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2017 US Open – Men's Singles
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Men's Singles
2017 US Open
Champion
Rafael Nadal
Runner-up
Kevin Anderson
Final score
6–3, 6–3, 6–4
Details
Draw
128 (16Q / 8WC)
Seeds
32
Events
Singles
men women boys girls
Doubles
men women mixed boys girls
Legends
men women mixed
WC Singles
men women quad
WC Doubles
men women quad
← 2016 · US Open · 2018 →
Main article: 2017 US Open (tennis)
Stan Wawrinka was the defending champion, but was unable to defend the title due to a knee injury that ended his season prematurely. Wawrinka's withdrawal ended his streak of 50 consecutive grand slam appearances, dating back to the 2005 French Open.[1]
Rafael Nadal won his 16th Major title and 3rd US Open title, defeating first time Major Title finalist Kevin Anderson, 6–3, 6–3, 6–4.[2] Nadal retained the ATP No. 1 singles ranking after Roger Federer lost in the quarterfinals. It was also Nadal's first hard court title since January 2014. Anderson was the first South African man to reach the US Open singles final since 1965 and any Grand Slam singles final since the 1984 Australian Open, as well as the lowest-ranked male player to reach the US Open singles final since the ATP rankings began in 1973.[3][4] Anderson was also the tallest Grand Slam finalist in history.[5]
Novak Djokovic withdrew due to an elbow injury that ended his tennis season, ending his streak of 51 consecutive grand slam appearances, dating back to the 2005 Australian Open.[6] Accordingly, this was the first men's singles draw at the US Open since 1971 to include neither finalist from the previous year's tournament. The withdrawals of Wawrinka and Djokovic, along with those of Andy Murray, Kei Nishikori (also ending his season), and Milos Raonic, meant that only 6 of the top 11 ranked players competed in the tournament. The draw was retrospectively adjusted after Murray's late withdrawal,[7] but the timing of the withdrawal meant that Nadal and Federer remained in the same half of the draw.[8] This meant it was the first Grand Slam since 2004 that did not feature Wawrinka, Djokovic and Murray in the tournament.
Federer broke the men's singles record for total appearances at Grand Slams with his 71st participation. Also, Andrey Rublev became the youngest man to reach the US Open quarterfinals since Andy Roddick in 2001, and Denis Shapovalov the youngest man to reach the fourth round of the US Open since Michael Chang in 1989.[9] Sam Querrey also became the first American man to reach the quarterfinals of the US Open since John Isner and Andy Roddick in 2011. Also, Pablo Carreño Busta made his first major semifinal appearance, becoming the first Spanish semifinalist since David Ferrer in 2012 other than Nadal.
Contents
1 Seeds
2 Qualifying
3 Draw
3.1 Key
3.2 Finals
3.3 Top half
3.3.1 Section 1
3.3.2 Section 2
3.3.3 Section 3
3.3.4 Section 4
3.4 Bottom half
3.4.1 Section 5
3.4.2 Section 6
3.4.3 Section 7
3.4.4 Section 8
4 References
5 External links
Seeds[edit]
01. Rafael Nadal (Champion)
02. Andy Murray (Withdrew due to a hip injury)
03. Roger Federer (Quarterfinals)
04. Alexander Zverev (Second round)
05. Marin Čilić (Third round)
06. Dominic Thiem (Fourth round)
07. Grigor Dimitrov (Second round)
08. Jo-Wilfried Tsonga (Second round)
09. David Goffin (Fourth round)
10. John Isner (Third round)
11. Roberto Bautista Agut (Third round)
12. Pablo Carreño Busta (Semifinals)
13. Jack Sock (First round)
14. Nick Kyrgios (First round)
15. Tomáš Berdych (Second round)
16. Lucas Pouille (Fourth round)
17. Sam Querrey (Quarterfinals)
18. Gaël Monfils (Third round, retired)
19. Gilles Müller (Second round)
20. Albert Ramos Viñolas (Second round)
21. David Ferrer (First round)
22. Fabio Fognini (First round)
23. Mischa Zverev (Fourth round)
24. Juan Martín del Potro (Semifinals)
25. Karen Khachanov (First round)
26. Richard Gasquet (First round)
27. Pablo Cuevas (First round)
28. Kevin Anderson (Final)
29. Diego Schwartzman (Quarterfinals)
30. Adrian Mannarino (Third round)
31. Feliciano López (Third round)
32. Robin Haase (First round)
33. Philipp Kohlschreiber (Fourth round)
Click on the seed number of a player to go to their draw section.
