23
98. Guntas G, Mitchell SF, Ostermeier M (2004)
A molecular switch created by in vitro
recombination of nonhomologous genes.
Chem Biol 11:1483–1487. doi:10.1016/j.
chembiol.2004.08.020
99. Ribeiro LF, Tullman J, Nicholes N et al (2016)
A xylose-stimulated xylanase–xylose binding
protein chimera created by random nonhomologous recombination. Biotechnol Biofuels
9:119. doi:10.1186/s13068-016-0529-7
100. Wright CM, Wright RC, Eshleman JR,
Ostermeier M (2011) A protein therapeutic
modality founded on molecular regulation.
Proc Natl Acad Sci 108:16206–16211.
doi:10.1073/pnas.1102803108
101. Yon F, Fried M (1989) Precise gene fusion by
PCR. Nucleic Acids Res 17:4145–4159
102. Yolov AA, Shabarova ZA (1990) Constructing
DNA by polymerase recombination. Nucleic
Acids Res 18:3983–3986. doi:10.1093/
nar/18.13.3983
103. Ohlendorf R, Schumacher CH, Richter F,
Möglich A (2016) Library-aided probing of
linker determinants in hybrid photoreceptors.
ACS
Synth
Biol
5(10):1117–1126.
doi:10.1021/acssynbio.6b00028
104. Gibson DG, Young L, Chuang R-Y et al
(2009) Enzymatic assembly of DNA molecules
up to several hundred kilobases. Nat Methods
6:343–345. doi:10.1038/nmeth.1318
105. Li MZ, Elledge SJ (2007) Harnessing homologous recombination in vitro to generate
recombinant DNA via SLIC. Nat Methods
4:251–256. doi:10.1038/nmeth1010
106. Quan J, Tian J (2009) Circular polymerase
extension cloning of complex gene libraries
and pathways. PLoS One 4:e6441.
doi:10.1371/journal.pone.0006441
107. Zhang Y, Werling U, Edelmann W (2012)
SLiCE: a novel bacterial cell extract-based
DNA cloning method. Nucleic Acids Res
40(8):e55. doi:10.1093/nar/gkr1288
108. Beyer HM, Gonschorek P, Samodelov SL
et al (2015) AQUA cloning: a versatile and
simple enzyme-free cloning approach. PLoS
One 10(9):e0137652. doi:10.1371/journal.
pone.0137652
109. Engler C, Kandzia R, Marillonnet S (2008) A
one pot, one step, precision cloning
method with high throughput capability.
PLoS One 3(11):e3647. doi:10.1371/journal.pone.0003647
110. Geu-Flores F, Nour-Eldin HH, Nielsen MT,
Halkier BA (2007) USER fusion: a rapid and
efficient method for simultaneous fusion and
cloning of multiple PCR products. Nucleic
Acids Res 35(7):e55. doi:10.1093/nar/
gkm106
111. Bitinaite J, Rubino M, Varma KH et al (2007)
USER friendly DNA engineering and cloning
method by uracil excision. Nucleic Acids Res
35:1992–2002. doi:10.1093/nar/gkm041
112. Nour-Eldin HH, Hansen BG, Nørholm
MHH et al (2006) Advancing uracil-excision
based cloning towards an ideal technique for
cloning PCR fragments. Nucleic Acids Res
34(18):e122. doi:10.1093/nar/gkl635
113. Stein V, Hollfelder F (2009) An efficient
method to assemble linear DNA templates for
in vitro screening and selection systems.
Nucleic Acids Res 37(18):e122. doi:10.1093/
nar/gkp589
114. Villiers BRM, Stein V, Hollfelder F (2010)
USER
friendly
DNA
recombination
(USERec): a simple and flexible near
homology- independent method for gene
library construction. Protein Eng Des Sel
23:1–8. doi:10.1093/protein/gzp063
115. Vinkenborg JL, Evers TH, Reulen SWA et al
(2007) Enhanced sensitivity of FRET-based
protease sensors by redesign of the GFP
dimerization
interface.
Chembiochem
8:1119–1121. doi:10.1002/cbic.200700109
116. Ohashi T, Galiacy SD, Briscoe G, Erickson
HP (2007) An experimental study of GFPbased FRET, with application to intrinsically
unstructured proteins. Protein Sci 16:1429–
1438. doi:10.1110/ps.072845607
117. Janssen BMG, Engelen W, Merkx M (2015)
DNA-directed control of enzyme-inhibitor
complex formation: a modular approach to
reversibly switch enzyme activity. ACS Synth
Biol 4:547–553. doi:10.1021/sb500278z
118. Banala S, Aper SJA, Schalk W, Merkx M
(2013) Switchable reporter enzymes based on
mutually exclusive domain interactions allow
antibody detection directly in solution. ACS
Chem Biol 8:2127–2132. doi:10.1021/
cb400406x
119. Smith GP (1985) Filamentous fusion phage:
novel expression vectors that display cloned antigens on the virion surface. Science 228:1315–
1317. doi:10.1126/science.4001944
120. Boder ET, Wittrup KD (1997) Yeast surface
display for screening combinatorial polypeptide libraries. Nat Biotechnol 15:553–557.
doi:10.1038/nbt0697-553
121. Gai SA, Wittrup KD (2007) Yeast surface display for protein engineering and characterization. Curr Opin Struct Biol 17:467–473.
doi:10.1016/j.sbi.2007.08.012
122. Wilson DS, Keefe AD, Szostak JW (2001)
The use of mRNA display to select highaffinity protein-binding peptides. Proc Natl
Acad Sci U S A 98:3750–3755. doi:10.1073/
pnas.061028198
Engineering Synthetic Protein Switches
98. Guntas G, Mitchell SF, Ostermeier M (2004)
A molecular switch created by in vitro
recombination of nonhomologous genes.
