Molecular knots in biology and chemistry

Journal of Physics Condensed Matter

Volumn 27, Issue 35, 2015, Pages

  Lim, Nicole C H ^a,b   Jackson, Sophie E ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITI BRUNEI DARUSSALAM   (Brunei Darussalam)

Author keywords

DNA knots; protein knots; protein slipknots; RNA pseudoknots; synthetic knots

Indexed keywords

PROTEINS; RNA; TOPOLOGY;

AESTHETIC APPEALS; COMPUTATIONAL STUDIES; MOLECULAR KNOTS; NATURALLY OCCURRING; PSEUDO-KNOTS; SYNTHETIC CHEMISTS; SYNTHETIC KNOTS; TOPOLOGICAL ENTITY;

NUCLEIC ACIDS;

BIOMATERIAL; MACROMOLECULE;

BIOPHYSICS; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; MACROMOLECULE; PROCEDURES;

BIOCOMPATIBLE MATERIALS; BIOPHYSICS; HUMANS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR;

EID: 84939644993     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/27/35/354101     Document Type: Article

References (292)

1. Airas U and Heinonen S 2002 Clinical significance of true umbilical knots: a population-based analysis Am. J. Perinatol. 19 127-32
2. (http://shortwhitecoats.com/2011/how-to-suture-a-wound-a-video-tutorial - ref-separator -
3. (www.womansday.com/style-beauty/fashion-style/how-to-tie-a-reef-knot)-118095 - slide-1 - ref-separator -
4. (http://library.med.utah.edu/WebPath/PLACHTML/PLAC028.html) - ref-separator -
5. Stray J E, Crisona N J, Belotserkovskii B P, Lindsley J E and Cozzarelli N R 2005 The saccharomyces cerevisiae Smc2/4 condensin compacts DNA into (+) chiral structures without net supercoiling J. Biol. Chem. 280 34723-34
6. Ponnuswamy N, Cougnon F B L, Clough J M, Pantoş G D and Sanders J K M 2012 Discovery of an organic trefoil knot Science 338 783-5
7. Arsuaga J, Vazquez M, McGuirk P, Trigueros S, Sumners D W L and Roca J 2005 DNA knots reveal a chiral organization of DNA in phage capsids Proc. Natl Acad. Sci. USA 102 9165-9
8. Buck D 2009 DNA topology Proc. Symp. in Applied Mathematics vol 66 ed D Buck and E Flapan (Providence, RI: American Mathematical Society) pp 1-33
9. Dean F B, Stasiak A, Koller T and Cozzarelli N R 1985 Duplex DNA knots produced by E. coli topoisomerase I. Structure and requirements for formation J. Biol. Chem. 260 4975-83
10. Giedroc D P and Cornish P V 2009 Frameshifting RNA pseudoknots: structure and mechanism Virus Res. 139 193-208
11. Gultyaev A P, Olsthoorn R C L, Pleij C W A and Westhof E 2012 RNA Structure: Pseudoknots. eLS (Chichester: Wiley)
12. Jackson S E 2012 Characterising the folding pathways of topologically knotted proteins Curr. Phys. Chem. 2 59-78
13. Mallam A L 2009 How does a knotted protein fold? Febs J. 276 365-75
14. Staple D W and Butcher S E 2005 Pseudoknots: RNA structures with diverse functions PLoS Biol. 3 e213
15. Virnau P, Mallam A and Jackson S 2011 Structures and folding pathways of topologically knotted proteins J. Phys.: Condens. Matter 23 033101
16. Ayme J-F, Beves J E, Campbell C J and Leigh D A 2013 Template synthesis of molecular knots Chem. Soc. Rev. 42 1700-12
17. Forgan R S, Sauvage J-P and Stoddart J F 2011 Chemical topology: complex molecular knots, links and entanglements Chem. Rev. 111 5434-64
18. Adams C C 2004 The Knot Book: An Elementary Introduction to the Mathematical Theory of Knots (Providence, RI: American Mathematical Society)
19. Mishra R and Bhushan S 2011 Knot theory in understanding proteins J. Math. Biol. 65 1187-213
20. Freyd P, Yetter D, Hoste J, Lickorish W B R, Millett K C and Ocneanu A 1985 A new polynomial invariant of knots and links Bull. Am. Math. Soc. 12 239-46
21. Jones V F R 1985 A polynomial invariant for knots via von neumann algebras Bull. Am. Math. Soc. 12 103-11
22. Ganzell S and Kapp A V 2008 Chirality versus HOMFLY and Kauffman polynomials J. Knot Theory Ramifications 17 1519
23. Ramadevi P, Govindarajan T R and Kaul R K 1994 Chirality of knots 942 and 1071 and Chern-Simons theory Mod. Phys. Lett. A 9 3205-17
24. Taylor W R and Lin K 2003 Protein knots: a tangled problem Nature 421 25
25. Koniaris K and Muthukumar M 1991 Self-entanglement in ring polymers J. Chem. Phys. 95 2873-81
26. Taylor W R 2000 A deeply knotted protein structure and how it might fold Nature 406 916-9
27. Khatib F, Weirauch M T and Rohl C A 2006 Rapid knot detection and application to protein structure prediction Bioinformatics 22 e252-9
28. Millett K C, Dobay A and Stasiak A 2005 Linear random knots and their scaling behavior Macromolecules 38 601-6
29. Watson J D and Crick F H C 1953 A structure for deoxyribose nucleic acid Nature 171 737-8
30. Liu L F, Depew R E and Wang J C 1976 Knotted single-stranded DNA rings: a novel topological isomer of circular single-stranded DNA formed by treatment with E.coli omega protein J. Mol. Biol. 106 439-52
31. Liu L F, Perkocha L, Calendar R and Wang J C 1981 Knotted DNA from bacteriophage capsids Proc. Natl Acad. Sci. USA 78 5498-502
32. Deweese J E, Osheroff M A and Osheroff N 2008 DNA topology and topoisomerases: teaching a 'knotty' subject Biochem. Mol. Biol. Educ. 37 2-10
33. Arsuaga J, Vazquez M, Trigueros S, Sumners D W L and Roca J 2002 Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids Proc. Natl Acad. Sci. USA 99 5373-7
34. Shaw S Y and Wang J C 1993 Knotting of a DNA chain during ring closure Science 260 533-6
35. Sogo J M, Stasiak A, Martinez-Robles M L, Krimer D B, Hernandez P and Schvartzman J B 1999 Formation of knots in partially replicated DNA molecules J. Mol. Biol. 286 637-43
