A reinterpretation of the infrared linear dichroism of oriented nucleic acid films and a calculation of some effective partial changes on the ribose phosphate backbone

Beetz, C. P.; Ascarelli, G.; Arnott, Struther

doi:10.1016/s0006-3495(79)85155-3

Cited by 15 publications

(5 citation statements)

References 31 publications

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“…The corresponding 6 angle was assumed to be >850 for the B form and >830 for the Z form (2,15 (13) and assuming that the two differently oriented groups contribute equally to the absorption of the band, we found Eq. 1 to be still valid, provided we define 6, the mean angle, as: The validity limits for the comparison of these 6 values with those deduced from models have been discussed (16,17) and can be considered to be at least qualitatively correct for PO2 stretching modes. Recent experimental work (18) supports this thesis which will be discussed elsewhere.…”

Section: Methodsmentioning

confidence: 99%

Comparison of poly(dG-dC).poly(dG-dC) conformations in oriented films and in solution.

Pilet¹,

Leng²

1982

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

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The structures of B and Z forms of poly(dGdC)'poly(dG-dC) in oriented hydrated films have been investigated by infrared spectroscopy. First, the infrared linear dichroism spectrum of poly(dG-dC) poly(dG-dC) in B form (high relative humidity and 2 M Na+) was recorded. The spectrum ofthe Z form was recorded at a lower relative humidity and higher sodium content (4 M). The experimental conditions were similar to those used in x-ray diffraction studies of left-handed poly(dG-dC)poly(dGdC) fibers. A qualitative agreement was found between the calculated values of the angles characteristic of the orientation of PO_ groups with respect to the helical axis in the Z, form and the experimental values. The infrared spectra of B and Z forms show some significant differences in H20 and 2H20. The deuteration rates of exchangeable protons involved in hydrogen bonds between guanine and cytosine residues were deduced from the changes in absorbance near 1700 cm.. In the B form, the exchange half-time is of the order of 20 min. In the Z form, the exchange half-time of some protons is very slow, of the order of 24 hr. Because of the similarity between these values and those previously reported for the high-salt and low-salt form of poly(dGdC).poly(dG-dC) in solution, we conclude that the high-salt form of poly(dG-dC)'poly(dG-dC) in solution belongs to the Z family.The discovery that alternating d(CpG)DNA fragments crystallize as a left-handed double helical molecule (1-3) raises the question of whether this form, termed Z DNA, exists in solution. In solution, poly(dG-dC)poly(dG-dC) can undergo a saltinduced cooperative transition (4, 5). The low-salt conformation of poly(dG-dC)poly(dG-dC) was shown to belong to the B family, whereas the high-salt conformation is assumed to belong to the Z family (1). Several lines of evidence support this assumption. The circular dichroism spectrum of the high-salt conformation is almost an inversion of the spectrum of the low-salt conformation (6).31P NMR spectra ofoligo[d(G-C)] have one and two peaks in low-and high-salt solutions, respectively (7). In the high-salt conformation, two exchanging protons have a halftime at least 50 times greater than that measured in low-salt conformation (8). These results are consistent with Z-and B-DNA conformations but do not firmly establish the existence of the Z form in solution.In this work, we studied the structures of B and Z forms of poly(dG-dC)-poly(dG-dC) in oriented hydrated films by infrared spectroscopy. We first report the infrared linear dichroism spectra ofthese two forms in deuterated and nondeuterated states. The spectra of both forms in H20 and 2H20 show some differences which allow the determination ofthe exchange rates of the protons involved in hydrogen bonds between base residues. These rates are of the same order of magnitude as those previously reported for the low-and high-salt form of poly(dGThe publication costs ofthis article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertis...

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Section: Methodsmentioning

confidence: 99%

Comparison of poly(dG-dC).poly(dG-dC) conformations in oriented films and in solution.

Pilet¹,

Leng²

1982

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

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“…Since/ is treated only as an unknown parameter the transition moment directions obtained will be, therefore, numerically correct in representing 'effective' angles as discussed in Section 3. A discrepancy between infrared LD and X-ray diffraction data regarding phosphate orientations (Beetz et al 1979) inspired Pohle et al ( , 1986 to critically examine the information from infra-red LD for A, B and C forms of DNA in relation to results from energy minimization, X-ray and NMR; the conclusion was a generally satisfactory agreement with the bulk of results of other methods. Both the German and the French group (Taillandier et al 1984(Taillandier et al , 1985Liquier et al 1975), specializing in infra-red LD, have also applied the method successfully for characterizing the conformation of DNA upon interaction with biologically relevant agents such as drugs and proteins (see below).…”

Section: £ Smentioning

confidence: 99%

Linear dichroism spectroscopy of nucleic acids

Nordén

Kubista

Kurucsev

1992

Quart. Rev. Biophys.

360

376

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This review will consider solution studies of structure and interactions of DNA and DNA complexes using linear dichroism spectroscopy, with emphasis on the technique of orientation by flow. The theoretical and experimental background to be given may serve, in addition, as a general introduction into the state of the art of linear dichroism spectroscopy, particularly as it is applied to biophysical problems.

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“…196 Although these values were shown to be reproducibly consistent in numerous p-IR studies, the use of stretching vibrations of the PO 2 − group in the DNA backbone was called into question due to discrepancies between p-IR and X-ray diffraction data. 198 It was argued that the approximation of the transition moment of these vibrations aligning with the O-P-O bisector and O---O line was imprecise as these approximations were made considering a simple PO 4 unit. However, in practice, as the phosphate is associated with the entire DNA molecule this approximation would not hold due to vibrational coupling and degenerate modes contributing to the 1090 and 1230 cm −1 peaks assigned to the stretching vibrations.…”

Section: Nucleic Acidsmentioning

confidence: 99%

Linearly Polarized Infrared Spectroscopy for the Analysis of Biological Materials

Gassner

Vongsvivut

et al. 2023

Appl Spectrosc

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The analysis of biological samples with polarized infrared spectroscopy (p-IR) has long been a widely practiced method for the determination of sample orientation and structural properties. In contrast to earlier works, which employed this method to investigate the fundamental chemistry of biological systems, recent interests are moving toward “real-world” applications for the evaluation and diagnosis of pathological states. This focal point review provides an up-to-date synopsis of the knowledge of biological materials garnered through linearly p-IR on biomolecules, cells, and tissues. An overview of the theory with special consideration to biological samples is provided. Different modalities which can be employed along with their capabilities and limitations are outlined. Furthermore, an in-depth discussion of factors regarding sample preparation, sample properties, and instrumentation, which can affect p-IR analysis is provided. Additionally, attention is drawn to the potential impacts of analysis of biological samples with inherently polarized light sources, such as synchrotron light and quantum cascade lasers. The vast applications of p-IR for the determination of the structure and orientation of biological samples are given. In conclusion, with considerations to emerging instrumentation, findings by other techniques, and the shift of focus toward clinical applications, we speculate on the future directions of this methodology.

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A reinterpretation of the infrared linear dichroism of oriented nucleic acid films and a calculation of some effective partial changes on the ribose phosphate backbone

Cited by 15 publications

References 31 publications

Comparison of poly(dG-dC).poly(dG-dC) conformations in oriented films and in solution.

Comparison of poly(dG-dC).poly(dG-dC) conformations in oriented films and in solution.

Linear dichroism spectroscopy of nucleic acids

Linearly Polarized Infrared Spectroscopy for the Analysis of Biological Materials

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