A compact form of double-stranded RNA in solutions containing poly(ethyleneglycol)

Evdokimov, Yu. M.; Pyatigorskaya, T.L.; Kadikov, V.A.; Polyvtsev, O.F.; Doskočil, J.; Koudelka, J.; Varshavsky, Ya.M.

doi:10.1093/nar/3.6.1533

Cited by 18 publications

(6 citation statements)

References 13 publications

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“…Compared with n = 2, the Δε/ε ratio can be increased about 50‐fold. The simulated length‐dependence of the CD spectra is thus in qualitative and quantitative agreement with the many‐fold increase observed for experimental ψ‐CD,9–16 even when the enhancement is not related to the dimer, but to an average straight DNA segment. Also the simulated slight frequency shift (e.g., n = 2 vs .…”

Section: Resultssupporting

confidence: 82%

“…A typical experimental CD Δε/ε ratio of a B‐form DNA is about 10 −3 –10 −4 . The value can increase about 10 times in conditions most favorable to the ψ‐effect 12, 15, 27. This indicates a presence of many factors destroying the ideal limit simulated in Figure 4.…”

Section: Resultsmentioning

confidence: 99%

“…These unusual ECD spectra were called ψ‐type (psi for “polymer and salt induced”) circular dichroism (CD) 9. Later, other types of DNA condensation, such as those achieved by multivalent metal ions or H1 histone, produced similar enhancements 5–17. It was also shown that the condensed DNA spectral enhancement is not restricted to ultraviolet light and electronic CD, but is observable also in the infrared region for the vibrational circular dichroism (VCD) 18…”

Section: Introductionmentioning

confidence: 86%

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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: Resultssupporting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 86%

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

Andrushchenko

Bouř

2008

J Comput Chem

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“…By condensation of DNA strands at high salt concentrations, ECD intensity significantly increased when compared, for example, with standard B‐DNA spectrum . Later, this so called ψ ‐type circular dichroism (“psi” for polymer and salt‐induced) was observed in a range of DNA samples . An analogous observation was reported in the infrared region for vibrational circular dichroism (VCD) …”

Section: Introductionmentioning

confidence: 63%

“…1 Later, this so called ψ-type circular dichroism ("psi" for polymer and salt-induced) was observed in a range of DNA samples. [1][2][3][4][5][6][7][8][9][10][11][12][13] An analogous observation was reported in the infrared region for vibrational circular dichroism (VCD). 14 For proteins, ECD enhancement in such an extent is not known.…”

Section: Introductionmentioning

confidence: 70%

Transition dipole coupling modeling of optical activity enhancements in macromolecular protein systems

Průša

Bouř

2017

Chirality

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Optical activity of regular molecular assemblies, such as protein fibrils or nucleic acid condensates, is often significantly stronger than for isolated molecules. Previous modeling suggested that this may be caused by the ordered quasi-periodic structure and a long-order synchronization of chromophore excitations. In the present study, we briefly review this phenomenon and investigate some aspects on simple models related to protein vibrational optical activity. The transition dipole coupling (TDC) model is used to generate vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra. While a linear arrangement of chromophores produced relatively simple couplet intensity patterns, a richer band structure was predicted for planar geometries. A stacking of β-sheet planes has been identified as another powerful source of the enhancement. The results do not completely reproduce experimental observations but are consistent with them and confirm that chiroptical methods may be extremely useful to study aggregation of chiral molecules.

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DNA interaction with Mn²⁺ ions at elevated temperatures: VCD evidence of DNA aggregation

2003

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Interaction of natural calf thymus DNA with Mn(2+) ions was studied at room temperature and at elevated temperatures in the range from 23 degrees C to 94 degrees C by means of IR absorption and vibrational circular dichroism (VCD) spectroscopy. The Mn(2+) concentration was varied between 0 and 1.3M (0 and 10 [Mn]/[P]). The secondary structure of DNA remained in the frame of the B-form family in the whole ion concentration range at room temperature. No significant DNA denaturation was revealed at room temperature even at the highest concentration of metal ions studied. However at elevated temperatures, DNA denaturation and a significant decrease of the melting temperature of DNA connected with a decrease of the stability of DNA induced by Mn(2+) ions occurred. VCD demonstrated sensitivity to DNA condensation and aggregation as well as an ability to distinguish between these two processes. No condensation or aggregation of DNA was observed at room temperature at any of the metal ion concentrations studied. DNA condensation was revealed in a very narrow range of experimental conditions at around 2.4 [Mn]/[P] and about 55 degrees C. DNA aggregation was observed in the presence of Mn(2+) ions at elevated temperatures during or after denaturation. VCD spectroscopy turned out to be useful for studying DNA condensation and aggregation due to its ability to distinguish between these two processes, and for providing information about DNA secondary structure in a condensed or aggregated state.

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A compact form of double-stranded RNA in solutions containing poly(ethyleneglycol)

Cited by 18 publications

References 13 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

Transition dipole coupling modeling of optical activity enhancements in macromolecular protein systems

DNA interaction with Mn²⁺ ions at elevated temperatures: VCD evidence of DNA aggregation

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A compact form of double-stranded RNA in solutions containing poly(ethyleneglycol)

Cited by 18 publications

References 13 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

Transition dipole coupling modeling of optical activity enhancements in macromolecular protein systems

DNA interaction with Mn2+ ions at elevated temperatures: VCD evidence of DNA aggregation

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DNA interaction with Mn²⁺ ions at elevated temperatures: VCD evidence of DNA aggregation