36. Bates A D and Maxwell A 1997 DNA topology: topoisomerases keep it simple Curr. Biol. 7 R778-81
37. Bates A D and Maxwell A 2005 DNA Topology (Oxford: Oxford University Press)
38. Buck D and Flapan E 2007 Predicting knot or catenane type of site-specific recombination products J. Mol. Biol. 374 1186-99
39. Wasserman S A, Dungan J M and Cozzarelli N R 1985 Discovery of a predicted DNA knot substantiates a model for site-specific recombination Science 229 171-4
40. Valencia K and Buck D 2011 Predicting knot and catenane type of products of site-specific recombination on twist knot substrates J. Mol. Biol. 411 350-67
41. Grindley N D, Whiteson K L and Rice P A 2006 Mechanisms of site-specific recombination Annu. Rev. Biochem. 75 567-605
42. Witz G and Stasiak A 2010 DNA supercoiling and its role in DNA decatenation and unknotting Nucl. Acids Res. 38 2119-33
43. Olavarrieta L, Hernandez P, Krimer D B and Schvartzman J B 2002 DNA knotting caused by head-on collision of transcription and replication J. Mol. Biol. 322 1-6
44. Lopez V, Martinez-Robles M L, Hernandez P, Krimer D B and Schvartzman J B 2012 Topo IV is the topoisomerase that knots and unknots sister duplexes during DNA replication Nucl. Acids Res. 40 3563-73
45. Liu L F, Davis J L and Calendar R 1981 Novel topologically knotted DNA from bacteriophage P4 capsids: studies with DNA topoisomerases Nucl. Acids Res. 9 3979-89
46. Wolfson J S, McHugh G L, Hooper D C and Swartz M N 1985 Knotting of DNA molecules isolated from deletion mutants of intact bacteriophage P4 Nucl. Acids Res. 13 6695-702
47. Isaken M, Julien B, Calendar R and Lindgvist B H 1999 Isolation of knotted DNA from coliphage P4 Methods Mol. Biol. 94 69-74
48. Micheletti C, Marenduzzo D, Orlandini E and Sumners D W L 2008 Simulations of knotting in confined circular DNA Biophys. J. 95 3591-9
49. Rollins G C, Petrov A S and Harvey S C 2008 The role of DNA twist in the packaging of viral genomes Biophys. J. 94 L38-40
50. Ashley C and Lee J S 2000 A triplex-mediated knot between separated polypurine-polyrimidine tracts in circular DNA blocks transcription by E.coli RNA polymerase DNA Cell Biol. 19 235-41
51. Portugal J and Rodriguez Campos A 1996 T7 RNA polymerase cannot transcribe through a highly knotted DNA template Nucl. Acids Res. 24 4890-94
52. Deibler R W, Mann J K, Sumners D W L and Zechiedrich E L 2007 Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation BMC Mol. Biol. 8 44
53. Buck G R and Zechiedrich E L 2004 DNA disentangling by type-2 topoisomerases J. Mol. Biol. 340 933-9
54. Deibler R W, Rahmati S and Zechiedrich E L 2001 Topoisomerase IV, alone, unkots DNA in E. coli Genes Dev. 15 748-61
55. Marenduzzo D, Micheletti C, Orlandini E and Sumners D W L 2013 Topological friction strongly affects viral DNA ejection Proc. Natl Acad. Sci. USA 110 20081-6
56. Mann J K 2007 DNA knotting: occurrences, consequences and resolution Electronic Theses, Treatises and Dissertations Paper 2754
57. Mirkin S M 2001 DNA topology: fundamentals Encyclopedia of Life Sciences (London: Nature Publishing Group) pp 1-11
58. Schvartzman J B, Martinez-Robles M L, Hernandez P and Krimer D B 2013 The benefit of DNA supercoiling during replication Biochem. Soc. Trans. 41 646-51
59. Doudna J A and Cate J H 1997 RNA structure: crystal clear? Curr. Opin. Struct. Biol. 7 310-6
60. Hermann T and Patel D J 1999 Stitching together RNA tertiary architectures J. Mol. Biol. 294 829-49
61. Rietveld K, van Poelgeest R, Pleij C W A, van Boom J H and Bosch L 1982 The tRNA-like structure at the 3′ terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA Nucl. Acids Res. 10 1929-46
62. Pleij C W A, Rietveld K and Bosch L 1985 A new principle of RNA folding based on pseudoknotting Nucl. Acids Res. 13 1717-31
63. Westhof E and Jaeger L 1992 RNA pseudoknots Curr. Opin. Struct. Biol. 2 327-33
64. Kim N, Shiffeldrim N, Gan H H and Schlick T 2004 Candidates for novel RNA topologies J. Mol. Biol. 341 1129-44
65. Ke A, Zhou K, Ding F, Cate J H and Doudna J A 2004 A conformational switch controls hepatitis delta virus ribozyme catalysis Nature 429 201-5
66. Theimer C A, Blois C A and Feigon J 2005 Structure of the human telomerase RNA pseudokont reveals conserved tertiary interactions essential for function Mol. Cell 17 671-82
67. Baril M, Dulude D, Steinberg S V and Brakier-Gingras L 2003 The frameshift stimulatory signal of human immunodeficiency virus type 1 group O is a pseudoknot J. Mol. Biol. 331 571-83
68. Brierley I, Gilbert R J C and Pennell S 2008 RNA pseudoknots and the regulation of protein synthesis Biochem. Soc. Trans. 36 684-9
69. Brierley I, Pennell S and Gilbert R J C 2007 Viral RNA pseudoknots: versatile motifs in gene expression and replication Nat. Rev. Microbiol. 5 598-610
70. Mans R M W, Pleij C W A and Bosch L 1991 Transfer RNA-like structures: structure, function and evolutionary significance Eur. J. Biochem. 201 303-24
71. Michel F and Westhof E 1990 Modelling of the 3D architecture of group I catalytic introns based on comparative sequence analysis J. Mol. Biol. 216 585-610
72. Thill G, Vasseur M and Tanner N K 1993 Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme Biochemistry 32 4254-62
73. Wadkins T S, Perrotta A T, Ferre-D'Amare A R, Doudna J A and Been M D 1999 A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes RNA 5 720-7
