D

Degeneracy:

It refers to the fact that multiple different codons may encode the same amino acid.

Denaturation:

With refer to nucleic acids, it refers to the conversion from double-stranded to the single-stranded state, often achieved by heating or alkaline conditions. This is also called "melting" DNA. With respect to proteins, refers to the disruption of tertiary and secondary structure, often achieved by heat, detergents, chaotropes, and sulfhydryl-reducing agents.

Denaturing Gel:

Its an agarose or acrylamide gel run under conditions which destroy secondary or tertiary protein or RNA structure.

Denaturing Gradient Gel Electrophoresis (DGGE):

Resolves partially denatured double stranded DNA in precisely conditions of temperature and denaturant concentration. Different alleles may denature to various extents under such conditions, and migrate differently on DGGE acrylamide gels.

Derivative Curve:

This curve is used in Tm analysis. It has the temperature in the x axis and the negative derivative of fluorescence (F) with respect to temperature (T), shown as dF/dT, on the y axis.

Deletion:

The absence of bases that are present in the wild-type DNA sequence.

Dideoxy Sequencing:

Enzymatic determination of DNA or RNA sequence by the method of Sanger and colleagues, based on the incorporation of chain terminating dideoxynucleotides in a growing nucleic acid strand copied by DNA polymerase or reverse transcriptase from a DNA or RNA template. Separate reactions include dideoxynucleotides containing A,C, G, or T bases. The reaction products represent a collection of new. labeled DNA strands of varying lengths, all terminating with a dideoxynucleotide at the 3' end and are separated in a polyacrylamide/urea gel to generate a sequence "ladder". This method is more commonly used than "Maxam-Gilbert" (chemical) sequencing.

Direct Repeats:

Identical or related sequences present in two or more copies in the same orientation in the same molecule of DNA.

Diploid:

A full set of genetic material, consisting of paired chromosomes one chromosome from each parental set.The diploid human genome has 46 chromosomes.

Divergence:

It is the percent difference in nucleotide sequence between two related DNA sequences or in amino acid sequences between two proteins.

DNA (Deoxyribonucleic Acid):

The molecule responsible for storing and transmitting genetic information. DNA is a double- stranded molecule held together by weak bonds between base pairs of nucleotides twisted around each other in the shape of a double helix. The four nucleotides in DNA contain the bases: adenine (A), guanine (G), cytosine (C), and thymine (T). In nature, base pairs form only between A and T and between G and C.

DNase:

Deoxyribonuclease, a class of enzymes which digest DNA. The most common is DNase I, an endonuclease which digests both single and double-stranded DNA.

DNA Ligase:

Enzymatic activity responsible for creating phosphodiester bonds between the 5' end of one strand of DNA and the 3' end of another strand. Requires the presence of a 5' phosphate on one strand, and a 3' Hydroxyl group on the second strand.

DNA Polymerase:

Enzymatic activity responsible for catalyzing the polymerization of DNA. Is dependent upon an annealed primer from which to initiate polymerization, and a DNA template from which to copy.

DNA Replication:

The use of existing DNA as a template for the synthesis of new DNA strands. In humans and other eukaryotes, replication occurs in the cell nucleus.

DNA Sequence:

The relative order of base pairs, whether in a fragment of DNA, a gene, a chromosome, or an entire genome. See base sequence analysis.

Domain:

A discrete portion of a protein with its own function. The combination of domains in a single protein determines its overall function.

Dominant:

Allele that determines phenotype in a heterozygous individual carrying another recessive allele.

Double Helix:

The helical shape assumed by DNA in which the two complementary strands hydrogen bond together in opposite orientations.

Dot Blot:

A technique for measuring the amount of one specific DNA or RNA in a complex mixture. The samples are spotted onto a hybridization membrane fixed and hybridized with a radioactive probe. The extent of labeling is proportional to the concentration of the target molecule in the sample.

Duplex:

A nucleic acid molecule in which two strands are base paired with each other.

dsDNA-binding Agent:

A molecule that emits fluorescence when bound to dsDNA. The prototype is SYBR® Green I. In real-time PCR, the fluorescence intensity increases proportionally to dsDNA (amplicon) concentration. The problem with DNA-binding agents is that they bind to all dsDNA products: specific amplicon or non-specific products (misprimed targets and primer-dimers included). For this reason, analysis using DNA-binding agents is usually coupled with melting analysis.

Dynamic Range:

The range of initial template concentrations over which accurate Ct values are obtained. If endogenous control is used for DDCt quantitation method, dynamic ranges of target and control should be comparable. In absolute quantitation, interpolation within this range is accurate but extrapolation beyond the dynamic range should be avoided. The larger the dynamic range, the greater the ability to detect samples with high and low copy number in the same run.