Sequence-specific local structural variations in solution structures of d(CGXX′CG)2 and d(CAXX′TG)2 self-complementary deoxyribonucleic acids

Lam, Sik Lok; Au-Yeung, Steve C. F.

doi:10.1006/jmbi.1996.0783

Cited by 20 publications

(12 citation statements)

References 54 publications

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“…ideal B-DNA, which depend on the nearest-neighbor bases. With CHARMM27, the three more sequence-dependent parameters, (tip, propeller twist, and buckle) show large deviations from the ideal values: up to 258 for the tip, 308 for the propeller twist, and 508 for the buckle at A:T basepairs; the maximum deviations observed in the analysis by Lam and Au-Yeung (1997) are 78, 108, and 98 respectively. In the x-ray structure of the d(CGATTAATCG) 2 decamer (Quintana et al, 1992), the maximum deviation in propeller twist between two A:T basepairs is 10.58 (between A6:B5 and B3:A8).…”

Section: Sequence Dependence Of the Conformational Flexibilitymentioning

confidence: 99%

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

Reddy

Leclerc

Karplus

2003

Biophysical Journal

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The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the latter two is the primary focus of this paper. The performance of each force field is evaluated first on its ability to reproduce the B-DNA decamer d(CGATTAATCG)(2) in solution with simulations in which the long-range electrostatics were treated by the particle mesh Ewald method; the crystal structure determined by Quintana et al. (1992) is used as the starting point for all simulations. A detailed analysis of the structural and solvation properties shows how well the different force fields can reproduce sequence-specific features. The results are compared with data from experimental and previous theoretical studies.

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Section: Sequence Dependence Of the Conformational Flexibilitymentioning

confidence: 99%

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

Reddy

Leclerc

Karplus

2003

Biophysical Journal

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“…In the following, we focus on two model oligomers: double-stranded d(G 5 C 5 ) and d(GC) 8 deoxyribonucleic acids. d(GC) 8 has alternating stacked G and C bases and is in the B-form, while d(G 5 C 5 ) is similar to poly(dG)−poly(dC) and is in the A-form. − The 2D IR spectra of these oligomers are distinct, exhibiting different peak frequencies, intensities, shapes, and cross-peaks. By utilizing the improved resolution and information content of 2D IR spectroscopy, we determine the couplings between the bases from simulations of the spectra and electronic structure calculations.…”

Section: Introductionmentioning

confidence: 99%

DNA Vibrational Coupling Revealed with Two-Dimensional Infrared Spectroscopy: Insight into Why Vibrational Spectroscopy Is Sensitive to DNA Structure

2006

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Two-dimensional infrared (2D IR) spectroscopy was used to study the carbonyl vibrational modes of guanine and cytosine bases in A- and B-form DNA. Located between 1600 and 1700 cm(-1), these modes are often used to monitor DNA secondary structure with traditional infrared spectroscopies such as FTIR, but traditional spectroscopies lack the necessary observables to unravel the coupling mechanisms that make these modes sensitive to secondary structure. By using 2D IR spectroscopy and electronic structure calculations on d(G(5)C(5)) and d(GC)(8) model nucleic acids, we find that hydrogen-bonded guanine/cytosine base pairs are primarily electrostatically coupled and that the coupling between these modes can be modeled with a transition dipole density approach. In comparison, electrostatics is insufficient to model stacked bases because of cooperative charge-sharing effects, but the coupling can be accurately calculated using a finite difference method. We find that the coupling is very strong for both hydrogen-bonded and stacked base geometries, creating vibrational modes that extend both across the base pairs and along the lengths of the helices. Our results provide a physical basis for understanding how strong coupling gives rise to the empirically established relationship between infrared spectroscopy and DNA/RNA secondary structure.

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“…The structure of the unmodified DNA : DNA duplex (named DCON) was previously determined by other authors. [14] Our results show that dFdC provokes local distortions in the duplexes that are more pronounced in the case of the RGEM hybrid. Interestingly, dFdC sugar adopts a North conformation when confronted to DNA, but prefers South puckers when confronted to an RNA strand.…”

Section: Introductionmentioning

confidence: 62%

Structural Effects of Incorporation of 2'‐Deoxy‐2'2'‐Difluorodeoxycytidine (Gemcitabine) in A‐ and B‐Form Duplexes

Cabrero

Martín-Pintado

Mazzini

et al. 2021

Chemistry A European J

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We report the structural effect of 2'‐deoxy‐2',2'‐difluorocytidine (dFdC) insertions in the DNA strand of a DNA : RNA hybrid duplex and in a self‐complementary DNA : DNA duplex. In both cases, the modification slightly destabilizes the duplex and provokes minor local distortions that are more pronounced in the case of the DNA : RNA hybrid. Analysis of the solution structures determined by NMR methods show that dFdC is an adaptable derivative that adopts North type sugar conformation when inserted in pure DNA, or a South sugar conformation in the context of DNA : RNA hybrids. In this latter context, South sugar pucker favors the formation of a 2'F⋅⋅H8 attractive interaction with a neighboring purine, which compensates the destabilizing effect of base pair distortions. These interactions share some features with pseudohydrogen bonds described previously in other nucleic acids structures with fluorine modified sugars.

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Sequence-specific local structural variations in solution structures of d(CGXX′CG)2 and d(CAXX′TG)2 self-complementary deoxyribonucleic acids

Cited by 20 publications

References 54 publications

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

DNA Vibrational Coupling Revealed with Two-Dimensional Infrared Spectroscopy: Insight into Why Vibrational Spectroscopy Is Sensitive to DNA Structure

Structural Effects of Incorporation of 2'‐Deoxy‐2'2'‐Difluorodeoxycytidine (Gemcitabine) in A‐ and B‐Form Duplexes

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