74. Tanaka Y, Hori T, Tagaya M, Sakamoto T, Kurihara Y, Katahira M and Uesugi S 2002 Imino proton NMR analysis of HDV ribozymes: nested double pseudoknot structure and Mg2+ ion-binding site close to the catalytic core in solution Nucl. Acids Res. 30 766-74
75. Lai M M 1995 The molecular biology of hepatitis delta virus Annu. Rev. Biochem. 64 259-86
76. Kuo M Y, Sharmeen L, Dinter-Gottlieb G and Taylor J 1988 Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus J. Virol. 62 4439-44
77. Ferre-D'Amare A R, Zhou K and Doudna J A 1998 Crystal structure of a hepatitis delata virus ribozyme Nature 395 567-74
78. Ferré-D'Amaré A R and Scott W G 2010 Small self-cleaving ribozymes Cold Spring Harb. Perspect. Biol. 2 a003574
79. Klein D J and Ferre-D'Amare A R 2006 Structural basis of glmS ribozyme activation by glucosamine-6-phosphate Science 313 1752-6
80. Salehi-Ashtiani K, Luptak A, Litovchick A and Szostak J W 2006 A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene Science 313 1788-92
81. Cech T R 2004 Beginning to understand the end of the chromosome Cell 116 273-9
82. Blackburn E H 2001 Switching and signalling at the telomere Cell 106 661-73
83. Blackburn E H and Collins K 2011 Telomerase: an RNP enzyme synthesizes DNA Cold Spring Harb. Perspect. Biol. 3 a003558
84. Shay J W and Wright W E 2006 Telomerase therapeutics for cancer: challenges and new directions Nat. Rev. Drug Discovery 5 577-84
85. Wong J M and Collins K 2003 Telomere maintenance and disease Lancet 362 983-8
86. Marciniak R A, Johnson F B and Guarente L 2000 Dyskeratosis congenita, telomeres and human ageing Trends Genetics 16 193-5
87. Chen J L, Blasco M A and Greider C W 2000 Secondary structure of vertebrate telomerase RNA Cell 100 503-14
88. Collins K 2006 The biogenesis and regulation of telomerase holoenzymes Nat. Rev. Mol. Cell Biol. 7 484-94
89. Gilley D and Blackburn E H 1999 The telomerase RNA pseudoknot is critical for the stable assembly of a catalytically active ribonucleoprotein Proc. Natl Acad. Sci. USA 96 6621-5
90. Tzfati Y, Knight Z, Roy J and Blackburn E H 2003 A novel pseudoknot element is essential for the action of a yeast telomerase Genes Dev. 17 1779-988
91. Comolli L R, Smirnov I, Xu L, Blackburn E H and James T L 2002 A molecular switch underlies a human telomerase disease Proc. Natl Acad. Sci. USA 99 16998-7003
92. Theimer C A, Finger L D, Trantirek L and Feigon J 2003 Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA Proc. Natl Acad. Sci. USA 100 449-54
93. Chen J L and Greider C W 2004 Telomerase RNA structure and function: implications for dyskeratosis congenita Trends Biochem. Sci. 29 183-92
94. Vulliamy T, Marrone A, Dokal I and Mason P J 2002 Association between aplastic anaemia and mutations in telomerase RNA Lancet 359 2168-70
95. Gesteland R F and Atkins J F 1996 Recoding: dynamic reprogramming of translation Annu. Rev. Biochem. 65 741-68
96. ten Dam E B, Pleij C W A and Bosch L 1990 RNA pseudoknots: translational frameshifting and readthrough on viral RNAs Virus Genes 4 121-36
97. Brierley I 1995 Ribosomal frameshifting viral RNAs J. Genetic Virol. 76 1885-92
98. Giedroc D P, Theimer C A and Nixon P L 2000 Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting J. Mol. Biol. 298 167-85
99. Somogyi P, Jenner A J, Brierley I and Inglis S C 1993 Ribosomal pausing during translation of an RNA pseudoknot Mol. Cell Biol. 13 6931-40
100. Takyar S, Hickerson R P and Noller H F 2005 mRNA helicase activity of the ribosome Cell 120 49-58
101. Plant E P and Dinman J D 2005 Torsional restraint: a new twist on frameshifting pseudoknots Nucl. Acids Res. 33 1825-33
102. Plant E P, Muldoon Jacobs K L, Harger J W, Meskauskas A, Jacobs J L, Baxter J L, Petrov A N and Dinman J D 2003 The 9 solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting RNA 9 168-74
103. Shen L X and Tinoco I 1995 The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus J. Mol. Biol. 247 963-78
104. Chen X, Kang H, Shen L X, Chamorro M, Varmus H E and Tinoco I 1996 A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNA J. Mol. Biol. 260 479-83
105. Michiels P J, Versleijen A A, Verlaan P W, Pleij C W A, Hilbers C W and Heus H A 2001 Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting J. Mol. Biol. 310 1109-23
106. Berry K E, Waghray S, Mortimer S A, Bai Y and Doudna J A 2011 Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning Structure 19 1456-66
107. Lukavsky P J 2009 Structure and function of HCV IRES domains Virus Res. 139 166-71
108. Niepmann M 2013 Hepatitis C virus RNA translation Hepatitis C Virus L from Molecular Virology to Antiviral Therapy, Current Topics in Microbiology and Immunology vol 369 ed R Bartenschlager (Berlin: Springer) pp 143-66
109. Berry K E, Waghray S and Doudna J A 2010 The HCV IRES pseudoknot positions the initiation codon on the 40S ribosomal subunit RNA 16 1559-69
110. Dreher T W and Miller W A 2006 Translational control in positive strand RNA plant viruses Virology 344 185-97
111. Kaur S, Gillet R, Li W, Gursky R and Frank J 2006 Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome Proc. Natl Acad. Sci. USA 103 16484-9
112. Keiler K C, Waller P R and Sauer R T 1996 Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA Science 271 990-3
113. Akutsu T 2000 Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots Discrete Appl. Math. 104 45-62
114. Rivas E and Eddy S R 1999 A dynamic programming algorithm for RNA structure prediction including pseudoknots J. Mol. Biol. 285 2053-68
