DNA

Palindromic Sequences

Restriction enzymes cut double-stranded DNA at specific locations based the pattern of bases found at those locations. These enzymes predictably cut both strands because the sequences they recognize are palindromic. That is the recognition sequences are short string of identical bases on both DNA strands.

Palindromic sequences are similar to language palindromes, but follow a distinct set of rules. Any string of bases can be made into a palindromic sequence by following these rules.

Restriction Enzymes

Restriction enzymes cut DNA at specific sites based on the sequence of bases along the strand at the cut site. These enzymes were first identified and studied in strains of the bacteria E. Coli in the 1950’s and 60’s. The term restriction was used to describe them because their activity restricted the growth of viruses that infect E. coli.

Restriction enzymes are nucleases - enzymes that cut nucleic acid polymers (i.e. DNA and RNA). There are two types of nuclease: endonuclease and exonuclease. Endonucleases make cuts within a DNA polymer. Exonucleases remove individual nucleotides* from the end of a strand. Restriction enzymes are a type of endonuclease - they cut at specific sites in the middle of DNA strands.

DNA migration in gel electrophoresis

Gel electrophoresis uses electricity to separate fragments of DNA based on their length. An understanding of how DNA migrates in an electrical field is needed in order to properly interpret the result of a gel electrophoresis run.

Gel Electrophoresis Overview

Electrophoresis is the movement of charged particles through an electrical field. Since the sugar-phosphate backbone of DNA has a negative charge, electrophoresis can be used to pull DNA through an electrical field towards the positive electrode of a circuit. Molecular biologists have exploited this behavior to develop techniques that separate, clean and analyze DNA fragments.

DNA Polymerase

DNA polymerases are the enzymes that replicate DNA in living cells. They do this by adding individual nucleotides to the 3-prime hydroxl group of a strand of DNA. The process uses a complementary, single strand of DNA as a template.

The energy required to drive the reaction comes from cutting high energy phosphate bonds on the nucleotide-triphosphate's used as the source of the nucleotides needed in the reaction.

Draft DNA structures

More components for making molecular biology illustrations. Below are the four nucleic acids in DNA*.

Double Stranded DNA

This is a dynamically generated, double strand of DNA*. It will be used in some molecular biology / genetics* illustrations planned for the site.
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