Chem Biol 11:1483–1487. doi:10.1016/j.
chembiol.2004.08.020
99. Ribeiro LF, Tullman J, Nicholes N et al (2016)
A xylose-stimulated xylanase–xylose binding
protein chimera created by random nonhomologous recombination. Biotechnol Biofuels
9:119. doi:10.1186/s13068-016-0529-7
100. Wright CM, Wright RC, Eshleman JR,
Ostermeier M (2011) A protein therapeutic
modality founded on molecular regulation.
Proc Natl Acad Sci 108:16206–16211.
doi:10.1073/pnas.1102803108
101. Yon F, Fried M (1989) Precise gene fusion by
PCR. Nucleic Acids Res 17:4145–4159
102. Yolov AA, Shabarova ZA (1990) Constructing
DNA by polymerase recombination. Nucleic
Acids Res 18:3983–3986. doi:10.1093/
nar/18.13.3983
103. Ohlendorf R, Schumacher CH, Richter F,
Möglich A (2016) Library-aided probing of
linker determinants in hybrid photoreceptors.
ACS
Synth
Biol
5(10):1117–1126.
doi:10.1021/acssynbio.6b00028
104. Gibson DG, Young L, Chuang R-Y et al
(2009) Enzymatic assembly of DNA molecules
up to several hundred kilobases. Nat Methods
6:343–345. doi:10.1038/nmeth.1318
105. Li MZ, Elledge SJ (2007) Harnessing homologous recombination in vitro to generate
recombinant DNA via SLIC. Nat Methods
4:251–256. doi:10.1038/nmeth1010
106. Quan J, Tian J (2009) Circular polymerase
extension cloning of complex gene libraries
and pathways. PLoS One 4:e6441.
doi:10.1371/journal.pone.0006441
107. Zhang Y, Werling U, Edelmann W (2012)
SLiCE: a novel bacterial cell extract-based
DNA cloning method. Nucleic Acids Res
40(8):e55. doi:10.1093/nar/gkr1288
108. Beyer HM, Gonschorek P, Samodelov SL
et al (2015) AQUA cloning: a versatile and
simple enzyme-free cloning approach. PLoS
One 10(9):e0137652. doi:10.1371/journal.
pone.0137652
109. Engler C, Kandzia R, Marillonnet S (2008) A
one pot, one step, precision cloning
method with high throughput capability.
PLoS One 3(11):e3647. doi:10.1371/journal.pone.0003647
110. Geu-Flores F, Nour-Eldin HH, Nielsen MT,
Halkier BA (2007) USER fusion: a rapid and
efficient method for simultaneous fusion and
cloning of multiple PCR products. Nucleic
Acids Res 35(7):e55. doi:10.1093/nar/
gkm106
111. Bitinaite J, Rubino M, Varma KH et al (2007)
USER friendly DNA engineering and cloning
method by uracil excision. Nucleic Acids Res
35:1992–2002. doi:10.1093/nar/gkm041
112. Nour-Eldin HH, Hansen BG, Nørholm
MHH et al (2006) Advancing uracil-excision
based cloning towards an ideal technique for
cloning PCR fragments. Nucleic Acids Res
34(18):e122. doi:10.1093/nar/gkl635
113. Stein V, Hollfelder F (2009) An efficient
method to assemble linear DNA templates for
in vitro screening and selection systems.
Nucleic Acids Res 37(18):e122. doi:10.1093/
nar/gkp589
114. Villiers BRM, Stein V, Hollfelder F (2010)
USER
friendly
DNA
recombination
(USERec): a simple and flexible near
homology- independent method for gene
library construction. Protein Eng Des Sel
23:1–8. doi:10.1093/protein/gzp063
115. Vinkenborg JL, Evers TH, Reulen SWA et al
(2007) Enhanced sensitivity of FRET-based
protease sensors by redesign of the GFP
dimerization
interface.
Chembiochem
8:1119–1121. doi:10.1002/cbic.200700109
116. Ohashi T, Galiacy SD, Briscoe G, Erickson
HP (2007) An experimental study of GFPbased FRET, with application to intrinsically
unstructured proteins. Protein Sci 16:1429–
1438. doi:10.1110/ps.072845607
117. Janssen BMG, Engelen W, Merkx M (2015)
DNA-directed control of enzyme-inhibitor
complex formation: a modular approach to
reversibly switch enzyme activity. ACS Synth
Biol 4:547–553. doi:10.1021/sb500278z
118. Banala S, Aper SJA, Schalk W, Merkx M
(2013) Switchable reporter enzymes based on
mutually exclusive domain interactions allow
antibody detection directly in solution. ACS
Chem Biol 8:2127–2132. doi:10.1021/
cb400406x
119. Smith GP (1985) Filamentous fusion phage:
novel expression vectors that display cloned antigens on the virion surface. Science 228:1315–
1317. doi:10.1126/science.4001944
120. Boder ET, Wittrup KD (1997) Yeast surface
display for screening combinatorial polypeptide libraries. Nat Biotechnol 15:553–557.
doi:10.1038/nbt0697-553
121. Gai SA, Wittrup KD (2007) Yeast surface display for protein engineering and characterization. Curr Opin Struct Biol 17:467–473.
doi:10.1016/j.sbi.2007.08.012
122. Wilson DS, Keefe AD, Szostak JW (2001)
The use of mRNA display to select highaffinity protein-binding peptides. Proc Natl
Acad Sci U S A 98:3750–3755. doi:10.1073/
pnas.061028198
Engineering Synthetic Protein Switches