A complete set of harmonic force constants describing the DNA deformation energetics at the base pair level was obtained using unrestrained atomic-resolution molecular dynamics simulations of selected duplex oligonucleotides and subsequent analysis of structural fluctuations from the simulated trajectories. The deformation was described by the six base pair conformational parameters (buckle, pr...

We have combined standard micrococcal nuclease (MNase) digestion of nuclei with a modified protocol for constructing paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrapped nucleosomes and subnucleosome-sized particles can occupy the same position within a ...

Brutlag, D., Atkinson, M. R., Setlow, P. & Kornberg, A. (1969) Biochem. Biophys. Res. Commun. 37, 982-989 Joyce, C. M. & Grindley, N. D. F. (1983) Proc. Natl. Acad. Sci. U .S .A . 80, 183G1834 Joyce, C. M., Ollis, D. L., Ruch, J., Steitz, T. A,, Knigsber, W. H. & Grindley, N. D. F. (19850) in Protein Structure. Function and Design (Oxender, D. ed.), UCLA Symposia in Molecular and Cellular Biolo...

A rotationally resolved electronic spectrum of the gas-phase dimer 2-aminopyridine.2-pyridone, an analog of the adenine.thymine base pair, has been observed and assigned, leading to precise measurements of its moments of inertia and preliminary determinations of its structure. A Watson-Crick configuration results, with N...H-N and N-H...O hydrogen bond lengths of 2.898 and 2.810 A, respectively...

RNAbow diagrams are a versatile tool for visualizing and comparing ensembles of RNA secondary structures. Previously, RNAbows have proved useful when investigating individual ensembles of folds, performing cluster analysis, and identifying conformational changes caused by single nucleotide polymorphisms [Aalberts and Jannen, RNA, 19, 475–478 (2013)]. This contest submission highlights their use...

Awareness of the harmful effects of radiation has increased interest in finding the mechanisms of DNA damage. Radical and anion formation among the DNA base pairs are thought to be important steps in such damage [Collins, G. P. (2003) Sci. Am. 289 (3), 26-27]. Energetic properties and optimized geometries of 10 radicals and their respective anions derived through hydrogen abstraction from the W...

In our previous communication we reported the enzymatic recognition of unnatural imidazopyridopyrimidine:naphthyridine (Im:Na) base pairs, i.e. ImO(N):NaN(O) and ImN(O):NaO(N), using the Klenow fragment exo(-) [KF (exo(-))]. We describe herein the successful results of (i) improved enzymatic recognition for ImN(O):NaO(N) base pairs and (ii) further primer extension reactions after the Im:Na bas...

Proton nuclear magnetic resonance (NMR) spectroscopy is employed to characterize the kinetics of base-pair opening in a series of nine-mer duplexes containing different single base mismatches. The imino protons from the different mismatched as well as fully matched duplexes are assigned from the imino-imino region in the WATERGATE NOESY spectra. The exchange kinetics of the imino protons are me...