Selected deoxyoctanucleotides and their daunomycin complexes: Infrared absorption and vibrational circular dichroism spectra

Tsankov, D.; Maharaj, V.; Sande, J.H. van de; Wieser, H.

doi:10.1016/j.vibspec.2006.06.018

Cited by 4 publications

(6 citation statements)

References 45 publications

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“…Most likely, the arrangement of DNA double helices into super‐helical threads11, 14 or other regular arrangements provide the necessary rigidity. Experimentally, a decrease of the VCD signal due to a disturbance of the regular double stranded DNA helix was observed upon interaction with various agents 51, 52. At normal physiological conditions DNA exists as a worm‐like chain with rather short straight segments, not favorable for the enhancement.…”

Section: Resultsmentioning

confidence: 99%

Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model

Andrushchenko

Bouř

2008

J Comput Chem

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An increased circular dichroism (CD) signal of large molecular aggregates formed upon DNA condensation was observed a long time ago, and is often referred to as w-CD. The effort to understand this phenomenon is further motivated by the latest DNA packing studies and advances in macromolecular chemistry. In the present work, the transition dipole coupling model describing interactions of molecules with light has been extended to handle systems of arbitrary size. The analytical formulae obtained retain the simplicity and computational speed of the standard approach. The origin of the w-effect was investigated on several model systems. The results suggest that the CD enhancement is primarily caused by delocalized phonon-like excitations in nucleic acid strands. The size of the system exhibiting the effect thus does not need to be comparable with or greater than the wavelength of the absorbed light. Small structural irregularities still allow for the enhancement while a larger disorder breaks it. The modeling is consistent with previous experimental electronic and vibrational CD studies, and makes it possible to correlate the enhancement with the geometry of the nucleic acid systems.

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Section: Resultsmentioning

confidence: 99%

Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model

Andrushchenko

Bouř

2008

J Comput Chem

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“…All seven octamers were generated in a canonical B-DNA geometry with the Tinker software. 81 Considering that the backbone absorption and VCD signal virtually does not depend on the base sequence, 33,43,115 the sugar-phosphate backbone was removed and only eight methylated base pairs preserving the original B-DNA arrangement were retained for each octamer (an example structure is shown in Fig. 11, right-hand side).…”

Section: Variations Of Dna Sequence: Employing the Continuum Solvent mentioning

confidence: 99%

“…24 First applications of the technique were mostly aimed at understanding the nature of nucleic acid VCD and establishing characteristic VCD signatures of different nucleic acid conformations, and were performed mainly by the groups of Keiderling in Chicago 6,[24][25][26][27][28][29] and Diem in New York. 14,18,19,[30][31][32] The group of Wieser in Calgary in 1995 expanded the use of VCD in nucleic acid field systematically investigating the effect of the base sequence variation on VCD spectra, 33 studying DNA and RNA interactions with metal ions 5,23,[34][35][36][37][38] and drugs, [39][40][41][42][43] and exploring atypical nucleic acid structures. 44 The pioneering work has been performed on home-built VCD instruments.…”

Section: Introductionmentioning

confidence: 99%

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

Andrushchenko

Bouř

2010

Chirality

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The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.

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“…Its intercalation into DNA causes selective inhibition of DNA replication and RNA transcription. A detailed review of the VCD results with daunomycin complexes of six different octanucleotides was published recently, 26 and it demonstrates the sensitivity of VCD in the nitrogen base region to intercalation of drugs into the different sequences of base pairs.…”

Section: Interactions With Porphyrins and Cyclic Derivativesmentioning

confidence: 99%

“…A clear separation of signals originating from two different proteins, one labeled with 13 C, was achieved for apo-13 C-CaM and unlabeled apo-Lac. VCD was used in the spectroscopic investigation of the interaction of four terpene trilactones from Ginkgo biloba with the peptide Ab (25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35) that serves as a model of amyloid beta peptide (Ab). 77 Such interaction is studied because of the possible inhibition of the pathological aggregation of Ab by G. biloba, which is used in the ''treatment'' of dementia.…”

Section: Protein-protein Interactionsmentioning

confidence: 99%

Bioinspired interactions studied by vibrational circular dichroism

Urbanová

2009

Chirality

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Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.

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Selected deoxyoctanucleotides and their daunomycin complexes: Infrared absorption and vibrational circular dichroism spectra

Cited by 4 publications

References 45 publications

Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model

Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

Bioinspired interactions studied by vibrational circular dichroism

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