115. Dirks R M and Pierce N A 2003 A partition function algorithm for nucleic acid secondary structure including pseudoknots J. Comput. Chem. 24 1664-77
116. Reeder J, Steffen P and Giegerich R 2007 pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows Nucl. Acids Res. 35 W320-4
117. Lyngsø R B and Pedersen C N 2000 RNA pseudoknot prediction in energy-based models J. Comput. Biol. 7 409-27
118. Chen X, He S M, Bu D, Zhang F, Wang Z, Chen R and Gao W 2008 FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space Bioinformatics 24 1994-2001
119. Andronescu M S, Pop C and Condon A E 2010 Improved free energy parameters for RNA pseudoknotted secondary structure prediction RNA 16 26-42
120. Sato K, Kato Y, Hamada M, Akutsu T and Asai K 2011 IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming Bioinformatics 27 i85-93
121. Bon M and Orland H 2011 TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots Nucl. Acids Res. 39 e93
122. Bon M, Micheletti C and Orland H 2013 McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots Nucl. Acids Res. 41 1895-900
123. Jabbari H and Condon A 2014 A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures BMC Bioinf. 15 1-17
124. Moss W N 2013 Computational prediction of RNA secondary structure Methods Enzymol. 530 3-65
125. Shapiro B A, Yingling Y G, Kasprzak W and Bindewald E 2007 Bridging the gap in RNA structure prediction Curr. Opin. Struct. Biol. 17 157-65
126. Akutsu T 2006 Recent advances in RNA secondary structure prediction with pseudoknots Curr. Bioinf. 1 115-29
127. van Batenburg F H D, Gultyaev A P, Pleij C W A, Ng J and Oliehoek J 2000 Pseudobase: a database with RNA pseudoknots Nucl. Acids Res. 28 201-4
128. Ren J, Rastegari B, Condon A and Hoos H H 2005 HotKnots: heuristic prediction of RNA secondary structures including pseudoknots RNA 11 1494-504
129. Byun Y and Han K 2006 Pseudoviewer: web application and web service for visualising RNA pseudoknots and secondary structures Nucl. Acids Res. 34 W416-22
130. Metzler D and Nebel M E 2008 Predicting RNA secondary structures with pseudoknots by MCMC sampling J. Math. Biol. 56 161-81
131. Bellaousov S and Matthews D H 2010 ProbKnot: fast prediction of RNA secondary structure including pseudoknots RNA 16 1870-80
132. Wang H, Di Gate R J and Seeman N C 1996 An RNA topoisomerase Proc. Natl Acad. Sci. USA 93 9477-82
133. Cao Z, Roszak A W, Gourlay L J, Lindsay J G and Isaacs N W 2005 Bovine mitochondrial peroxiredoxin III forms a two-ring catenane Structure 13 1661-4
134. Boutz D R, Cascio D, Whitelegge J, Perry L J and Yeates T O 2007 Discovery of a thermophilic protein complex stabilized by topologically interlinked chains J. Mol. Biol. 368 1332-44
135. Haglund E, Sulkowska J I, Noel J K, Lammert H, Onuchic J N and Jennings P A 2014 Pierced lasso bundles are a new class of knot-like motifs Plos Comput. Biol. 10 e1003613
136. McDonald N Q and Hendrickson W A 1993 A structural superfamily of growth factors containing a cystine knot motif Cell 73 421-4
137. Craik D J, Daly N L and Waine C 2001 The cystine knot motif in toxins and implications for drug design Toxicon 39 43-60
138. Craik D J, Cemazar M, Wang C K and Daly N L 2006 The cyclotide family of circular miniproteins: nature's combinatorial peptide template Biopolymers 84 250-66
139. Taylor W R 2007 Protein knots and fold complexity: some new twists Comput. Biol. Chem. 31 151-62
140. King N P, Yeates E O and Yeates T O 2007 Identification of rare slipknots in proteins and their implications for stability and folding J. Mol. Biol. 373 153-66
141. Noel J K, Sulkowska J I and Onuchic J N 2010 Slipknotting upon native-like loop formation in a trefoil knot protein Proc. Natl Acad. Sci. USA 107 15403-8
142. Sulkowska J I, Rawdon E J, Millett K C, Onuchic J N and Stasiak A 2012 Conservation of complex knotting and slipknotting patterns in proteins Proc. Natl Acad. Sci. USA 109 E1715-23
143. Burman R, Gunasekera S, Stromstedt A A and Goransson U 2014 Chemistry and biology of cyclotides: circular plant peptides outside the box J. Nat. Prod. 77 724-36
144. Craik D J, Cemazar M and Daly N L 2007 The chemistry and biology of cyclotides Curr. Opin. Drug Discovery Dev. 10 176-84
145. Iyer S and Acharya K R 2011 Tying the knot: the cystine signature and molecular-recognition processes of the vascular endothelial growth factor family of angiogenic cytokines FEBS J. 278 4304-22
146. Jiang X, Dias J A and He X 2014 Structural biology of glycoprotein hormones and their receptors: insights to signaling Mol. Cell Endocrinol. 382 424-51
147. Mansfield M L 1994 Are there knots in proteins? Nat. Struct. Biol. 1 213-4
148. Lua R C and Grosberg A Y 2006 Statistics of knots, geometry of conformations, and evolution of proteins PLoS Comput. Biol. 2 e45
149. Virnau P, Mirny L A and Kardar M 2006 Intricate knots in proteins: function and evolution Plos Comput. Biol. 2 1074-9
150. Lai Y, Chen C and Hwang J K 2012 pKNOT v.2: the protein KNOT web server Nucl. Acids Res. 40 W228-31
151. Kolesov G, Virnau P, Kardar M and Mirny L A 2007 Protein knot server: detection of knots in protein structures Nucl. Acids Res. 35 W425-8
152. Jamroz M, Niemyska W, Rawdon E J, Stasiak A, Millett K C, Sulkowski P and Sulkowska J I 2014 KnotProt: a database of proteins with knots and slipknots Nucl. Acids Res. 43(DI) D306-14
153. Rawdon E J, Millett K C, Sulkowska J I and Stasiak A 2013 Knot localization in proteins Biochem. Soc. Trans. 41 538-41