Qualifying[edit]
Main article: 2017 US Open – Men's Singles Qualifying
Draw[edit]
Key[edit]
Q = Qualifier
WC = Wild Card
LL = Lucky Loser
Alt = Alternate
SE = Special Exempt
PR = Protected Ranking
w/o = Walkover
r = Retired
d = Defaulted
Finals[edit]
Quarterfinals Semifinals Final
1 Rafael Nadal 6 6 6
Andrey Rublev 1 2 2
1 Rafael Nadal 4 6 6 6
24 Juan Martín del Potro 6 0 3 2
3 Roger Federer 5 6 68 4
24 Juan Martín del Potro 7 3 710 6
1 Rafael Nadal 6 6 6
28 Kevin Anderson 3 3 4
17 Sam Querrey 65 711 3 67
28 Kevin Anderson 77 69 6 79
28 Kevin Anderson 4 7 6 6
12 Pablo Carreño Busta 6 5 3 4
12 Pablo Carreño Busta 6 6 6
29 Diego Schwartzman 4 4 2
Top half[edit]
Section 1[edit]
First Round Second Round Third Round Fourth Round
1 R Nadal 78 6 6
D Lajović 66 2 2 1 R Nadal 4 6 6 6
T Daniel 6 4 4 6 6 T Daniel 6 3 2 2
WC T Paul 1 6 6 2 2 1 R Nadal 63 6 6 6
Y Sugita 6 6 6 LL L Mayer 77 3 1 4
WC G Blancaneaux 2 2 0 Y Sugita 77 4 3 4
LL L Mayer 3 6 6 6 LL L Mayer 63 6 6 6
26 R Gasquet 6 2 4 2 1 R Nadal 6 6 6
22 F Fognini 4 68 6 0 A Dolgopolov 2 4 1
Q S Travaglia 6 710 3 6 Q S Travaglia 66 5 0
V Troicki 3 6 3 6 6 V Troicki 78 7 6
N Gombos 6 3 6 4 3 V Troicki 1 0 4
J-L Struff 6 3 2 6 3 A Dolgopolov 6 6 6
A Dolgopolov 3 6 6 1 6 A Dolgopolov 3 6 77 6
R Harrison 4 2 64 15 T Berdych 6 1 65 2
15 T Berdych 6 6 77
Section 2[edit]
First Round Second Round Third Round Fourth Round
9 D Goffin 6 2 6 6
J Benneteau 4 6 4 2 9 D Goffin 3 77 62 77 6
S Darcis 1 2 0 G Pella 6 65 77 64 3
G Pella 6 6 6 9 D Goffin 7 5
Q M Marterer 3 6 1 4 18 G Monfils 5 1r
D Young 6 1 6 6 D Young 3 77 4 6 5
J Chardy 66 3 4 18 G Monfils 6 63 6 2 7
18 G Monfils 78 6 6 9 D Goffin 5 65 3
27 P Cuevas 5 63 1 A Rublev 7 77 6
D Džumhur 7 77 6 D Džumhur 4 6 6 6
Q C-M Stebe 5 6 6 6 Q C-M Stebe 6 4 0 1
N Kicker 7 3 1 1 D Džumhur 4 4 7 4
A Bedene 1 4 4 A Rublev 6 6 5 6
A Rublev 6 6 6 A Rublev 7 77 6
Q V Šafránek 1 4 2 7 G Dimitrov 5 63 3
7 G Dimitrov 6 6 6
Section 3[edit]
First Round Second Round Third Round Fourth Round
3 R Federer 4 6 6 1 6
F Tiafoe 6 2 1 6 4 3 R Federer 6 63 4 6 6
B Kavčič 3 7 4 3 M Youzhny 1 77 6 4 2
M Youzhny 6 5 6 6 3 R Federer 6 6 7
F Verdasco 6 0 31 F López 3 3 5
V Pospisil 2 0r F Verdasco 3 2 6 1
A Kuznetsov 4 64 77 2 31 F López 6 6 3 6
31 F López 6 77 65 6 3 R Federer 6 6 7
33 P Kohlschreiber 6 6 6 33 P Kohlschreiber 4 2 5
Q T Smyczek 1 4 4 33 P Kohlschreiber 6 6 3
Q V Millot 1 0 6 6 4 S Giraldo 2 1 0r
S Giraldo 6 6 4 4 6 33 P Kohlschreiber 7 6 6
M Jaziri 77 4 6 5 6 PR J Millman 5 2 4
T Monteiro 65 6 3 7 4 M Jaziri 1 61 1
PR J Millman 6 1 6 6 PR J Millman 6 77 6
14 N Kyrgios 3 6 4 1
Section 4[edit]
First Round Second Round Third Round Fourth Round
11 R Bautista Agut 6 4 6 77
A Seppi 2 6 2 61 11 R Bautista Agut 6 6 77
D Brown 6 6 6 D Brown 1 3 63
T Bellucci 4 3 2 11 R Bautista Agut 3 3 4
WC P Kypson 4 69 1 24 JM del Potro 6 6 6
Q A Menéndez-Maceiras 6 711 6 Q A Menéndez-Maceiras 2 3 63
H Laaksonen 4 63 65 24 JM del Potro 6 6 77
24 JM del Potro 6 77 77 24 JM del Potro 1 2 6 77 6
30 A Mannarino 6 6 6 6 D Thiem 6 6 1 61 4
PR R Berankis 2 4 2 30 A Mannarino 6 64 6 6
