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Restriction endonucleases: natural and directed evolution

Author(s):

Gupta, R
(Gupta, Richa)
2
;
Capalash, N
(Capalash, Neena)
2
;
Sharma, P
(Sharma, Prince)
1


Source:
APPLIED

MICROBIOLOGY AND BIOTECHNOLOGY


Volume:

94


Issue:

3


Pages:

583
-
599


DOI:

10.1007/s00253
-
012
-
3961
-
z


Published:

MAY 2012

Times Cited:

0 (from Web of Science)

Cited References:

130

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Abstract:

Type II restriction endonucleases (REs) are highly sequence
-
specific compared with other
classes of nucleases. PD
-
(D/E)XK nucleases, initially represented by only type II REs, now comprise
a large and extremely diverse superfamily of proteins and, althoug
h sharing a structurally conserved
core, typically display little or no detectable sequence similarity except for the active site motifs.
Sequence similarity can only be observed in methylases and few isoschizomers. As a consequence,
REs are classified acc
ording to combinations of functional properties rather than on the basis of
genetic

relatedness. New alignment matrices and classification systems based on structural core
connectivity and cleavage mechanisms have been developed to characterize new REs and

related
proteins. REs recognizing more than 300 distinct specificities have been identified in RE
database

(REBASE: http://rebase.neb.com/cgi
-
bin/statlist) but still the need for newer specificities is increasing
due to the advancement in molecular biolog
y and applications. The enzymes have undergone
constant evolution through structural changes in protein scaffolds which include random mutations,
homologous recombinations, insertions, and deletions of coding DNA sequences but rational
mutagenesis or direc
ted evolution delivers protein variants with new functions in accordance with
defined biochemical or environmental pressures. Redesigning through random mutation, addition or
deletion of amino acids, methylation
-
based selection, synthetic molecules, combin
ing recognition and
cleavage domains from different enzymes, or combination with domains of additional functions
change the cleavage specificity or substrate preference and stability. There is a growing number of
patents awarded for the creation of enginee
red REs with new and enhanced properties.

Accession Number:

WOS:000302283700003

Document Type:

Review

Language:

English

Author Keywords:

Restriction enzymes;
Engineering
; Evolution; Mutation; Applications

KeyWords Plus:

ZINC
-
FINGER NUCLEASES; SEQ
UENCE
-
SPECIFIC CLEAVAGE; DNA
-
BINDING;
NICKING ENDONUCLEASES; RECOGNITION SEQUENCE; MODIFICATION ENZYMES; HOMING
ENDONUCLEASE; MODIFICATION SYSTEM; CRYSTAL
-
STRUCTURE; MAMMALIAN
-
CELLS

Reprint Address:

Sharma, P (reprint author), Panjab Univ, Dept Microbiol
, Chandigarh 160014,
India.

Addresses:


1. Panjab Univ, Dept Microbiol, Chandigarh 160014, India

2. Panjab Univ, Dept Biotechnol, Chandigarh 160014, India

E
-
mail Address:

princess@pu.ac.in


Funding:

Funding
Agency

Grant Number

Department of Biotechnology, New Delhi, India





[Show funding text]





Publisher:

SPRINGER, 233 SPRING ST, NEW YORK, NY 10013 USA

Web of Science Categories:

Biotechnology & Applied Microbiology

Research Areas:

Biotechnology & Applied Microbiology

IDS Number:

918XB

ISSN:

0175
-
7598