154. Bölinger D, Sulkowska J I, Hsu H-P, Mirny L A, Kardar M, Onuchic J N and Virnau P 2010 A Stevedore's protein knot Plos Comput. Biol. 6 e1000731
155. Takusagawa F, Kamitori S and Markham G D 1996 Structure and function of S-adenosylmethionine synthetase: crystal structures of S-adenosylmethionine synthetase with ADP, BrADP, and PPi at 28 angstroms resolution Biochemistry 35 2586-96
156. Takusagawa F, Kamitori S, Misaki S and Markham G D 1996 Crystal structure of S-adenosylmethionine synthetase J. Biol. Chem. 271 136-47
157. Ahn H J, Kim H W, Yoon H J, Lee B I, Suh S W and Yang J K 2003 Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition EMBO J. 22 2593-603
158. Finn R D et al 2014 Pfam: the protein families database Nucl. Acids Res. 42 D222-30
159. Chiang P K, Gordon R K, Tal J, Zeng G C, Doctor B P, Pardhasaradhi K and McCann P P 1996 S-adenosylmethionine and methylation FASEB J. 10 471-80
160. Lim K, Zhang H, Tempczyk A, Krajewski W, Bonander N, Toedt J, Howard A, Eisenstein E and Herzberg O 2003 Structure of the YibK methyltransferase from haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot Proteins-Struct. Funct. Genetics 51 56-67
161. Nureki O et al 2002 An enzyme with a deep trefoil knot for the active-site architecture Acta Crystallogr. D Biol. Crystallogr. 58 1129-37
162. Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H and Yokoyama S 2004 Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme Structure 12 593-602
163. Zarembinski T I, Kim Y, Peterson K, Christendat D, Dharamsi A, Arrowsmith C H, Edwards A M and Joachimiak A 2003 Deep trefoil knot implicated in RNA binding found in an archaebacterial protein Proteins 50 177-83
164. Shi D, Morizono H, Yu X, Roth L, Caldovic L, Allewell N M, Malamy M H and Tuchman M 2005 Crystal structure of N-acetylornithine transcarbamylase from xanthomonas campestris: a novel enzyme in a new arginine biosynthetic pathway found in several eubacteria J. Biol. Chem. 280 14366-9
165. Shi D, Gallegos R, DePonte J 3rd, Morizono H, Yu X, Allewell N M, Malamy M and Tuchman M 2002 Crystal structure of a transcarbamylase-like protein from the anaerobic bacterium bacteroides fragilis at 2.0 a resolution J. Mol. Biol. 320 899-908
166. van Roon A M, Loening N M, Obayashi E, Yang J C, Newman A J, Hernandez H, Nagai K and Neuhaus D 2008 Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif Proc. Natl Acad. Sci. USA 105 9621-6
167. Biou V, Dumas R, Cohen-Addad C, Douce R, Job D and Pebay-Peyroula E 1997 The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 A resolution EMBO J. 16 3405-15
168. Leung E W and Guddat L W 2009 Conformational changes in a plant ketol-acid reductoisomerase upon Mg(2+) and NADPH binding as revealed by two crystal structures J. Mol. Biol. 389 167-82
169. Das C, Hoang Q Q, Kreinbring C A, Luchansky S J, Meray R K, Ray S S, Lansbury P T, Ringe D and Petsko G A 2006 Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1 Proc. Natl Acad. Sci. USA 103 4675-80
170. Johnston S C, Larsen C N, Cook W J, Wilkinson K D and Hill C P 1997 Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 a resolution EMBO J. 16 3787-96
171. Johnston S C, Riddle S M, Cohen R E and Hill C P 1999 Structural basis for the specificity of ubiquitin C-terminal hydrolases EMBO J. 18 3877-87
172. Wagner J R, Brunzelle J S, Forest K T and Vierstra R D 2005 A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome Nature 438 325-31
173. Wagner J R, Zhang J, Brunzelle J S, Vierstra R D and Forest K T 2007 High resolution structure of Deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution J. Biol. Chem. 282 12298-309
174. Yeates T, Norcross T S and King N P 2007 Knotted and topologically complex proteins as models for studying folding and stability Curr. Opin. Chem. Biol. 11 595-603
175. Bornschlogl T, Anstrom D M, Mey E, Dzubiella J, Rief M and Forest K T 2009 Tightening the knot in phytochrome by single-molecule atomic force microscopy Biophys. J. 96 1508-14
176. Soler M A, Nunes A and Faisca P F 2014 Effects of knot type in the folding of topologically complex lattice proteins J. Chem. Phys. 141 025101
177. Andersson F I, Werrell E F, McMorran L, Crone W J K, Das C, Hsu S-T D and Jackson S E 2011 The effect of parkinson's-disease-associated mutations on the deubiquitinating enzyme UCH-L1 J. Mol. Biol. 407 261-72
178. Sulkowska J I, Sulkowski P, Szymczak P and Cieplak M 2008 Stabilizing effect of knots on proteins Proc. Natl Acad. Sci. USA 105 19714-9
179. Sayre T C, Lee T M, King N P and Yeates T O 2011 Protein stabilization in a highly knotted protein polymer Protein Eng. Des. Sel.: PEDS 24 627-30
180. Soler M A and Faisca P F N 2013 Effects of knots on protein folding properties Plos One 8 e74755
181. Wang T and Ikai A 1999 Protein stretching III: force-extension curves of tethered bovine carbonic anhydrase B to the silicon substrate under native, intermediate and denaturing conditions Japan. J. Appl. Phys. 38 3912-7
182. Alam M T, Yamada T, Carlsson U and Ikai A 2002 The importance of being knotted: effects of the C-terminal knot structure on enzymatic and mechanical properties of bovine carbonic anhydrase II FEBS Lett. 519 35-40
183. Dzubiella J 2013 Tightening and untying the knot in human carbonic anhydrase III J. Phys. Chem. Lett. 4 1829-33
184. Wang T, Arakawa H and Ikai A 2001 Force measurement and inhibitor binding assay of monomer and engineered dimer of bovine carbonic anhydrase B Biochem. Biophys. Res. Commun. 285 9-14