WC B Fratangelo 77 6 3 77 WC B Fratangelo 3 77 1 2
I Karlović 62 4 6 64 30 A Mannarino 5 3 4
M Baghdatis 4 4 3 6 D Thiem 7 6 6
WC T Fritz 6 6 6 WC T Fritz 4 4 6 5
WC A De Minaur 4 1 1 6 D Thiem 6 6 4 7
6 D Thiem 6 6 6
Bottom half[edit]
Section 5[edit]
First Round Second Round Third Round Fourth Round
17 S Querrey 6 6 6
G Simon 4 3 4 17 S Querrey 6 6 6
WC C Eubanks 2 4 2 D Sela 4 1 4
D Sela 6 6 6 17 S Querrey 4 6 6 6
Q R Albot 7 4 6 6 Q R Albot 6 2 4 4
E Escobedo 5 6 2 4 Q R Albot 6 79 5 0 77
Y-h Lu 4 6 6 6 Y-h Lu 2 67 7 6 62
25 K Khachanov 6 2 3 3 17 S Querrey 6 6 6
23 M Zverev 77 4 4 7 6 23 M Zverev 2 2 1
WC T-S Kwiatkowski 65 6 6 5 3 23 M Zverev 6 6 3 63 7
LL L Lacko 3 2 65 B Paire 3 2 6 77 5
B Paire 6 6 77 23 M Zverev 6 6 77
H Zeballos 6 68 4 3 10 J Isner 4 3 65
H Chung 3 710 6 6 H Chung 3 4 5
P-H Herbert 1 3 6 3 10 J Isner 6 6 7
10 J Isner 6 6 4 6
Section 6[edit]
First Round Second Round Third Round Fourth Round
13 J Sock 2 612 6 7 4
J Thompson 6 714 1 5 6 J Thompson 6 2 6 4 2
Q J-P Smith 65 4 6 64 T Fabbiano 2 6 3 6 6
T Fabbiano 77 6 3 77 T Fabbiano 2 4 4
J Sousa 6 3 64 2 P Lorenzi 6 6 6
P Lorenzi 4 6 77 6 P Lorenzi 64 6 77 6
B Tomic 6 3 4 4 19 G Müller 77 3 64 3
19 G Müller 3 6 6 6 P Lorenzi 4 3 77 4
28 K Anderson 6 6 6 28 K Anderson 6 6 64 6
Q JC Aragone 3 3 1 28 K Anderson 6 7 6
A Giannessi 4 77 2 5 PR E Gulbis 3 5 4
PR E Gulbis 6 63 6 7 28 K Anderson 6 6 6
J Veselý 65 62 2 B Ćorić 4 3 2
B Ćorić 77 77 6 B Ćorić 3 7 77 77
Q D King 69 5 4 4 A Zverev 6 5 61 64
4 A Zverev 711 7 6
Section 7[edit]
First Round Second Round Third Round Fourth Round
8 J-W Tsonga 6 6 6
M Copil 3 3 4 8 J-W Tsonga 4 4 63
Q D Shapovalov 7 6 6 Q D Shapovalov 6 6 77
D Medvedev 5 1 2 Q D Shapovalov 3 6 6 1
N Almagro 4 62 65 K Edmund 6 3 3 0r
S Johnson 6 77 77 S Johnson 5 2 64
K Edmund 6 7 6 K Edmund 7 6 77
32 R Haase 3 5 3 Q D Shapovalov 62 64 63
20 A Ramos Viñolas 4 77 7 63 7 12 P Carreño Busta 77 77 77
D Istomin 6 64 5 77 5 20 A Ramos Viñolas 6 4 6 3 0
M Fucsovics 3 6 4 6 63 Q N Mahut 4 6 4 6 6
Q N Mahut 6 2 6 2 77 Q N Mahut 3 4 3
PR D Tursunov 67 1 0r 12 P Carreño Busta 6 6 6
Q C Norrie 79 6 0 Q C Norrie 2 4 3
Q E King 3 2 65 12 P Carreño Busta 6 6 6
12 P Carreño Busta 6 6 77
Section 8[edit]
First Round Second Round Third Round Fourth Round
16 L Pouille 6 6 6
R Bemelmans 3 4 4 16 L Pouille 7 6 4 3 6
J Donaldson 6 4 6 78 J Donaldson 5 4 6 6 4
N Basilashvili 0 6 3 66 16 L Pouille 2 6 6 6
PR A Haider-Maurer 63 1r Q M Kukushkin 6 3 4 4
E Donskoy 77 5 E Donskoy 4 4 5
Q M Kukushkin 4 6 6 6 Q M Kukushkin 6 6 7
21 D Ferrer 6 3 2 1 16 L Pouille 63 5 6 2
29 D Schwartzman 6 6 6 29 D Schwartzman 77 7 2 6
C Berlocq 2 1 3 29 D Schwartzman 6 6 7
PR T Kokkinakis 77 6 1 62 3 J Tipsarević 2 4 5
J Tipsarević 65 3 6 77 6 29 D Schwartzman 4 7 7 6
R Dutra Silva 5 6 3 4 5 M Čilić 6 5 5 4
F Mayer 7 0 6 6 F Mayer 3 3 3
T Sandgren 4 3 6 3 5 M Čilić 6 6 6
5 M Čilić 6 6 3 6
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References[edit]
Jump up ^ "Stan Wawrinka ruled out for rest of 2017 season after surgery on knee". The Guardian. August 4, 2017. Retrieved August 4, 2017.
