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A palindromic sequence is a nucleic acid sequence in a double-stranded DNA or RNA molecule whereby reading in a certain direction (e.g. 5' to 3') on one strand is identical to the sequence in the same direction (e.g. 5' to 3') on the complementary strand. This definition of palindrome thus depends on complementary strands being palindromic of ...
Many of them are palindromic, meaning the base sequence reads the same backwards and forwards. [29] In theory, there are two types of palindromic sequences that can be possible in DNA. The mirror-like palindrome is similar to those found in ordinary text, in which a sequence reads the same forward and backward on a single strand of DNA, as in ...
Several databases exist for restriction sites and enzymes, of which the largest noncommercial database is REBASE. [5] [6] Recently, it has been shown that statistically significant nullomers (i.e. short absent motifs which are highly expected to exist) in virus genomes are restriction sites indicating that viruses have probably got rid of these motifs to facilitate invasion of bacterial hosts. [7]
This structure is thought to destabilize the binding of RNA polymerase enzyme to DNA (hence terminating transcription). Dyad symmetry is known to have a role in the rho independent method of transcription termination in E. coli. [citation needed] Regions of dyad symmetry in the DNA sequence stall the RNA polymerase enzyme as it transcribes them.
For example, there are two PstI recognition sites in the following DNA sequence fragment, starting at base 9 and 31 respectively. A recognition sequence is a specific sequence, usually very short (less than 10 bases). Depending on the degree of specificity of the protein, a DNA-binding protein can bind to more than one specific sequence.
A: Inverted Repeat Sequences; B: Loop; C: Stem with base pairing of the inverted repeat sequences. The illustration shows an inverted repeat undergoing cruciform extrusion. DNA in the region of the inverted repeat unwinds and then recombines, forming a four-way junction with two stem-loop structures. The cruciform structure occurs because the ...
A restriction fragment is a DNA fragment resulting from the cutting of a DNA strand by a restriction enzyme (restriction endonucleases), a process called restriction. [1] Each restriction enzyme is highly specific, recognising a particular short DNA sequence, or restriction site, and cutting both DNA strands at specific points within this site.
These are known as palindromic (P) nucleotides due to the palindromic nature of the sequence produced when DNA repair enzymes resolve the overhang. [18] The process of hairpin opening by Artemis is a crucial step of V(D)J recombination and is defective in the severe combined immunodeficiency (scid) mouse model .