The pH-dependent structure of calf thymus DNA studied by Raman spectroscopy

O’Connor, Timothy; Mansy, Samir; Bina, Minou; McMillin, David R.; Brück, Marie-Christin; Tobias, R. Stuart

doi:10.1016/0301-4622(82)87016-6

Cited by 52 publications

(33 citation statements)

References 31 publications

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“…A subsequent Raman spectroscopic study on calf thymus DNA, on the otherhand, proposed the first protonation sites in DNA to be adenines and cytosines suggesting the formation of a C-type conformation. 51 Later studies on oligonucleotides using NMR assigned the first protonation sites to be N3 of cytosines resulting in Hoogsteen base pairing. 57,58 Base protonation has been shown to promote the formation of triple helical structure, 59 H-form DNA, 24 parallel stranded structure, 60 and facilitate B-Z interconversion in synthetic alternating GC polymer.…”

Section: E Protonated Dna Structurementioning

confidence: 99%

Molecular aspects on the interaction of protoberberine, benzophenanthridine, and aristolochia group of alkaloids with nucleic acid structures and biological perspectives

Maiti

Kumar

2006

Medicinal Research Reviews

164

103

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Alkaloids occupy an important position in chemistry and pharmacology. Among the various alkaloids, berberine and coralyne of the protoberberine group, sanguinarine of the benzophenanthridine group, and aristololactam-beta-d-glucoside of the aristolochia group have potential to form molecular complexes with nucleic acid structures and have attracted recent attention for their prospective clinical and pharmacological utility. This review highlights (i) the physicochemical properties of these alkaloids under various environmental conditions, (ii) the structure and functional aspects of various forms of deoxyribonucleic acid (DNA) (B-form, Z-form, H(L)-form, protonated form, and triple helical form) and ribonucleic acid (RNA) (A-form, protonated form, and triple helical form), and (iii) the interaction of these alkaloids with various polymorphic DNA and RNA structures reported by several research groups employing various analytical techniques like absorbance, fluorescence, circular dichroism, and NMR spectroscopy; electrospray ionization mass spectrometry, thermal melting, viscosity, and DNase footprinting as well as molecular modeling and thermodynamic studies to provide detailed binding mechanism at the molecular level for structure-activity relationship. Nucleic acids binding properties of these alkaloids are interpreted in relation to their biological activity.

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Section: E Protonated Dna Structurementioning

confidence: 99%

Molecular aspects on the interaction of protoberberine, benzophenanthridine, and aristolochia group of alkaloids with nucleic acid structures and biological perspectives

Maiti

Kumar

2006

Medicinal Research Reviews

164

103

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“…Instead of looking for and presenting obvious spectral differences between a few selected Raman spectra taken under definite conditions, more complex and less apparent spectral changes can be discerned, studied and interpreted as a function of a particular physicochemical parameter (intensive variable [1] ), gradually varied over a given range. Thermal-induced structural transitions of biomolecules, [2,3] acid-base titrations [4,5] or kinetic studies [6,7] monitored by Raman spectroscopy can be taken as an archetype of particular but frequent Raman experiments when a biological analyte is dissolved in an aqueous buffer to rather low concentration, and spectral changes are studied as a function of temperature, pH and time, respectively. Instead of laborious visual inspection and manual identification of spectral changes, extensive series of Raman spectra can be analyzed by multivariate statistical methods [8] (factor analysis, principal component analysis).…”

Section: Introductionmentioning

confidence: 99%

SVD‐based method for intensity normalization, background correction and solvent subtraction in Raman spectroscopy exploiting the properties of water stretching vibrations

Palacký

Mojzeš

Bok

2011

J Raman Spectroscopy

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A semiautomated method combining intensity normalization with effective elimination of the solvent signal and non-Raman background is presented for Raman spectra of biochemical and biological analytes in aqueous solutions. The method is particularly suitable for rapid and effortless preprocessing of extensive datasets taken as a function of gradually varied physicochemical parameters, e.g. analyte and/or ligand concentration, temperature, pH, pressure, ionic strength, time, etc. For intensity normalization, the strong Raman OH stretching band of water in the range of 2700-3900 cm −1 recorded together with the analyte spectrum in the fingerprint region below 1800 cm −1 is employed as internal intensity standard. Concomitant dependences of the solvent Raman spectra are taken into account and, in some cases, turned into advantage. Once the Raman spectra of the solvent are acquired for a particular range of the parameter varied, solvent contribution can be subtracted correctly from any analyte spectrum taken within this range. The procedure presented can be efficiently applied only for the analytes having their own Raman signal in the range of OH stretching vibrations much weaker than that of the solvent. However, this is the case for a great number of biochemical and biological samples. Accuracy, reliability and robustness of the method were tested under the conditions of spontaneous Raman, resonance Raman and surface-enhanced Raman scattering. Serviceability of the method is demonstrated by several real-world examples.

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“…Therefore, it is important to study the effects of acid-fixed DNA structures in more detail and to analyse the non-B-DNA conformations formed during biopolymer protonation. Vibrational spectroscopy is a powerful tool, which has been often used to characterize the nature of acid-DNA interaction [6,9,[11][12][13].…”

Section: Introductionmentioning

confidence: 99%