We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and ...

Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only b...

Estimation of demographic history from nucleotide sequences represents an important component of many studies in molecular ecology. For example, knowledge of a population's history can allow us to test hypotheses about the impact of climatic and anthropogenic factors. In the past, demographic analysis was typically limited to relatively simple population models, such as exponential or logistic ...

FARRIS, J. S., AND M. KÄLLERSJÖ. 1998. Asymmetry and explanations. Cladistics 14:159–166. FARRIS, J. S., M. KÄLLERSJÖ, AND J. E. DE LAET. 2001. Branch lengths do not indicate support—Even in maximum likelihood. Cladistics 17:298–299. FELSENSTEIN, J. 1993. PHYLIP: Phylogeny inference package, version 3.5c. Documentation and program. Department of Genetics, Univ. Washington, Seattle. KIMURA, M. 1...

We report the complete nucleotide sequence of a plasmid carrying the multiresistance gene cfr. This plasmid was isolated from an Escherichia coli strain of swine origin in 2011. This 37,672-bp plasmid, pSD11, had an IncX4 backbone similar to those of the IncX4 plasmids obtained from the United States and Australia, in which the cfr gene was flanked by two copies of IS26 and a truncated Tn1331 w...

DNA has a well-defined structural transition--the denaturation of its double-stranded form into two single strands--that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA denaturation, one can engineer DNA 'heattronic' devices that have a rapidly increasing thermal conductance over a narrow temperature range across the denaturation ...

A 10.5-base periodicity found earlier is inherent in both eu- and prokaryotic coding nucleotide sequences. In the case of noncoding eukaryotic sequences no periodicity is found, so the 10.5-base oscillation seemingly does not correlate with the nucleosomal organization of DNA. It is shown that the DNA fragments, coding the alpha-helical protein segments, manifest the pronounced 10.5-base period...

Short nucleotide sequences at the 3'-termini of adenovirus types 2 and 5 DNA have been determined using T4 DNA polymerase as described by P. T. Englund (1972). The terminal sequences of both serotypes appear to be completely identical. Both molecular ends of type 2 as well as of type 5 DNA terminate with the sequence ...pCpC...pGpApTpG3', consistent with the presence of an inverted terminal rep...

Base sequences BS m,n are quadruples A;B;C;D of {±1}-sequences, with A and B of length m and C and D of length n, such that the sum of their nonperiodic autocorrelation functions is a δfunction. Normal sequences NS n are base sequences A;B;C;D ∈ BS n, n such that A B. We introduce a definition of equivalence for normal sequences NS n and construct a canonical form. By using this canonical form,...