dPrimer v1.0

	This Macintosh software is for use in calculating Tm values for  degenerate primer. 
The launched dPrimer program provides two small windows for the input of either amino acids or nucleotides. A brief instruction is also given for the use of symbols for input. The amino acids can be converted to degenerate oligonucleotides by checking the ÔA.A. to DNAÕ button. The oligonucleotides can also be converted to reversed and complementary sequences by checking the Ôreverse & complementÕ. The default maximum degeneracy is set at 5000, which can be adjusted accordingly. The thermodynomic parameters for both PCR and hybridization have been set in the program, and user can  select one of them by checking the corresponding button. The program will begin the calculation if the ÔProcessÕ buttom has been checked. All results will then be shown in the large window on the right. Although the dPrimer program is designed for degenerate oligonucleotides, the Tm of a regular oligonuleotide can also be calculated with a degeneracy of 1. 
	Using the program dPrimer, we were able to calculate individual Tm of all possible oligonucleotides in a degenerate primer or probe. The range of Tm was given as minimum Tm (Min. Tm) and maximum Tm (Max. Tm). The mean Tm and standard deviation (S.D.) were also provided. The length of the degenerate oligonucleotides could easily adjusted in the input windows for quick calculation  if a desired range of Tm is required.
	Considering that most degenerate oligonucleotides are designed for PCR amplification, DNA library screenings or Southern blot, we include only thermodynomic data for the formation of DNA duplex in the program. Therefore, the Tm obtained using the program is only accurate when the degenerate oligonucleotids are annealing or hybidizing to DNA templates.
	Although dPrimer will give users a Tm range that covers all individual oligonucleotides in a degenerate primer or probe, it does not not provide an optimal annealing or probing temperature, and the Tm of the oligonucleotide that actually forms DNA duplex is also not clear.
	This program use the nearest neighbor interaction model  (Breslauer K. et al., 1986, Proc. Natl. Acad. Sci. USA, Vol. 83. pp. 3746-3750.) to calculate the Tm value as shown in the following equation: 

Tm  = ÆH/(ÆS + R * ln(c/4)) - 273.15 +16.6 log [salt]

where ÆH and ÆS are the enthalpy and entropy for the helix formation of an oligonucleotide deplux, respectively; R is the molar gas constant; c is the total concentration of the annealing oligonucleotide; and [salt] is the K+ concentration. 
	Please sent questions and comments to me at the address below, preferably by e-mail.
							Haoyuan Chen, Ph. D.
							Department of Biochemistry
							Emory University
							Atlanta, Ga 30322.
							
							Tel: (404)727-5621 (O)

							E-mail: hchen@bimcore.emory.edu