Jump up ^ "US Open final 2017: Rafa Nadal wins 16th Major title to complete a Nadal-Federer 2017 clean sweep". The Telegraph. 11 September 2017. Retrieved 19 September 2017.
Jump up ^ http://www.tennis.com/pro-game/2017/09/kevin-anderson-pablo-carreno-busta-2017-us-open-semifinals-new-york/69281/
Jump up ^ "Rafael Nadal defeats Kevin Anderson in US Open final for 16th grand slam title". Guardian. 11 September 2017. Retrieved 19 September 2017.
Jump up ^ http://www.tennis.com/pro-game/2017/09/us-open-nadal-anderson-seems-a-mismatch-but-upsets-happen/69295/
Jump up ^ "Novak Djokovic: Twelve-time Grand Slam champion will not play again in 2017". BBC Sport. July 26, 2017. Retrieved July 26, 2017.
Jump up ^ Marshall, Ashley (2017-08-26). "Murray pulls out of 2017 US Open". US Open. Retrieved 2017-08-26.
Jump up ^ http://www.news.com.au/sport/tennis/us-open-mens-draw-is-a-whos-who-of-tennis-battlers/news-story/ae62666ab04e0749c916f4e2826c1992
Jump up ^ "U.S. Open: Denis Shapovalov gets easy win as injured Edmund retires". CBC Sports. Retrieved October 3, 2017.
External links[edit]
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(2005) Roger Federer
(2006) Roger Federer
(2007) Roger Federer
(2008) Roger Federer
(2009) Juan Martín del Potro
(2010) Rafael Nadal
(2011) Novak Djokovic
(2012) Andy Murray
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(2014) Marin Čilić
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(2016) Stan Wawrinka
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Restriction enzyme
From Wikipedia, the free encyclopedia
Jump to: navigation, search
Restriction Enzyme Glossary
Restriction[hide]
The cutting of DNA at specific sites
Enzyme[hide]
A protein that catalyzes a chemical reaction
Molecular recognition[hide]
Used by restriction enzymes to locate specific sequences of DNA on which to bind and subsequently cleave
Recognition sequence[hide]
The DNA sequence to which restriction enzymes bind
Restriction site[hide]
The site of the DNA sequence where it cleaved by the restriction enzyme
v
t
e
A restriction enzyme or restriction endonuclease is an enzyme that cleaves DNA into fragments at or near specific recognition sites within the molecule known as restriction sites.[1][2][3] Restriction enzymes are commonly classified into five types, which differ in their structure and whether they cut their DNA substrate at their recognition site, or if the recognition and cleavage sites are separate from one another. To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix.
These enzymes are found in bacteria and archaea and provide a defense mechanism against invading viruses.[4][5] Inside a prokaryote, the restriction enzymes selectively cut up foreign DNA in a process called restriction; meanwhile, host DNA is protected by a modification enzyme (a methyltransferase) that modifies the prokaryotic DNA and blocks cleavage. Together, these two processes form the restriction modification system.[6]
Over 3000 restriction enzymes have been studied in detail, and more than 600 of these are available commercially.[7] These enzymes are routinely used for DNA modification in laboratories, and they are a vital tool in molecular cloning.[8][9][10]
Contents
[hide]
1 History
2 Origins
3 Recognition site
4 Types
4.1 Type l
4.2 Type II
4.3 Type III
4.4 Type IV
4.5 Type V
4.6 Artificial restriction enzymes
5 Nomenclature
6 Applications
7 Examples
8 See also
9 References
10 External links
History[edit]
The term restriction enzyme originated from the studies of phage λ, a virus that infects bacteria, and the phenomenon of host-controlled restriction and modification of such bacterial phage or bacteriophage.[11] The phenomenon was first identified in work done in the laboratories of Salvador Luria and Giuseppe Bertani in the early 1950s.[12][13] It was found that, for a bacteriophage λ that can grow well in one strain of Escherichia coli, for example E. coli C, when grown in another strain, for example E. coli K, its yields can drop significantly, by as much as 3-5 orders of magnitude. The host cell, in this example E. coli K, is known as the restricting host and appears to have the ability to reduce the biological activity of the phage λ. If a phage becomes established in one strain, the ability of that phage to grow also becomes restricted in other strains. In the 1960s, it was shown in work done in the laboratories of Werner Arber and Matthew Meselson that the restriction is caused by an enzymatic cleavage of the phage DNA, and the enzyme involved was therefore termed a restriction enzyme.[4][14][15][16]
The restriction enzymes studied by Arber and Meselson were type I restriction enzymes, which cleave DNA randomly away from the recognition site.[17] In 1970, Hamilton O. Smith, Thomas Kelly and Kent Wilcox isolated and characterized the first type II restriction enzyme, HindII, from the bacterium Haemophilus influenzae.[18][19] Restriction enzymes of this type are more useful for laboratory work as they cleave DNA at the site of their recognition sequence. Later, Daniel Nathans and Kathleen Danna showed that cleavage of simian virus 40 (SV40) DNA by restriction enzymes yields specific fragments that can be separated using polyacrylamide gel electrophoresis, thus showing that restriction enzymes can also be used for mapping DNA.[20] For their work in the discovery and characterization of restriction enzymes, the 1978 Nobel Prize for Physiology or Medicine was awarded to Werner Arber, Daniel Nathans, and Hamilton O. Smith.[21] The discovery of restriction enzymes allows DNA to be manipulated, leading to the development of recombinant DNA technology that has many applications, for example, allowing the large scale production of proteins such as human insulin used by diabetics.[12][22]
