Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion

We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides—it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations

Development of a contact call in black-capped chickadees (<em>Poecile atricapillus</em>) hand-reared in different acoustic environments

The tseet contact call, common to black-capped (Poecile atricapillus) and mountain chickadees (P. gambeli), is the most frequently produced vocalization of each species. Previous work has characterized the tseet call of black-capped and mountain chickadees from different geographic locations in terms of nine acoustic features. In the current study, using similar methods, the tseet call of black-capped chickadees that were hand reared with either conspecifics, heterospecifics (mountain chickadees), or in isolation from adult chickadees are described. Analysis of call features examined which acoustic features were most affected by rearing environment, and revealed that starting frequency and the slope of the descending portion of the tseet call differed between black-capped chickadees reared with either conspecific or heterospecific adults. Birds reared in isolation from adults differed from the other hand-reared groups on almost every acoustic feature. Chickadee tseet calls are more individualized when they are reared with adult conspecifics or heterospecifics compared to chickadees that are reared in isolation from adults. The current results suggest a role of learning in this commonly used contact call