Restriction endonuclease palindrome sequences

Restriction endonucleases cleave DNA base sequences that are palindromes, meaning that the sequence reads the same as the complement when both are read in the (5 ) to (3 ) direction. Thus, the sequence in (c), CTCGAG is recognized. The sequence in (a), GAATTC, is also a palindrome and is recognized by a restriction endonuclease. The sequence in (b) is not recognized. 

The first step in DNA sequencing is to cleave the enormous chain at known points to produce smaller, more manageable pieces, a task accomplished by the use of restriction endonucleases. Each different restriction enzyme, of which more than 3500 are known and approximately 200 are commercially available, cleaves a DNA molecule at a point in the chain where a specific base sequence occurs. For example, the restriction enzyme Alul cleaves between G and C in the four-base sequence AG-CT. Note that the sequence is a palindrome, meaning that the sequence (5 )-AGCT-(3 ) is the same as its complement (3 )-TCGA-(5 ) when both are read in the same 5 — 3 direction. The same is true for other restriction endonucleases. 

The sequence of DNA recognized by a specific restriction endonuclease is often palindromic. A palindrome is something that reads the same way backward and forward (Fig. 6-2). The sequence of the bottom strand read in the 5 to 3 direction is the same as that of the top strand read in the 5 to 3 direction. The usual analogy for a verbal palindrome is a sentence that reads the same way backward and forward. Madam, I m Adam is the usual example. It s not exactly the same way for DNA palindromes. The top strand does not read the same from the left as from the right the top strand read from left to right is the same as the bottom strand read from right to left. 

Double stranded DNA can be enzymatically cleaved by commercially available endonucleases (restriction enzymes). These enzymes recognise specific, usually palindromic, sequences and cut specifically at those positions. 

Thousands of restriction endonucleases have been discovered in different bacterial species, and more than 100 different DNA sequences are recognized by one or more of these enzymes. The recognition sequences are usually 4 to 6 bp long and palindromic (see Fig. 8-20). Table 9-2 lists sequences recognized by a few type II restriction endonucleases. In some cases, the interaction between a restriction endonuclease and its target sequence has been elucidated in exquisite molecular detail for example, Figure 9-2 shows the complex of the type II restriction endonuclease EcoRV and its target sequence. 

Restriction endonucleases recognize short stretches of DNA (generally four or six base pairs) that contain specific nucleotide sequences. These sequences, which differ for each restriction endonuclease, are palindromes, that is, they exhibit two-fold rotational symmetry (Figure... 

Correct answer = D. The vast majority of restriction endonucleases recognize palindromes, and AAGCTT is the only palindrome among the choices. Because the sequence of only one DNA strand is given, one must determine the base sequence of the complementary strand. To be a palindrome, both strands must have the same sequence when read in the 5 —>3 direction. Thus, the complement of 5 AAGCTT3 is also 5 AAGCTT3. ... 

The most striking specificity in DNA hydrolysis is displayed by the restriction endonucleases which are discussed further in Chapter 26. These fussy catalysts cleave only at points within or close to a defined sequence of several nucleotides in double-stranded DNA. For example, the enzyme EcoR I cuts only at the following palindromic sequence ... 

The cuts in the two strands are made at the points indicated by the arrows. This one endonuclease will cut almost any DNA into long pieces averaging about 5000 base pairs each. These pieces can in turn be cleaved by other restriction endonucleases to form smaller fragments. Since there are about 2400 of these enzymes known, with 188 different specificities,536 it is possible to cut any piece of DNA down to a size of 100-500 base pairs, ideal for sequencing.537 539 Each fragment has known sequences at the two ends. Some restriction enzymes cleave outside their specific recognition sequence (see Table 26-2). Some recognize 16-nucleotide palindromes and cut at rare sites. 

The type II restriction endonucleases, which are the ones most widely used in molecular biology, are relatively small 50- to 100-kDa monomeric or dimeric proteins. About 2400 different enzymes with 188 different specificities had been isolated by 1995.83/84 The sites of attack, in most instances, are nucleotide sequences with a twofold axis of local symmetry.85 For example, the following sites of cleavage have been identified for two restriction endonucleases encoded by the DNA of R-factor plasmids of E. coli and for a restriction enzyme from Hemophilus influenzae. In the diagrams i are sites of cleavage, are sites of methyla-tion, and are local twofold axes (centers of palindromes) N can be any nucleotide with a proper base pairing partner. 

New England Biolabs, Inc. catalogue 1982-83 contains up to date restriction endonuclease maps of pBR322, M13mp8, phage A and SV40 DNA updated lists of restriction endonucleases, M13 primers, linkers and adapters as well as cross indexes of palindromic recognition sequences and much other useful data. A valuable up to date compendium obtainable from ... 

DNA sequencing Maxam-Gilbert method restriction endonuclease restriction fragment palindrome Sanger dideoxy method DNA synthesis DMT ether phosphoramidite phosphite polymerase chain reaction (PCR)... 

The recognition sites for restriction endonucleases arc specific palindromic sequences of DNA"" not more than 8 bp long. A number of these palindromes are listed in Table 6-2. A palindrome is a. sequence of letters that reads the same way forward and backward, for instance "A man. a plan, a canal Panama ." "DNA-land," "Did Hannah sec bees Hannah did." Restriction endonucleases cleave DNA at palindromic sites to yield several types of cuts ... 

B. Most of the sequences recognized by restriction endonucleases are palindromes that is, they have the same nucleotide sequence on both strands when read in the 5 to 3 direction. Since choice B has the only sequence that will be a palindrome when paired with its complementary strand, it is the most likely to be a site recognized by a restriction endonuclease (it is the site recognized by the restriction endonuclease Pstl). 

Cutting DNA Molecules into Small Fragments Restriction enzymes are endonucleases produced by bacteria that typically recognize specific 4- to 8-bp sequences, called restriction sites, and then cleave both DNA strands at this site. Restriction sites commonly are short palindromic sequences. that is, the restriction-site sequence is the same on each DNA strand when read in the 5 3 direction (Figure 9-10). 

Restriction enzymes (endonucleases) typically cut DNA at specific 4- to 8-bp palindromic sequences, producing defined fragments that often have self-complementary single-stranded tails (sticky ends). 

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