degree of protonation revealed that complex formation is already observable at 2 M NaCl. The influence of salt together with 5 M urea suggests that in addition to electrostatic interactions probably hydrogen bonding may favour specific complexes. Affinity of protonated histidines to AT-rich regions is strongly supported by the complexes formed with (dA.dT)-containing polymers. The psi-type structure occurs with poly(dA-dT)-poly(dA-dT) while poly(dA)-poly(dT) is restricted to form a similar psi-state on interaction with highly protonated poly-L-histidine. Differences in the helix winding properties due to variation in the sequence is suggested as a possible factor in the formation of the psi-type complexes. The mechanism of interaction including hydrogen bonding of histidine side-chains with an AT pair at high degree of protonation and with GC-regions at lower degree of protonation in the polypeptide structure is discussed.

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Section: Resultssupporting

confidence: 64%

Conformation and reactivity of DNA in the complex with protein. IV.Circular dichroism of poly-L-histidine model complexes with DNA polymers and specificity of the interaction

Burckhardt¹,

Zimmer²,

Luck³

1976

Nucleic Acids Research

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“…Many other articles have been published dealing with the protonation of different polynucleotides, and for almost all studies C‐containing sequences have been selected, since this base is generally considered the preferred site of protonation 14–24…”

Section: Introductionmentioning

confidence: 99%

Titration of poly(dA‐dT) · poly(dA‐dT) in solution at variable NaCl concentration

et al. 2004

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CD and uv absorption data showed that high molecular weight poly(dA-dT) . poly(dA-dT), at 298 K, undergoes an acid-induced transition from B-double helix to random coil in NaCl solutions of different concentrations, ranging from 0.005 to 0.600M. Similarly, titration of the polynucleotide with a strong base causes duplex-to-single strands transition. The base- and acid-induced transitions were both reversible by back-titration (with an acid or, respectively, with a base): the apparent pKa were the same in both directions. However, the number of protons per titratable site (adenine N1) required to reach half-denaturation was in great excess over the stoichiometric value; to a much larger extent, the same effect was observed also for the deprotonation of the N3H sites of thymine. Moreover, in the basic denaturation experiments, at low salt concentrations ([NaCl]< or =0.300M) less acid than calculated was needed to back-titrate the base excess to half-denaturation. Both effects could be qualitatively justified on the basis of the counterion condensation theory of polyelectrolytes and considering the energy barrier created by the negatively charged phosphodiester groups to the penetration of the OH- ions inside the double helix and the screening effect of the Na+ ions on such charges, in the deprotonation experiments.

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“…6 and 7 we find that log AAn = (n -1) log(1 -4) + log(4)AAt0) (8) The data of Using 4 = 0.08, we may state that under our experimental conditions each impulse caused 8% of the intact poly(A) .2 poly(U) molecules to undergo the conformational transition described by Eq. 1.…”

Section: Resultsmentioning

confidence: 74%

“…The polymer fractions with mean sedimentation coefficients of s2 --5 were selected. Poly(A) and poly(U), dissolved in 0.1 M NaCl-5 mM Na-phosphate buffer (pH 7.1), were mixed in the molar ratio 1:2 and equilibrated for [4][5][6] days at 17°to permit complete complex formation. The complex poly(A) -2 poly(U) was titrated with 1 N HCl to pH 4.5 and equilibrated until no further change in A260 was observed.…”

Section: Methodsmentioning

confidence: 99%

Long-Lived Conformation Changes Induced by Electric Impulses in Biopolymers

Neumann

Katchalsky

1972

Proc. Natl. Acad. Sci. U.S.A.

141

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Electric impulses are capable of inducing long-lived conformational changes in (metastable) biopolymers. Results of experiments with poly(A) 2 poly(U) and ribosomal RNA, which are known to develop metastabilities, are reported. A polarization mechanism is proposed to explain the structural transitions observed in the biopolymers exposed to the impulses. In accordance with this idea, the applied electric field (of about 20 kV/cm and decaying exponentially, with a decay time of about 10 $sec) induces large dipole moments by shifting the ionic atmosphere of multistranded polynucleotide helices. This shift, in turn, causes strand repulsion and partial unwinding. The fields used in our experiments are of the same order of magnitude as those in nerve impulses. The significance of the impulse experiments with regard to the question of biological memory recording is briefly discussed.The initial step in the recording of biological memory is probably a physical, and not a biochemical, process (1, 2). A plausible mechanism for physical memory imprinting in living organisms is based on conformational transitions of metastable macromolecules or of macromolecular organizations, such as membranes (2, 3). Since metastabilities can lead to hysteresis, and because hysteresis loops were observed in several biopolymers (2, 4-6), these polymers could be possible matrices for a memory imprint. Such matrices should be able to record the electric impulses that are the information signals of the nervous system. Thus, we determined whether electric impulses can cause long-lived conformational changes in biopolymers. On physicochemical grounds, such long-lived changes are expected in domain structures capable of developing metastable states. Here, we report that electric impulses of about 20 kV/cm, and of a duration of a few Asec, do indeed induce long-lived conformational transitions in macromolecular complexes of polynucleotides (7), analyze this impulse effect, and suggest an explanation in terms of the physical chemistry of polyelectrolytes.The polynucleotides investigated consist of polyriboadenylate, poly(A), and polyribouridylate, poly(U), mixed in the molar ratio 1: 2 in aqueous NaCl solution. At sufficiently high salt concentration and neutral pH, these polymers form a three-stranded helical complex, poly(A) -2 poly(U). The basepairing scheme of this complex (8, 9) is depicted in Fig. 1. The complex polyA-2 poly(U) can develop metastability, which underlies the time-independent hysteresis loops observed in potentiometric and spectrophotometric acid-base titrations (10). Such a hysteresis cycle is shown in Fig. 2 . This barrier, which is mainly electrostatic, is strengthened by the mutual repulsion of the poly(A) -2 poly(U) triple helixes arising from the high density of negatively charged phosphates along these multistranded molecules (10). When the pH is lowered, the extent of protonation is increased. This further loosens the triple helix, lowering the nucleation barrier. Therefore, around pH'm (see Fig. 2) the "transc...

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Studies on conformational changes in the DNA structure induced by protonation: Reversible and irreversible acid titrations and sedimentation measurements

Cited by 30 publications

References 48 publications

Conformation and reactivity of DNA in the complex with protein. IV.Circular dichroism of poly-L-histidine model complexes with DNA polymers and specificity of the interaction

Conformation and reactivity of DNA in the complex with protein. IV.Circular dichroism of poly-L-histidine model complexes with DNA polymers and specificity of the interaction

Titration of poly(dA‐dT) · poly(dA‐dT) in solution at variable NaCl concentration

Long-Lived Conformation Changes Induced by Electric Impulses in Biopolymers

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