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For: Altona C, Pikkemaat JA, Overmars FJ. Three-way and four-way junctions in DNA: a conformational viewpoint. Curr Opin Struct Biol 1996;6:305-16. [PMID: 8804833 DOI: 10.1016/s0959-440x(96)80048-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Number Cited by Other Article(s)
1
Jabbari A, Sameiyan E, Yaghoobi E, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. Aptamer-based targeted delivery systems for cancer treatment using DNA origami and DNA nanostructures. Int J Pharm 2023;646:123448. [PMID: 37757957 DOI: 10.1016/j.ijpharm.2023.123448] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/14/2023] [Accepted: 09/24/2023] [Indexed: 09/29/2023]
2
Gerasimova YV, Nedorezova DD, Kolpashchikov DM. Split light up aptamers as a probing tool for nucleic acids. Methods 2021;197:82-88. [PMID: 33992774 DOI: 10.1016/j.ymeth.2021.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022]  Open
3
Kolpashchikov DM, Spelkov AA. Binary (Split) Light‐up Aptameric Sensors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201914919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
4
Kolpashchikov DM, Spelkov AA. Binary (Split) Light-up Aptameric Sensors. Angew Chem Int Ed Engl 2020;60:4988-4999. [PMID: 32208549 DOI: 10.1002/anie.201914919] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Indexed: 12/12/2022]
5
Kashida H, Azuma H, Maruyama R, Araki Y, Wada T, Asanuma H. Efficient Light‐Harvesting Antennae Resulting from the Dense Organization of Dyes into DNA Junctions through d ‐Threoninol. Angew Chem Int Ed Engl 2020;59:11360-11363. [DOI: 10.1002/anie.202004221] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Indexed: 01/07/2023]
6
Kashida H, Azuma H, Maruyama R, Araki Y, Wada T, Asanuma H. Efficient Light‐Harvesting Antennae Resulting from the Dense Organization of Dyes into DNA Junctions through d ‐Threoninol. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
7
Xia Y, Zheng KW, He YD, Liu HH, Wen CJ, Hao YH, Tan Z. Transmission of dynamic supercoiling in linear and multi-way branched DNAs and its regulation revealed by a fluorescent G-quadruplex torsion sensor. Nucleic Acids Res 2019;46:7418-7424. [PMID: 29982790 PMCID: PMC6101514 DOI: 10.1093/nar/gky534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/31/2018] [Indexed: 01/20/2023]  Open
8
Brady RA, Kaufhold WT, Brooks NJ, Foderà V, Di Michele L. Flexibility defines structure in crystals of amphiphilic DNA nanostars. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019;31:074003. [PMID: 30523829 DOI: 10.1088/1361-648x/aaf4a1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
9
Zuffo M, Xie X, Granzhan A. Strength in Numbers: Development of a Fluorescence Sensor Array for Secondary Structures of DNA. Chemistry 2019;25:1812-1818. [DOI: 10.1002/chem.201805422] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 12/16/2022]
10
van Buuren BN, Schleucher J, Wijmenga SS. NMR Structural Studies on a DNA Four-Way Junction: Stacking Preference and Localization of the Metal-ion Binding Site. J Biomol Struct Dyn 2016;17 Suppl 1:237-43. [PMID: 22607430 DOI: 10.1080/07391102.2000.10506627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
11
Mohri K, Nishikawa M, Takahashi N, Shiomi T, Matsuoka N, Ogawa K, Endo M, Hidaka K, Sugiyama H, Takahashi Y, Takakura Y. Design and development of nanosized DNA assemblies in polypod-like structures as efficient vehicles for immunostimulatory CpG motifs to immune cells. ACS NANO 2012;6:5931-40. [PMID: 22721419 DOI: 10.1021/nn300727j] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
12
Evstigneev MP, Parkinson JA, Lantushenko AO, Kostjukov VV, Pahomov VI. Hexamer oligonucleotide topology and assembly under solution phase NMR and theoretical modeling scrutiny. Biopolymers 2010;93:1023-38. [PMID: 20623667 DOI: 10.1002/bip.21515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
13
Song G, Ren J. Recognition and regulation of unique nucleic acid structures by small molecules. Chem Commun (Camb) 2010;46:7283-94. [DOI: 10.1039/c0cc01312a] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