Origins[edit]
Restriction enzymes likely evolved from a common ancestor and became widespread via horizontal gene transfer.[23][24] In addition, there is mounting evidence that restriction endonucleases evolved as a selfish genetic element.[25]
Recognition site[edit]
A palindromic recognition site reads the same on the reverse strand as it does on the forward strand when both are read in the same orientation
Restriction enzymes recognize a specific sequence of nucleotides[2] and produce a double-stranded cut in the DNA. The recognition sequences can also be classified by the number of bases in its recognition site, usually between 4 and 8 bases, and the number of bases in the sequence will determine how often the site will appear by chance in any given genome, e.g., a 4-base pair sequence would theoretically occur once every 4^4 or 256bp, 6 bases, 4^6 or 4,096bp, and 8 bases would be 4^8 or 65,536bp.[26] Many of them are palindromic, meaning the base sequence reads the same backwards and forwards.[27] 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 GTAATG. The inverted repeat palindrome is also a sequence that reads the same forward and backward, but the forward and backward sequences are found in complementary DNA strands (i.e., of double-stranded DNA), as in GTATAC (GTATAC being complementary to CATATG).[28] Inverted repeat palindromes are more common and have greater biological importance than mirror-like palindromes.
EcoRI digestion produces "sticky" ends,
whereas SmaI restriction enzyme cleavage produces "blunt" ends:
Recognition sequences in DNA differ for each restriction enzyme, producing differences in the length, sequence and strand orientation (5' end or 3' end) of a sticky-end "overhang" of an enzyme restriction.[29]
Different restriction enzymes that recognize the same sequence are known as neoschizomers. These often cleave in different locales of the sequence. Different enzymes that recognize and cleave in the same location are known as isoschizomers.
Types[edit]
Naturally occurring restriction endonucleases are categorized into four groups (Types I, II III, and IV) based on their composition and enzyme cofactor requirements, the nature of their target sequence, and the position of their DNA cleavage site relative to the target sequence.[30][31][32] DNA sequence analyses of restriction enzymes however show great variations, indicating that there are more than four types.[33] All types of enzymes recognize specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements,[34][35] as summarised below:
Type I enzymes (EC 3.1.21.3) cleave at sites remote from a recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (EC 2.1.1.72) activities.
Type II enzymes (EC 3.1.21.4) cleave within or at short specific distances from a recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.
Type III enzymes (EC 3.1.21.5) cleave at sites a short distance from a recognition site; require ATP (but do not hydrolyse it); S-adenosyl-L-methionine stimulates the reaction but is not required; exist as part of a complex with a modification methylase (EC 2.1.1.72).
Type IV enzymes target modified DNA, e.g. methylated, hydroxymethylated and glucosyl-hydroxymethylated DNA
Type l[edit]
Type I restriction enzymes were the first to be identified and were first identified in two different strains (K-12 and B) of E. coli.[36] These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions—one containing 3–4 nucleotides, and another containing 4–5 nucleotides—separated by a non-specific spacer of about 6–8 nucleotides. These enzymes are multifunctional and are capable of both restriction and modification activities, depending upon the methylation status of the target DNA. The cofactors S-Adenosyl methionine (AdoMet), hydrolyzed adenosine triphosphate (ATP), and magnesium (Mg2+) ions, are required for their full activity. Type I restriction enzymes possess three subunits called HsdR, HsdM, and HsdS; HsdR is required for restriction; HsdM is necessary for adding methyl groups to host DNA (methyltransferase activity), and HsdS is important for specificity of the recognition (DNA-binding) site in addition to both restriction (DNA cleavage) and modification (DNA methyltransferase) activity.[30][36]
Type II[edit]
Type II site-specific deoxyribonuclease
Structure of the homodimeric restriction enzyme EcoRI (cyan and green cartoon diagram) bound to double stranded DNA (brown tubes).[37] Two catalytic magnesium ions (one from each monomer) are shown as magenta spheres and are adjacent to the cleaved sites in the DNA made by the enzyme (depicted as gaps in the DNA backbone).
