Phosphodiester Backbone
Definition
The repeating sugar-phosphate chain that forms the structural scaffold of each DNA strand. The backbone is highly charged and hydrophilic, faces outward from the helix, and gives DNA its characteristic negative charge at physiological pH, which is exploited in gel electrophoresis.
- Structure
- Repeating sugar-phosphate chain of each DNA strand
- Orientation
- Faces outward from the double helix
- Charge
- Highly negatively charged at physiological pH
- Forensic relevance
- Basis for separation in gel electrophoresis
Common questions
Why does the backbone's negative charge matter for STR typing?+
That uniform negative charge lets DNA fragments migrate through a gel or capillary matrix toward the positive electrode at a rate governed mainly by size, which is the physical basis for separating and sizing STR alleles.
Is the backbone involved in encoding genetic information?+
No, the backbone is purely structural; the base sequence attached to it carries the genetic information, while the sugar-phosphate chain provides the stable scaffold the bases are strung along.
Does backbone damage differ from base damage in degraded forensic samples?+
Yes, backbone cleavage physically breaks the DNA strand into shorter fragments limiting which STR loci can amplify, whereas base damage, such as deamination, can cause sequence errors without necessarily shortening the strand.
Related terms
- Antiparallel Orientation
- The two strands of the DNA double helix run in opposite directions: one strand reads 5' to 3', its complement reads 3'...
- Base Complementarity
- The specific pairing rules that govern double-stranded DNA: adenine pairs with thymine (2 hydrogen bonds) and guanine pairs with cytosine (3 hydrogen...
- Denaturation
- The separation of double-stranded DNA into two single strands by disrupting the hydrogen bonds between base pairs. In PCR, denaturation is achieved...
- Deoxyribonucleotide
- The monomer unit of DNA, consisting of a deoxyribose sugar, a phosphate group, and one of four nitrogenous bases (adenine, thymine, guanine,...
- GC Content
- The proportion of base pairs in a DNA molecule that are guanine-cytosine. Because G-C pairs form three hydrogen bonds (versus two for...