DNA and RNA oligomers are used in a myriad of diverse biological and biochemical
experiments. These oligonucleotides are designed to have unique biophysical, chemical …

Revised Manuscript Received February 24, 1994® abstract: DNA-RNA hybrid duplexes are
found in many important biological processes and are involved in developing modes of …

We developed OligoCalc as a web-accessible, client-based computational engine for
reporting DNA and RNA single-stranded and double-stranded properties, including …

We present a brief, and largely personal, history of computer simulations of DNA and RNA
oligonucleotides, with an emphasis on duplex structures and the Amber force fields. Both …

Optimization of probe design for array‐based experiments requires improved predictability
of oligonucleotide hybridization behavior. Currently, designing oligonucleotides capable of …

The thermodynamic contributions to duplex formation of all 32 possible single-nucleotide
dangling ends on a Watson–Crick pair are reported. In most instances, dangling ends are …

Abstract DiProDB (http://diprodb. fli-leibniz. de) is a database of conformational and
thermodynamic dinucleotide properties. It includes datasets both for DNA and RNA, as well …

MATERIALS AND METHODS Oligonucleotide Synthesis. DNA and RNA oligonucle-otides
were synthesized using standard phosphoramidite procedures as described elsewhere …

The physical principles of DNA hybridization and folding are described within the context of
how they are important for designing optimal PCRs. The multi-state equilibrium model for …

Motivated by the analysis of natural and engineered DNA and RNA systems, we present the
first algorithm for calculating the partition function of an unpseudoknotted complex of …