Biomedical subjects

J D Bashford

Publications and source records attributed to J D Bashford.

4 recordsLinked to original sources

PubMed2005

A base-pairing model of duplex formation. I. Watson-Crick pairing geometries.

We present a base-pairing model of oligonucleotide duplex formation and show in detail its equivalence to the nearest-neighbor dimer methods from fits to free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids containing only Watson-Crick pairs. For completeness, the corresponding RNA-RNA parameters are included. In this approach, the connection between rank-deficient polymer and rank-determinant oligonucleotide parameter sets for DNA duplexes is transparent. The method is generalized to include RNA-DNA hybrids where the rank-deficient model with 11 dimer parameters in fact provides slightly improved predictions relative to the standard method with 16 independent dimer parameters (DeltaG mean errors of 4.5 and 5.4%, respectively).

Base Pairing↗

PubMed2004

An algebraic model of RNA duplex formation.

We propose a simple algebraic description of the two-body interactions of bases in RNA thermodynamics showing in detail qualitative equivalence with conventional nearest-neighbor models. The process of obtaining base content, polymer, and oligomer parameters is illustrated, and for duplexes containing Watson-Crick pairs, fits to oligonucleotide duplex heat-of-formation data are shown to be statistically equivalent to existing models.

Base Pairing↗

PubMed1998

A supersymmetric model for the evolution of the genetic code.

A model is presented for the structure and evolution of the eukaryotic and vertebrate mitochondrial genetic codes, based on the representation theory of the Lie superalgebra A(5,0) approximately sl(6/1). A key role is played by pyrimidine and purine exchange symmetries in codon quartets.

Animals↗

PubMedDate not supplied

The genetic code as a periodic table: algebraic aspects.

The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, A=(-1,0), C=(0,-1), G=(0,1), U=(1,0), data can be fitted as low order polynomials of the six coordinates in the 64-dimensional codon weight space. The work confirms and extends the recent studies by Siemion et al. (1995. BioSystems 36, 231-238) of the conformational parameters. Fundamental patterns in the data such as codon periodicities, and related harmonics and reflection symmetries, are here associated with the structure of the set of basis monomials chosen for fitting. Results are plotted using the Siemion one-step mutation ring scheme, and variants thereof. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.

Amino Acids↗