14
Wu B, Girard F, van Buuren B, Schleucher J, Tessari M, Wijmenga S. Global structure of a DNA three-way junction by solution NMR: towards prediction of 3H fold. Nucleic Acids Res 2004;32:3228-39. [PMID: 15199171 PMCID: PMC434450 DOI: 10.1093/nar/gkh645] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
15
Hickman AB, Ronning DR, Perez ZN, Kotin RM, Dyda F. The nuclease domain of adeno-associated virus rep coordinates replication initiation using two distinct DNA recognition interfaces. Mol Cell 2004;13:403-14. [PMID: 14967147 DOI: 10.1016/s1097-2765(04)00023-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Revised: 12/08/2003] [Accepted: 12/09/2003] [Indexed: 12/13/2022]
16
Li G, Tolstonog GV, Sabasch M, Traub P. Type III intermediate filament proteins interact with four-way junction DNA and facilitate its cleavage by the junction-resolving enzyme T7 endonuclease I. DNA Cell Biol 2003;22:261-91. [PMID: 12823903 DOI: 10.1089/104454903321908656] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
17
Assenberg R, Weston A, Cardy DLN, Fox KR. Sequence-dependent folding of DNA three-way junctions. Nucleic Acids Res 2002;30:5142-50. [PMID: 12466538 PMCID: PMC137952 DOI: 10.1093/nar/gkf637] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
18
Cromsigt J, van Buuren B, Schleucher J, Wijmenga S. Resonance assignment and structure determination for RNA. Methods Enzymol 2002;338:371-99. [PMID: 11460559 DOI: 10.1016/s0076-6879(02)38229-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
19
van Buuren BNM, Hermann T, Wijmenga SS, Westhof E. Brownian-dynamics simulations of metal-ion binding to four-way junctions. Nucleic Acids Res 2002;30:507-14. [PMID: 11788713 PMCID: PMC99837 DOI: 10.1093/nar/30.2.507] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
20
Woods KC, Martin SS, Chu VC, Baldwin EP. Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction. J Mol Biol 2001;313:49-69. [PMID: 11601846 DOI: 10.1006/jmbi.2001.5012] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
21
Wang DY, Sen D. A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate. J Mol Biol 2001;310:723-34. [PMID: 11453683 DOI: 10.1006/jmbi.2001.4811] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
22
van Buuren BN, Overmars FJ, Ippel JH, Altona C, Wijmenga SS. Solution structure of a DNA three-way junction containing two unpaired thymidine bases. Identification of sequence features that decide conformer selection. J Mol Biol 2000;304:371-83. [PMID: 11090280 DOI: 10.1006/jmbi.2000.4224] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
23
Makube N, Klump H, Pikkemaat J, Altona C. Thermodynamic properties of an intramolecular DNA four-way junction. Arch Biochem Biophys 1999;364:53-60. [PMID: 10087164 DOI: 10.1006/abbi.1998.1061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
24
Kettani A, Bouaziz S, Gorin A, Zhao H, Jones RA, Patel DJ. Solution structure of a Na cation stabilized DNA quadruplex containing G.G.G.G and G.C.G.C tetrads formed by G-G-G-C repeats observed in adeno-associated viral DNA. J Mol Biol 1998;282:619-36. [PMID: 9737926 DOI: 10.1006/jmbi.1998.2030] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
25
Fenley MO, Manning GS, Marky NL, Olson WK. Excess counterion binding and ionic stability of kinked and branched DNA. Biophys Chem 1998;74:135-52. [PMID: 9760723 DOI: 10.1016/s0301-4622(98)00171-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
26
Overmars FJ, Altona C. NMR study of the exchange rate between two stacked conformers of a model Holliday junction. J Mol Biol 1997;273:519-24. [PMID: 9356242 DOI: 10.1006/jmbi.1997.1340] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
27
Overmars FJ, Lanzotti V, Galeone A, Pepe A, Mayol L, Pikkemaat JA, Altona C. Design and NMR study of an immobile DNA four-way junction containing 38 nucleotides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997;249:576-83. [PMID: 9370369 DOI: 10.1111/j.1432-1033.1997.00576.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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