Nanoscale alpha-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson-Crick ba...

Structural details are reported for a novel right-handed polynucleotide double helix stabilized by vertical base stacking and hydrogen bonding. The primary difference between this duplex and the familiar Watson-Crick horizontally stabilized polynucleotide complex arises in the glycosyl rotation of the heterocyclic bases with respect to the sugar-phate backbone. In the vertical double helix the ...

Molecules that reversibly bind DNA and trigger the formation of non-Watson-Crick secondary structures would be useful in the design of dynamic DNA nanostructures and as potential leads for new therapeutic agents. We demonstrate that coralyne, a small crescent-shaped molecule, promotes the formation of a duplex secondary structure from homo-adenine oligonucleotides. AFM studies reveal that the s...

This April it will be 50 years since the discovery of the double helical structure of DNA by Jim Watson and Francis Crick. Since then, the genomes of a wide range of bacteria, archaea, viruses and several eukaryotes have been entirely decoded, and the human genome is fast approaching completion. This issue illustrates the diversity of the field of genomics, which was born out of their discovery...

The BPS (http://bps.rutgers.edu) is a database of RNA base-pair structures, higher-order base interactions and isosteric pairs (base pairs with similar shape). The main functions of the BPS are to find and annotate the structural and chemical features of the Watson-Crick and non-Watson-Crick (noncanonical) base pairs in high-resolution RNA structures, and to provide a user-friendly interface to...

Watson and Crick’s postulation in 1953, exactly 50 years ago, of a double helical structure for DNA, heralded a revolution in our understanding of biology at the molecular level. The fact that it immediately suggested a possible copying mechanism for the genetic material aroused the maximum interest, but the structure itself (often referred to as the B-DNA structure, by association with the cor...

Watson-Crick finite automata were first proposed in [2] inspired by formal language theory, finite states machines and some ingredients from DNA computing such as working with molecules as double stranded complementary strings. Here, we define different kinds of local testability in this model. Mainly, we will explore local testability in the upper (lower) strand and in the double strand.