A theory of aggregation in the thermal denaturation region of multistrand biopolymers

Shibata, John H.; Schurr, J. Michael

doi:10.1002/bip.1981.360200308

Cited by 26 publications

(15 citation statements)

References 29 publications

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“…Even better would be a theoretical model to quantify DNA aggregation and denaturation upon heating in the presence of divalent cations. Such a model has been developed (Shibata and Schurr, 1981) for DNA aggregation during thermal denaturation. We have shown (Duguid and Bloomfield, 1995) that this model can be used to explain DNA aggregation and melting in the presence of divalent metal cations.…”

Section: Discussionmentioning

confidence: 99%

Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+

Duguid

Bloomfield

Benevides

et al. 1995

Biophysical Journal

188

157

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Differential scanning calorimetry, laser Raman spectroscopy, optical densitometry, and pH potentiometry have been used to investigate DNA melting profiles in the presence of the chloride salts of Ba2+, Sr2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+. Metal-DNA interactions have been observed for the molar ratio [M2+]/[PO2-] = 0.6 in aqueous solutions containing 5% by weight of 160 bp mononucleosomal calf thymus DNA. All of the alkaline earth metals, plus Mn2+, elevate the melting temperature of DNA (Tm > 75.5 degrees C), whereas the transition metals Co2+, Ni2+, and Cd2+ lower Tm. Calorimetric (delta Hcal) and van't Hoff (delta HVH) enthalpies of melting range from 6.2-8.7 kcal/mol bp and 75.6-188.6 kcal/mol cooperative unit, respectively, and entropies from 17.5 to 24.7 cal/K mol bp. The average number of base pairs in a cooperative melting unit () varied from 11.3 to 28.1. No dichotomy was observed between alkaline earth and transition DNA-metal complexes for any of the thermodynamic parameters other than their effects on Tm. These results complement Raman difference spectra, which reveal decreases in backbone order, base unstacking, distortion of glycosyl torsion angles, and rupture of hydrogen bonds, which occur after thermal denaturation. Raman difference spectroscopy shows that transition metals interact with the N7 atom of guanine in duplex DNA. A broader range of interaction sites with single-stranded DNA includes ionic phosphates, the N1 and N7 atoms of purines, and the N3 atom of pyrimidines. For alkaline earth metals, very little interaction was observed with duplex DNA, whereas spectra of single-stranded complexes are very similar to those of melted DNA without metal. However, difference spectra reveal some metal-specific perturbations at 1092 cm-1 (nPO2-), 1258 cm-1 (dC, dA), and 1668 cm-1 (nC==O, dNH2 dT, dG, dC). Increased spectral intensity could also be observed near 1335 cm-1 (dA, dG) for CaDNA. Optical densitometry, employed to detect DNA aggregation, reveals increased turbidity during the melting transition for all divalent DNA-metal complexes, except SrDNA and BaDNA. Turbidity was not observed for DNA in the absence of metal. A correlation was made between DNA melting, aggregation, and the ratio of Raman intensities I1335/I1374. At room temperature, DNA-metal interactions result in a pH drop of 1.2-2.2 units for alkaline earths and more than 2.5 units for transition metals. Sr2+, Ba2+, and Mg2+ cause protonated sites on the DNA to become thermally labile. These results lead to a model that describes DNA aggregation and denaturation during heating in the presence of divalent metal cations; 1) The cations initially interact with the DNA at phosphate and/or base sites, resulting in proton displacement. 2) A combination of metal-base interactions and heating disrupts the base pairing within the DNA duplex. This allows divalent metals and protons to bind to additional sites on the DNA bases during the aggregation/melting process. 3) Strands whose bases have swung open upon disruption are linke...

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Section: Discussionmentioning

confidence: 99%

Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+

Duguid

Bloomfield

Benevides

et al. 1995

Biophysical Journal

188

157

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“…2). Since the OH − anion could fundamentally affect the interchain H-bonds (Bluhm et al, 1982;Bo et al, 1987;Shibata & Schurr, 1981;Sletmoen & Stokke, 2008;Tabata et al, 1981), the macromolecular conformation could be ascribed as the main cause of these differences. Alkali effects on rheological behavior were lower on EPS II and even less marked on EPS I (Table 1, Fig.…”

Section: Alkaline Treatmentmentioning

confidence: 99%

Effects of thermal, alkaline and ultrasonic treatments on scleroglucan stability and flow behavior

Viñarta

Delgado

Figueroa

et al. 2013

Carbohydrate Polymers

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“…In the triple helical to single‐stranded transitional region, a dynamic equilibrium between the breaking and formation of hydrogen bonds occurs. The number of interacting residues required to suppress complete strand separation is independent of the degree of polymerization of the strands 45. On the other hand, the probability that there within the original triplex is a region of hydrogen bonds sufficiently long to stabilize it increases with increasing molecular weight of the sample.…”

Section: Properties and Structure Of Denatured And Renatured (13)‐β‐mentioning

confidence: 99%

Higher order structure of (1,3)‐β‐D‐glucans and its influence on their biological activities and complexation abilities

2008

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(1,3)‐β‐D‐Glucans form a group of biologically active biopolymers that exist in different structural organizations depending on the environmental conditions. The biological effect of (1,3)‐β‐D‐glucans is a core issue stimulating large research efforts of the molecular properties and their consequences for action as biological response modifiers. The fascination for these molecules increased further following the finding of their ability to form complexes of defined geometry with a number of structures, ranging from linear architectures as polymers or carbon nanotubes, to globular structures as gold particles or dye molecules. The fascinating information concerning the relationship between sample treatment history and molecular organization has not yet reached out to all the contributors within the field, resulting in unnecessary apparent inconsistencies in the literature. In addition to environmental conditions, the sample history is known to influence on the precise structural organization of these molecules. The present knowledge related to the structure of native as well as denatured, renatured and annealed (1,3)‐β‐D‐glucans is reviewed. The influence of their structural organization on the biological activity and complexation abilities is discussed, and some factors hindering progress in the understanding of their biological effects or complexation abilities are pointed out. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 310–321, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley. com

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A theory of aggregation in the thermal denaturation region of multistrand biopolymers

Cited by 26 publications

References 29 publications

Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+

Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+

Effects of thermal, alkaline and ultrasonic treatments on scleroglucan stability and flow behavior

Higher order structure of (1,3)‐β‐D‐glucans and its influence on their biological activities and complexation abilities

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