Identifiers
EC number
3.1.21.4
CAS number
9075-08-5
Databases
IntEnz
IntEnz view
BRENDA
BRENDA entry
ExPASy
NiceZyme view
KEGG
KEGG entry
MetaCyc
metabolic pathway
PRIAM
profile
PDB structures
RCSB PDB PDBe PDBsum
Gene Ontology
AmiGO / QuickGO
[show]Search
PMC
articles
PubMed
articles
NCBI
proteins
Typical type II restriction enzymes differ from type I restriction enzymes in several ways. They form homodimers, with recognition sites that are usually undivided and palindromic and 4–8 nucleotides in length. They recognize and cleave DNA at the same site, and they do not use ATP or AdoMet for their activity—they usually require only Mg2+ as a cofactor.[27] These enzymes cleave the phosphodiester bond of double helix DNA. It can either cleave at the center of both strands to yield a blunt end. Or it can cleave at a staggered position leaving overhangs called sticky ends.[38] These are the most commonly available and used restriction enzymes. In the 1990s and early 2000s, new enzymes from this family were discovered that did not follow all the classical criteria of this enzyme class, and new subfamily nomenclature was developed to divide this large family into subcategories based on deviations from typical characteristics of type II enzymes.[27] These subgroups are defined using a letter suffix.
Type IIB restriction enzymes (e.g., BcgI and BplI) are multimers, containing more than one subunit.[27] They cleave DNA on both sides of their recognition to cut out the recognition site. They require both AdoMet and Mg2+ cofactors. Type IIE restriction endonucleases (e.g., NaeI) cleave DNA following interaction with two copies of their recognition sequence.[27] One recognition site acts as the target for cleavage, while the other acts as an allosteric effector that speeds up or improves the efficiency of enzyme cleavage. Similar to type IIE enzymes, type IIF restriction endonucleases (e.g. NgoMIV) interact with two copies of their recognition sequence but cleave both sequences at the same time.[27] Type IIG restriction endonucleases (e.g., Eco57I) do have a single subunit, like classical Type II restriction enzymes, but require the cofactor AdoMet to be active.[27] Type IIM restriction endonucleases, such as DpnI, are able to recognize and cut methylated DNA.[27] Type IIS restriction endonucleases (e.g., FokI) cleave DNA at a defined distance from their non-palindromic asymmetric recognition sites;[27] this characteristic is widely used to perform in-vitro cloning techniques such as Golden Gate cloning. These enzymes may function as dimers. Similarly, Type IIT restriction enzymes (e.g., Bpu10I and BslI) are composed of two different subunits. Some recognize palindromic sequences while others have asymmetric recognition sites.[27]
Type III[edit]
Type III restriction enzymes (e.g., EcoP15) recognize two separate non-palindromic sequences that are inversely oriented. They cut DNA about 20–30 base pairs after the recognition site.[39] These enzymes contain more than one subunit and require AdoMet and ATP cofactors for their roles in DNA methylation and restriction, respectively.[40] They are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5–6 bp-long asymmetric DNA sequences and cleave 25–27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F).[34][41]
Type IV[edit]
Type IV enzymes recognize modified, typically methylated DNA and are exemplified by the McrBC and Mrr systems of E. coli.[33]
Type V[edit]
Type V restriction enzymes (e.g., the cas9-gRNA complex from CRISPRs[42]) utilize guide RNAs to target specific non-palindromic sequences found on invading organisms. They can cut DNA of variable length, provided that a suitable guide RNA is provided. The flexibility and ease of use of these enzymes make them promising for future genetic engineering applications.[42][43]
Artificial restriction enzymes[edit]
Artificial restriction enzymes can be generated by fusing a natural or engineered DNA binding domain to a nuclease domain (often the cleavage domain of the type IIS restriction enzyme FokI).[44] Such artificial restriction enzymes can target large DNA sites (up to 36 bp) and can be engineered to bind to desired DNA sequences.[45] Zinc finger nucleases are the most commonly used artificial restriction enzymes and are generally used in genetic engineering applications,[46][47][48][49] but can also be used for more standard gene cloning applications.[50] Other artificial restriction enzymes are based on the DNA binding domain of TAL effectors.[51][52]
In 2013, a new technology CRISPR-Cas9, based on a prokaryotic viral defense system, was engineered for editing the genome, and it was quickly adopted in laboratories.[53] For more detail, read CRISPR (Clustered regularly interspaced short palindromic repeats).
In 2017 a group in Illinois announced using an Argonaute protein taken from Pyrococcus furiosus (PfAgo) along with guide DNA to edit DNA as artificial restriction enzymes.[54]
Artificial ribonucleases that act as restriction enzymes for RNA are also being developed. A PNA-based system, called PNAzymes, has a Cu(II)-2,9-dimethylphenanthroline group that mimics ribonucleases for specific RNA sequence and cleaves at a non-base-paired region (RNA bulge) of the targeted RNA formed when the enzyme binds the RNA. This enzyme shows selectivity by cleaving only at one site that either does not have a mismatch or is kinetically preferred out of two possible cleavage sites.[55]
Nomenclature[edit]
Derivation of the EcoRI name
Abbreviation
Meaning
Description
E Escherichia genus
co coli specific species
R RY13 strain
I First identified order of identification
in the bacterium
Since their discovery in the 1970s, many restriction enzymes have been identified; for example, more than 3500 different Type II restriction enzymes have been characterized.[56] Each enzyme is named after the bacterium from which it was isolated, using a naming system based on bacterial genus, species and strain.[57][58] For example, the name of the EcoRI restriction enzyme was derived as shown in the box.