185. Szymczak P 2013 Tight knots in proteins: can they block the mitochondrial pores? Biochem. Soc. Trans. 41 620-4
186. Huang L and Makarov D E 2008 Translocation of a knotted polypeptide through a pore J. Chem. Phys. 129 121107
187. Daggett V and Fersht A 2003 The present view of the mechanism of protein folding Nat. Rev. Mol. Cell Biol. 4 497-502
188. Daggett V and Fersht A R 2003 Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28 18-25
189. Fersht A R and Daggett V 2002 Protein folding and unfolding at atomic resolution Cell 108 573-82
190. Jackson S E 1998 How do small single-domain proteins fold? Fold. Des. 3 R81-91
191. Jackson S E and Fersht A R 1991 Folding of chymotrypsin inhibitor 2.1. Evidence for a two-state transition Biochemistry 30 10428-35
192. Dill K A and Chan H S 1997 From Levinthal to pathways to funnels Nat. Struct. Biol. 4 10-9
193. Onuchic J N and Wolynes P G 2004 Theory of protein folding Curr. Opin. Struct. Biol. 14 70-5
194. Mallam A, Rogers J M and Jackson S 2010 Experimental detection of knotted conformations in denatured proteins Proc. Natl Acad. Sci. USA 107 8189-94
195. Mallam A L and Jackson S E 2005 Folding studies on a knotted protein J. Mol. Biol. 346 1409-21
196. Mallam A L and Jackson S E 2006 Probing nature's knots: the folding pathway of a knotted homodimeric protein J. Mol. Biol. 359 1420-36
197. Mallam A L and Jackson S E 2007 The dimerization of an alpha/beta-knotted protein is essential for structure and function Structure 15 111-22
198. Mallam A L and Jackson S E 2007 A comparison of the folding of two knotted proteins: YbeA and YibK J. Mol. Biol. 366 650-65
199. Mallam A L and Jackson S E 2012 Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins Nat. Chem. Biol. 8 147-53
200. Mallam A L, Morris E R and Jackson S E 2008 Exploring knotting mechanisms in protein folding Proc. Natl Acad. Sci. USA 105 18740-5
201. Mallam A L, Onuoha S C, Grossmann J G and Jackson S E 2008 Knotted fusion proteins reveal unexpected possibilities in protein folding Mol. Cell 30 642-8
202. Purta E, Kaminska K H, Kasprzak J M, Bujnicki J M and Douthwaite S 2008 YbeA is the m(3)Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA Rna Soc. 14 2234-44
203. Hsieh S J, Mallam A L, Jackson S E and Hsu S T 2013 Backbone NMR assignments of a topologically knotted protein in urea-denatured state Biomol. NMR Assign. 8 283-5
204. Andrews B T, Capraro D T, Sulkowska J I, Onuchic J N and Jennings P A 2013 Hysteresis as a marker for complex, overlapping landscapes in proteins J. Phys. Chem. Lett. 4 180-8
205. Wang P, Yang L, Liu P, Gao Y Q and Zhao X S 2013 Single-molecule detection reveals knot sliding in TrmD denaturation Chemistry 19 5909-16
206. Lim N C H and Jackson S E 2015 Mechanistic insights into the folding of knotted proteins in vitro and in vivo J. Mol. Biol. 427 248-58
207. King N P, Jacobitz A W, Sawaya M R, Goldschmidt L and Yeates T O 2010 Structure and folding of a designed knotted protein Proc. Natl Acad. Sci. USA 107 20732-7
208. Wang T, Arakawa H and Ikai A 2001 Force measurement and inhibitor binding assay of monomer and engineered dimer of bovine carbonic anhydrase B Biochem. Biophys. Res. Commun. 285 9-14
209. Andersson F I, Pina D G, Mallam A L, Blaser G and Jackson S E 2009 Untangling the folding mechanism of the 5(2)-knotted protein UCH-L3 Febs J. 276 2625-35
210. Wallin S, Zeldovich K B and Shakhnovich E I 2007 The folding mechanics of a knotted protein J. Mol. Biol. 368 884-93
211. Sulkowska J I, Sulkowski P and Onuchic J 2009 Dodging the crisis of folding proteins with knots Proc. Natl Acad. Sci. USA 106 3119-24
212. Sulkowska J I, Noel J K, Ramirez-Sarmiento C A, Rawdon E J, Millett K C and Onuchic J 2013 Knotting pathways in proteins Biochem. Soc. Trans. 41 523-7
213. Prentiss M C, Wales D J and Wolynes P G 2010 The energy landscape, folding pathways and the kinetics of a knotted protein Plos Comput. Biol. 6 e1000835
214. Tuszynska I and Bujnicki J M 2010 Predicting atomic details of the unfolding pathway for YibK, a knotted protein from the SPOUT superfamily J. Biomol. Struct. Dyn. 27 511-20
215. Sulkowska J I, Sulkowski P, Szymczak P and Cieplak M 2010 Untying knots in proteins J. Am. Chem. Soc. 132 13954-6
216. Faisca P F N, Travasso R D M, Charters T, Nunes A and Cieplak M 2010 The folding of knotted proteins: insights from lattice simulations Phys. Biol. 7 16009
217. Soler M A and Faisca P F N 2012 How difficult is it to fold a knotted protein? In silico insights from surface-tethered folding experiments Plos One 7 e52343
218. Skrbic T, Micheletti C and Faccioli P 2012 The role of non-native interactions in the folding of knotted proteins Plos Comput. Biol. 8 e1002504
219. Covino R, Skrbić T, Beccara S A, Faccioli P and Micheletti C 2013 The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations Biomolecules 4 1-19
220. Sulkowska J I, Sulkowski P and Onuchic J 2009 Jamming proteins with slipknots and their free energy landscape Phys. Rev. Lett. 103 268103
221. He C, Genchev G Z, Lu H and Li H 2012 Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations J. Am. Chem. Soc. 134 10428-35
222. He C, Lamour G, Xiao A, Gsponer J and Li H 2014 Mechanically tightening a protein slipknot into a trefoil knot J. Am. Chem. Soc. 136 11946-55
