1988 # The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids

**Abstract:** An algorithm is presented which solves the problem of obtaining a rigorous helicoidal description of an irregular nucleic acid segment. Central to this approach is the definition of a function describing simultaneously the curvature of the nucleic acid segment in question and the corresponding stepwise variation of helicoidal parameters along the segment. Minimisation of this function leads to an optimal distribution of the conformational irregularity of the segment between these two components. Further, it is…

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“…Since the reference frames used in 3DNA roughly coincide with the frames used in CompDNA 43 and Curves 44,45 , the 3DNA base-pair and basepair step parameters closely resemble the values determined with CompDNA and the local parameters from Curves (except when DNA is highly kinked and the Curves values tend to be larger 29 ). The discrepancies are more pronounced with programs, such as SCHNAaP/ CEHS [26][27][28] , Newhelix/Freehelix 42 , and RNA 40 , that employ very different reference frames 30 .…”

confidence: 56%

“…Since the reference frames used in 3DNA roughly coincide with the frames used in CompDNA 43 and Curves 44,45 , the 3DNA base-pair and basepair step parameters closely resemble the values determined with CompDNA and the local parameters from Curves (except when DNA is highly kinked and the Curves values tend to be larger 29 ). The discrepancies are more pronounced with programs, such as SCHNAaP/ CEHS [26][27][28] , Newhelix/Freehelix 42 , and RNA 40 , that employ very different reference frames 30 .…”

confidence: 56%

“…We used CURVES, an algorithm designed to extract the measure of DNA groove dimensions and nucleobase stacking geometries (43)(44)(45). CURVES models the DNA backbone with a cubic spline interpolation of phosphate positions, allowing for continuous groove measurements throughout most of the structured DNA in the complex, albeit this treatment does not define groove dimensions at the DNA ends.…”

confidence: 99%

“…Helicoidal analysis suggested a 10° decrease of the twist angle between base pairs X 6 ·T 17 and Y 7 ·T 16 , resulting in an unwinding of the duplex (89). An approximate 10° bending of the cross-linked duplex was calculated using the program CURVES (90,91), probably a consequence of placing the two hydroxyl groups at C β and C γ in the anti conformation with respect to the C β -C γ bond, which did not allow the four carbon cross-link to exist in the extended chain conformation. …”

confidence: 99%