Thermodynamic properties of DNA sequences: characteristic values for the human genome.
BACKGROUND
Central to many molecular biology techniques as ubiquitous as PCR and Southern blotting is the design of oligonucleotide (oligo) probes and/or primers possessing specific thermodynamic properties. Here, we use validated theoretical methods to generate distributions of predicted thermodynamic properties for DNA oligos of various lengths. These distributions facilitate immediate appreciation of typical thermodynamic values for oligos of various lengths.


RESULTS
Distributions of melting temperature (Tm), free energy (DeltaG(T)o), and fraction hybridized or fraction bound (Fb), are presented for oligos of length 10-50 bases sampled from the human genome. The effects of changing temperature, oligo and salt concentrations, constraining G+C content, and introducing mismatches are exemplified. Our results provide the first survey of typical and limiting thermodynamic values evaluated on a genomic scale. Described numbers comprise useful 'rules of thumb' that are applicable to most technologies dependent upon DNA oligo design.
Koehler
Ryan T
RT
Applied Biosystems 850 Lincoln Centre Drive, Foster City, CA 94404, USA. koehlert@appliedbiosystems.com
Peyret
Nicolas
N
D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D004252:DNA Mutational Analysis / Q000379:methods; D015894:Genome, Human; D006801:Humans; D017403:In Situ Hybridization / Q000379:methods*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013816:Thermodynamics; D044366:Transition Temperature
D004247:DNA