Applications[edit]
Main article: Restriction digest
Isolated restriction enzymes are used to manipulate DNA for different scientific applications.
They are used to assist insertion of genes into plasmid vectors during gene cloning and protein production experiments. For optimal use, plasmids that are commonly used for gene cloning are modified to include a short polylinker sequence (called the multiple cloning site, or MCS) rich in restriction enzyme recognition sequences. This allows flexibility when inserting gene fragments into the plasmid vector; restriction sites contained naturally within genes influence the choice of endonuclease for digesting the DNA, since it is necessary to avoid restriction of wanted DNA while intentionally cutting the ends of the DNA. To clone a gene fragment into a vector, both plasmid DNA and gene insert are typically cut with the same restriction enzymes, and then glued together with the assistance of an enzyme known as a DNA ligase.[59][60]
Restriction enzymes can also be used to distinguish gene alleles by specifically recognizing single base changes in DNA known as single nucleotide polymorphisms (SNPs).[61][62] This is however only possible if a SNP alters the restriction site present in the allele. In this method, the restriction enzyme can be used to genotype a DNA sample without the need for expensive gene sequencing. The sample is first digested with the restriction enzyme to generate DNA fragments, and then the different sized fragments separated by gel electrophoresis. In general, alleles with correct restriction sites will generate two visible bands of DNA on the gel, and those with altered restriction sites will not be cut and will generate only a single band. A DNA map by restriction digest can also be generated that can give the relative positions of the genes.[63] The different lengths of DNA generated by restriction digest also produce a specific pattern of bands after gel electrophoresis, and can be used for DNA fingerprinting.
In a similar manner, restriction enzymes are used to digest genomic DNA for gene analysis by Southern blot. This technique allows researchers to identify how many copies (or paralogues) of a gene are present in the genome of one individual, or how many gene mutations (polymorphisms) have occurred within a population. The latter example is called restriction fragment length polymorphism (RFLP).[64]
Artificial restriction enzymes created by linking the FokI DNA cleavage domain with an array of DNA binding proteins or zinc finger arrays, denoted zinc finger nucleases (ZFN), are a powerful tool for host genome editing due to their enhanced sequence specificity. ZFN work in pairs, their dimerization being mediated in-situ through the FokI domain. Each zinc finger array (ZFA) is capable of recognizing 9–12 base pairs, making for 18–24 for the pair. A 5–7 bp spacer between the cleavage sites further enhances the specificity of ZFN, making them a safe and more precise tool that can be applied in humans. A recent Phase I clinical trial of ZFN for the targeted abolition of the CCR5 co-receptor for HIV-1 has been undertaken.[65]
Others have proposed using the bacteria R-M system as a model for devising human anti-viral gene or genomic vaccines and therapies since the RM system serves an innate defense-role in bacteria by restricting tropism by bacteriophages.[66] There is research on REases and ZFN that can cleave the DNA of various human viruses, including HSV-2, high-risk HPVs and HIV-1, with the ultimate goal of inducing target mutagenesis and aberrations of human-infecting viruses.[67][68][69] Interestingly, the human genome already contains remnants of retroviral genomes that have been inactivated and harnessed for self-gain. Indeed, the mechanisms for silencing active L1 genomic retroelements by the three prime repair exonuclease 1 (TREX1) and excision repair cross complementing 1(ERCC) appear to mimic the action of RM-systems in bacteria, and the non-homologous end-joining (NHEJ) that follows the use of ZFN without a repair template.[70][71]
Examples[edit]
See also: List of restriction enzyme cutting sites
Examples of restriction enzymes include:[72]
Enzyme
Source
Recognition Sequence
Cut
EcoRI Escherichia coli
5'GAATTC
3'CTTAAG
5'---G     AATTC---3'
3'---CTTAA     G---5'
EcoRII Escherichia coli
5'CCWGG
3'GGWCC
5'---     CCWGG---3'
3'---GGWCC     ---5'
BamHI Bacillus amyloliquefaciens
5'GGATCC