223. Potestio R, Micheletti C and Orland H 2010 Knotted versus unknotted proteins: evidence of knot-promoting loops PLoS Comput. Biol. 6 e1000864
224. Krissinel E and Henrick K 2004 Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallogr. D Biol. Crystallogr. 60 2256-68
225. Villeret V, Clantin B, Tricot C, Legrain C, Roovers M, Stalon V, Glansdorff N and Van Beeumen J 1998 The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures Proc. Natl Acad. Sci. USA 95 2801-6
226. Sulkowska J I, Noel J K, Ramirez-Sarmiento C A, Rawdon E J, Millett K C and Onuchic J N 2013 Knotting pathways in proteins Biochem. Soc. Trans. 41 523-7
227. Covino R, Skrbić T, Beccara S A, Faccioli P and Micheletti C 2013 The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations Biomolecules 4 1-19
228. Krobath H and Faisca P F 2013 Interplay between native topology and non-native interactions in the folding of tethered proteins Phys. Biol. 10 016002
229. Skrbic T, Micheletti C and Faccioli P 2012 The role of non-native interactions in the folding of knotted proteins PLoS Comput. Biol. 8 e1002504
230. Onuchic J N and Wolynes P G 2004 Theory of protein folding Curr. Opin. Struct. Biol. 14 70-5
231. Wasserman E 1960 The preparation of interlocking rings: a catenane J. Am. Chem. Soc. 82 4433-4
232. Beves J E, Campbell C J, Leigh D A and Pritchard R G 2013 Tetrameric cyclic double helicates as a scaffold for a molecular solomon link Angew. Chem. Int. Edn 52 6464-7
233. Schouwey C, Holstein J J, Scopelliti R, Zhurov O, Nagornov K O, Tsybin Y O, Smart O S, Bricogne G and Severin K 2014 Self-assembly of a giant molecular Solomon link from 30 subcomponents Angew. Chem. Int. Edn 53 11261-5
234. Chichak K S, Cantrill S J, Pease A R, Chiu S-H, Cave G W V, Atwood J L and Stoddart J F 2004 Molecular borromean rings Science 304 1308-12
235. Forgan R S, Spruell J M, Olsen J-C, Stern C L and Stoddart J F 2009 Towards the stepwise assembly of molecular borromean rings. A donor-acceptor ring-in-ring complex J. Mex. Chem. Soc. 53 134-8
236. Leigh D A, Pritchard R G and Stephens A J 2014 A star of david catenane Nat. Chem. 6 978-82
237. Safarowsky O, Vogel E and Vögtle F 2000 Amide-based [3]catenanes and [2]catenanes with aliphatic chains Eur. J. Org. Chem. 2000 499-505
238. Crowley J D, Goldup S M, Lee A-L, Leigh D A and McBurney R T 2009 Active metal template synthesis of rotaxanes, catenanes and molecular shuttles Chem. Soc. Rev. 38 1530-41
239. Dietrich-Buchecker C O, Sauvage J-P and Kintzinger J P 1983 Une nouvelle famille de molecules: les metallo-catenanes Tetrahedron Lett. 24 5095-8
240. Hamilton D G, Davies J E, Prodi L and Sanders J K M 1998 Synthesis, structure and photophysics of neutral pi-associated [2]catenanes Chem.- A Eur. J. 4 608-20
241. Beves J E 2012 Metal template synthesis of molecular knots and links CHIMIA Int. J. Chem. 66 170-3
242. Lukin O and Vögtle F 2005 Knotting and threading of molecules: chemistry and chirality of molecular knots and their assemblies Angew. Chem. Int. Edn 44 1456-77
243. Frisch H L and Wasserman E 1961 Chemical topology J. Am. Chem. Soc. 83 3789-95
244. Dietrich-Buchecker C O and Sauvage J-P 1989 A synthetic molecular trefoil knot Angew. Chem. Int. Edn Engl. 28 189-92
245. Seeman N C 1998 Nucleic acid nanostructures and topology Angew. Chem. Int. Edn 37 3220-38
246. Du S M, Stollar B D and Seeman N C 1995 A synthetic DNA molecule in three knotted topologies J. Am. Chem. Soc. 117 1194-200
247. Carina R F, Dietrich-Buchecker C and Sauvage J-P 1996 Molecular composite knots J. Am. Chem. Soc. 118 9110-6
248. Beves J E, Blight B A, Campbell C J, Leigh D A and McBurney R T 2011 Strategies and tactics for the metal-directed synthesis of rotaxanes, knots, catenanes and higher order links Angew. Chem. Int. Edn 50 9260-327
249. Cesario M, Dietrich-Buchecker C O, Gullhem J, Pascard C and Sauvage J-P 1985 Molecular-structure of a catenand and its copper(I) catenate - complete rearrangement of the interlocked macrocyclic ligands by complexation J. Chem. Soc. Chem. Commun. 1985 244-7
250. Sauvage J-P and Dietrich-Buchecker C 1999 Molecular knots- from early attempts to high-yield template synthesis Molecular Catenanes, Rotaxanes and Knots: a Journey Through the World of Molecular Topology ed J-P Sauvage and C Dietrich-Buchecker (Weinheim: Wiley-VCH)
251. Walba D M 1985 Topological stereochemistry Tetrahedron 41 3161-212
252. Dietrich-Buchecker C O, Sauvage J-P, De Cian A and Fischer J 1994 High-yield synthesis of a dicopper(I) trefoil knot containing 1, 3-phenylene groups as bridges between the chelate units J. Chem. Soc. Chem. Commun. 1994 2231-2
253. Dietrich-Buchecker C O, Rapenne G and Sauvage J-P 1997 Efficient synthesis of a molecular knot by copper(I)-induced formation of the precursor followed by ruthenium(II)-catalysed ring closing metathesis Chem. Commun. 1997 2053-4
254. Rapenne G, Dietrich-Buchecker C O and Sauvage J-P 1999 Copper(I)- or Iron(II)-templated synthesis of molecular knots containing two tetrahedral or octahedral coordination sites J. Am. Chem. Soc. 121 994-1001
255. Perret-Aebi L-E, von Zelewsky A, Dietrich-Buchecker C and Sauvage J-P 2004 Stereoselective synthesis of a topologically chiral molecule: the trefoil knot Angew. Chem. Int. Edn 43 4482-5
256. Adams H, Ashworth E, Breault G A, Guo J, Hunter C A and Mayers P C 2001 Knot tied around an octahedral metal centre Nature 411 763
257. Sokolov V I 1973 Topological ideas in stereochemistry Russ. Chem. Rev. 42 452-63
