PrimerDigital

PrimerAnalyser

comprehensive primer test, the melting temperature calculation for standard and degenerate oligonucleotides including LNA and other modifications, PCR efficiency, dimers detection and dilution and resuspension calculator

*IUPAC DNA degenerate code is an extended vocabulary of 15 letters which allows the description of ambiguous DNA code. Each letter represents a combination of one or several nucleotides:
B=(C,G,T), D=(A,G,T), H=(A,C,T), K=(G,T), M=(A,C), N=(A,C,G,T), R=(A,G), S=(G,C), V=(A,C,G), W=(A,T), Y=(C,T).  
U=Uracil; I=Inosine.   LNA: dA=E, dC=F, dG=J, dT=L. 

**SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc.Natl.Acad.Sci.USA, 95:1460-1465.

McTigue, Patricia M, Peterson, Raymond J, and Kahn, Jason D (2004) Sequence-Dependent Thermodynamic Parameters for Locked Nucleic Acid (LNA)-DNA Duplex Formation. Biochemistry, 43, 5388-5405.

Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37(42):14719-35.

Contact
Dr. Ruslan Kalendar

Java application needs a Java Virtual Machines (Sun) (the Java Runtime Environment (JRE) or complete Java Development Kit (JDK), for programmers only, can be downloaded from java.com).

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