3'CCTAGG
5'---G     GATCC---3'
3'---CCTAG     G---5'
HindIII Haemophilus influenzae
5'AAGCTT
3'TTCGAA
5'---A     AGCTT---3'
3'---TTCGA     A---5'
TaqI Thermus aquaticus
5'TCGA
3'AGCT
5'---T   CGA---3'
3'---AGC   T---5'
NotI Nocardia otitidis
5'GCGGCCGC
3'CGCCGGCG
5'---GC   GGCCGC---3'
3'---CGCCGG   CG---5'
HinFI Haemophilus influenzae
5'GANTC
3'CTNAG
5'---G   ANTC---3'
3'---CTNA   G---5'
Sau3AI Staphylococcus aureus
5'GATC
3'CTAG
5'---     GATC---3'
3'---CTAG     ---5'
PvuII* Proteus vulgaris
5'CAGCTG
3'GTCGAC
5'---CAG  CTG---3'
3'---GTC  GAC---5'
SmaI* Serratia marcescens
5'CCCGGG
3'GGGCCC
5'---CCC  GGG---3'
3'---GGG  CCC---5'
HaeIII* Haemophilus aegyptius
5'GGCC
3'CCGG
5'---GG  CC---3'
3'---CC  GG---5'
HgaI[73] Haemophilus gallinarum
5'GACGC
3'CTGCG
5'---NN  NN---3'
3'---NN  NN---5'
AluI* Arthrobacter luteus
5'AGCT
3'TCGA
5'---AG  CT---3'
3'---TC  GA---5'
EcoRV* Escherichia coli
5'GATATC
3'CTATAG
5'---GAT  ATC---3'
3'---CTA  TAG---5'
EcoP15I Escherichia coli
5'CAGCAGN25NN 3'GTCGTCN25NN
5'---CAGCAGN25 NN---3' 3'---GTCGTCN25NN ---5'
KpnI[74] Klebsiella pneumoniae
5'GGTACC
3'CCATGG
5'---GGTAC  C---3'
3'---C  CATGG---5'
PstI[74] Providencia stuartii
5'CTGCAG
3'GACGTC
5'---CTGCA  G---3'
3'---G  ACGTC---5'
SacI[74] Streptomyces achromogenes
5'GAGCTC
3'CTCGAG
5'---GAGCT  C---3'
3'---C  TCGAG---5'
SalI[74] Streptomyces albus
5'GTCGAC
3'CAGCTG
5'---G  TCGAC---3'
3'---CAGCT  G---5'
ScaI*[74] Streptomyces caespitosus
5'AGTACT
3'TCATGA
5'---AGT  ACT---3'
3'---TCA  TGA---5'
SpeI Sphaerotilus natans
5'ACTAGT
3'TGATCA
5'---A  CTAGT---3'
3'---TGATC  A---5'
SphI[74] Streptomyces phaeochromogenes
5'GCATGC
3'CGTACG
5'---GCATG  C---3'
3'---C  GTACG---5'
StuI*[75][76] Streptomyces tubercidicus
5'AGGCCT
3'TCCGGA
5'---AGG  CCT---3'
3'---TCC  GGA---5'
XbaI[74] Xanthomonas badrii
5'TCTAGA
3'AGATCT
5'---T  CTAGA---3'
3'---AGATC  T---5'
Key:
* = blunt ends
N = C or G or T or A
W = A or T
See also[edit]
Detailed articles about certain restriction enzymes: EcoRI, HindIII, BglII.
Homing endonuclease
Isoschizomer.
List of homing endonuclease cutting sites
List of restriction enzyme cutting sites
Molecular weight size marker
Restriction map
Star activity
CRISPR
CAS9
References[edit]
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Jump up ^ A. Pingoud (2004). Restriction Endonucleases (Nucleic Acids and Molecular Biology). Springer. p. 3. ISBN 9783642188510.
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Jump up ^ "Stu I from Streptomyces tubercidicus". Sigma-Aldrich. Retrieved 2008-06-07.
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External links[edit]
Library resources about
Restriction enzymes
Resources in your library
Resources in other libraries
General Information:
DNA Restriction Enzymes at the US National Library of Medicine Medical Subject Headings (MeSH)
Firman K (2007-11-24). "Type I Restriction-Modification". University of Portsmouth. Retrieved 2008-06-06.
Goodsell DS (2000-08-01). "Restriction Enzymes". Molecule of the Month. RCSB Protein Data Bank. Archived from the original on 2008-05-31. Retrieved 2008-06-06.
Simmer M, Secko D (2003-08-01). "Restriction Endonucleases: Molecular Scissors for Specifically Cutting DNA". The Science Creative Quarterly. Retrieved 2008-06-06.
Databases:
Roberts RJ, Vincze T, Posfai, J, Macelis D. "REBASE". Archived from the original on 2016-12-30. Retrieved 2008-06-06. Restriction Enzyme Database
Software:
Bikandi J, San Millán R, Rementeria A, Garaizar J. "Restriction enzyme digest of DNA". insilico.ehu.es. Retrieved 2008-06-06.
Palmer M. "WatCut". University of Waterloo, Ontario, Canada. Retrieved 2008-06-06. An on-line tool for restriction analysis, silent mutation scanning, SNP-RFLP analysis
Vincze T, Posfai J, Roberts RJ. "NEBcutter V2.0". New England Biolabs Inc. Retrieved 2008-06-06. Restriction enzyme finder
"Restriction enzyme digest of DNA software". BioPHP: PHP for Bioinformatics. Retrieved 2008-06-06. Online tool, free source code
"pDRAW32". AcaClone software. Retrieved 2008-06-06. Freeware DNA cloning, sequence analysis and plasmid/DNA plotting software
Čermák V. "Restriction Analyzer". Retrieved 2016-08-22. Free online tool for restriction analysis
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Restriction sites

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Enzyme substrate (biology)

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DNA binding domain

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