258. Guo J, Mayers P C, Breault G A and Hunter C A 2010 Synthesis of a molecular trefoil knot by folding and closing on an octahedral coordination template Nat. Chem. 2 218-22
259. Barran P E, Cole H L, Goldup S M, Leigh D A, McGonigal P R, Symes M D, Wu J and Zengerle M 2011 Active-metal template synthesis of a molecular trefoil knot Angew. Chem. Int. Edn 50 12280-4
260. Ayme J-F, Gil-Ramirez G, Leigh D A, Lemonnier J-F, Markevicius A, Muryn C A and Zhang G 2014 Lanthanide template synthesis of a molecular trefoil knot J. Am. Chem. Soc. 136 13142-5
261. Carver F J, Hunter C A and Shannon R J 1994 Directed macrocyclisation reactions J. Chem. Soc. Chem. Commun. 1994 1277-80
262. Safarowsky O, Nieger M, Fröhlich R and Vögtle F 2000 A molecular knot with twelve amide groups- one-step synthesis, crystal structure, chirality Angew. Chem. Int. Edn 39 1616-8
263. Feigel M, Ladberg R, Engels S, Herbst-Irmer R and Fröhlich R 2006 A trefoil knot made of amino acids and steroids Angew. Chem. Int. Edn 45 5698-702
264. Ponnuswamy N, Cougnon F B L, Pantoş G D and Sanders J K M 2014 Homochiral and meso figure eight knots and a solomon link J. Am. Chem. Soc. 136 8243-51
265. Ashton P R, Matthews O A, Menzer S, Raymo F M, Spencer N, Stoddart J F and Williams D J 1997 Molecular Meccans, 27. A template-directed synthesis of a molecular trefoil knot Liebigs Annalen der Chem. 1997 2485-94
266. Woods C R, Benaglia M, Toyota S, Hardcastle K and Siegel J S 2001 Trinuclear copper(I)-bipyridine triskellion: template/cantilever control of coordination complex stereochemistry in a trefoil knot precursor Angew. Chem. Int. Edn 40 749-51
267. Arias K I, Zysman-Colman E, Loren J C, Linden A and Siegel J S 2011 Synthesis of a D3-symmetric 'trefoil' knotted cyclophane Chem. Commun. 47 9588-90
268. Prakasam T, Lusi M, Elhabiri M, Platas-Iglesias C, Olsen J-C, Asfari Z, Cianférani-Sanglier S, Debaene F, Charbonnière LJ and Trabolsi A 2013 Simultaneous self-assembly of a [2]catenane, a trefoil knot, and a solomon link from a simple pair of ligands Angew. Chem. Int. Edn 125 10140-4
269. Ayme J-F, Beves J E, Leigh D A, McBurney R T, Rissanen K and Schultz D 2011 A synthetic molecular pentafoil knot Nat. Chem. 4 15-20
270. Rapenne G, Dietrich-Buchecker C and Sauvage J-P 1996 Resolution of a molecular trefoil knot J. Am. Chem. Soc. 118 10932-3
271. Hasenknopf B and Lehn J M 1996 Trinucleaer double helicates of iron(II) and nickel(II)- self-assembly and resolution into helical enantiomers Helv. Chim. Acta 79 1643-50
272. Meyer M, Albrecht-Gary A-M, Dietrich-Buchecker C O and Sauvage J-P 1997 Dicopper(I) trefoil knots: topological and structural effects on the demetalation rates and mechanism J. Am. Chem. Soc. 119 4599-607
273. Meluzzi D, Smith D E and Arya G 2010 Biophysics of knotting Annual Review of Biophysics vol 39 ed D C Rees and J R Williamson (Palo Alto, CA: Annual Reviews) pp 349-66
274. Trigueros S and Roca J 2007 Production of highly knotted DNA by means of cosmid circularization inside phage capsids BMC Biotechnol. 7 94
275. Bao X R, Lee H J and Quake S R 2003 Behaviour of complex knots in single DNA molecules Phys. Rev. Lett. 91 265506
276. Hagerman P J 1988 Flexibility of DNA Annu. Rev. Biophys. Biophys. Chem. 17 265-86
277. Murphy M C, Rasnik I, Cheng W, Lohman T M and Ha T 2004 Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy Biophys. J. 86 2530-7
278. Kebbekus P, Draper D E and Hagerman P 1995 Persistence length of RNA Biochemistry 34 4354-7
279. Bizarro C V, Alemany A and Ritort F 2012 Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods Nucl. Acids Res. 40 6922-35
280. Bucka A and Stasiak A 2002 Construction and electrophoretic migration of single-stranded DNA knots and catenanes Nucl. Acids Res. 30 e24
281. Seeman N C 2007 An overview of structural DNA nanotechnology Mol. Biotechnol. 37 246-57
282. Seeman N C 1998 DNA nanotechnology: novel DNA constructions Annu. Rev. Biophys. Biomol. Struct. 27 225-48
283. Seeman N C 1996 The design and engineering of nucleic acid nanoscale assemblies Curr. Opin. Struct. Biol. 6 519-26
284. Seeman N C 2003 Biochemistry and structural DNA nanotechnology: an evolving symbiotic relationship Biochemistry 42 7259-68
285. Wang H, Du S M and Seeman N C 1993 Tight single-stranded DNA knots J. Biomol. Struct. Dyn. 10 853-63
286. Au-Yeung H Y, Pantos G D and Sanders J K 2011 Dynamic combinatorial donor-acceptor catenanes in water: access to unconventional and unexpected structures J. Org. Chem. 76 1257-68
287. Lam R T S, Belenguer A, Roberts S L, Naumann C, Jarrosson T, Otto S and Sanders J K M 2005 Amplification of acetylcholine-binding catenanes from dynamic combinatorial libraries Science 308 667-9
288. Au-Yeung H Y, Dan Pantos G and Sanders J K M 2009 Dynamic combinatorial synthesis of a catenane based on donor-acceptor interactions in water Proc. Natl Acad. Sci. USA 106 10466-70
289. Micheletti C, Di Stefano M and Orland H 2015 Absence of knots in known RNA structures Proc. Natl Acad. Sci. USA 112 2052-7
290. Wüst T, Reith D and Virnau P 2015 Sequence determines degree of knottedness in a coarse-grained protein model Phys. Rev. Lett. 114 028102
291. Virnau P, Rieger F C and Reith D 2013 Influence of chain stiffness on knottedness in single polymers Biochem. Soc. Trans. 41 528-32
292. Cebrian J et al 2015 Electrophoretic mobility of supercoiled, catenated and knotted DNA molecules Nucl. Acids Res. 43 e24