References:

(1) Miescher, J. F. Ueber Die Chemische Zusammensetzung Der Eiterzellen. Med. Untersuchungen 1871, 4, 441–460.
(2) Hall, K.; Sankaran, N. DNA Translated: Friedrich Miescher’s Discovery of Nuclein in Its Original Context. Br. J. Hist. Sci. 2021, 1–9.
(3) Altmann, R. Über Nucleinsäuren (On Nucleic Acids). Arch. Anat. Physiol. 1889, 1, 524–536.
(4) Klein, W.; Thannhauser, S. J. Experimentelle Studien Uber Den Nucleinstoffwechsel. XXXV. Die Pyrimidinnucleotide Aus Thymusnucleinsaure. Z. Physiol Chem. 1935, 231, 96.
(5) Howard, G. A.; Lythgoe, B.; Todd, A. R. A Synthesis of Cytidine. J. Chem. Soc. 1947, 1052–1054.
(6) Clark, V. M.; Kirby, G. W.; Todd, A. The Use of Phosphoramidic Esters in Acylations. A New Preparation of Adenosine-5’-Pyrophosphate and Adenosine-5’- Triphosphate. J. Chem. Soc. 1957, 1497–1501.
(7) Chargaff, E.; Vischer, E.; Doniger, R.; Green, C.; Misani, F. The Composition of the Desoxypentose Nucleic Acids of Thymus and Spleen. J. Biol. Chem. 1949, 177 (1), 405–416.
(8) Crick, F.; Watson, J. Molecular Structure of Nucleic Acids. Nature 1953, 171, 737–738.
(9) Pauling, L.; Corey, R. Structure of the Nucleic Acids. Nature 1953, 171, 346.
(10) Hargittai, I. The Tetranucleotide Hypothesis: A Centennial. Struct. Chem. 2009, 20, 753–756.
(11) Furberg, S. On the Structure of Nucleic Acids. Acta Chem. Scand. 1952, 6, 634–640.
(12) Astbury, W. T. X-Ray Studies of Nucleic Acids. Symp. Soc. Exp. Biol. 1947, 1, 66–76.
(13) Wilkins, M. H.; Randall, J. T. Crystallinity in Sperm Heads: Molecular Structure of Nucleoprotein in Vivo. Biochim. biophys. acta 1953, 10, 192–193.
(14) Wilkins, M. H. F.; Stokes, A. R.; Wilson, H. R. Molecular Structure of Deoxypentose Nucleic Acids. Nature 1953, 171, 738–740.
(15) Franklin, R. E.; Gosling, R. . Molecular Configuration in Sodium Thymonucleate. Nature 1953, 171, 740–741.
(16) Maddox, B. Rosalind Franklin: The Dark Lady of DNA; HarperCollins: New York, 2002.
(17) Crick, F.; Watson, J. D. The Complementary Structure of Deoxyribonucleic Acid. Proc. R. Soc. A. 1954, 223, 80–96.
(18) Blackburn, M. G.; Gait, M. J.; Loakes, D.; Williams, D. M. DNA and RNA Structure. In Nucleic Acids in Chemistry and Biology; RSC Publishing: Cambridge, 2006; pp 13–76.
(19) Ussery, D. W. DNA Structure: A-, B- and Z-DNA Helix Families. In Encyclopedia of Life Sciences; John Wiley & Sons, Ltd: Chichester, UK, 2002.
(20) Hud, N. V.; Polak, M. DNA-Cation Interactions: The Major and Minor Grooves Are Flexible Ionophores. Curr. Opin. Struct. Biol. 2001, 11 (3), 293–301.
(21) Privalov, P. L.; Dragan, A. I.; Crane-Robinson, C.; Breslauer, K. J.; Remeta, D. P.; Minetti, C. A. S. A. What Drives Proteins into the Major or Minor Grooves of DNA? J. Mol. Biol. 2007, 365 (1), 1–9.
(22) Wang, A. H. J.; Quigley, G. J.; Kolpak, F. J.; Crawford, J. L.; van Boom, J. H.; van der Marel, G.; Rich, A. Molecular Structure of a Left-Handed Double Helical DNA Fragment at Atomic Resolution. Nature 1979, 282, 680–686.
(23) Rich, A.; Nordheim, A.; Wang, A. H. J. The Chemistry and Biology of Left-Handed Z-DNA. Annu. Rev. Biochem. 1984, 53, 791–846.
(24) Peck, L. J.; Nordheim, A.; Rich, A.; Wang, J. C. Flipping of Cloned d(PCpG)n d(PCpG)n DNA Sequences from Right- to Left-Handed Helical Structure by Salt , Co ( III ), or Negative Supercoiling. Biochemistry 1982, 79, 4560–4564.
(25) Leontis, N. B.; Westhof, E. Geometric Nomenclature and Classification of RNA Base Pairs. RNA 2001, 7 (4), 499–512.
(26) Felsenfeld, G.; Rich, A. Studies on the Formation of Two- and Three-Stranded Polyribonucleotides. Biochim Biophys Acta 1957, 26 (3), 457–468.
(27) Hoogsteen, K. The Structure of Crystals Containing a Hydrogen-Bonded Complex of 1-Methylthymine and 9-Methyladenine. Acta Crystallogr. 1959, 12 (10), 822–823.
(28) Phan, A. T.; Guéron, M.; Leroy, J. L. The Solution Structure and Internal Motions of a Fragment of the Cytidine-Rich Strand of the Human Telomere. J. Mol. Biol. 2000, 299 (1), 123–144.
(29) Dong, Y.; Yang, Z.; Liu, D. DNA Nanotechnology Based on I-Motif Structures. Accounts Chem. Res. 2014, 47 (6), 1853–1860.
(30) Gehring, K.; Leroy, J. L.; Guéron, M. A Tetrameric DNA Structure with Protonated Cytosine.Cytosine Base Pairs. Nature 1993, 363 (6429), 561–565.
(31) Zeraati, M.; Langley, D. B.; Schofield, P.; Moye, A. L.; Rouet, R.; Hughes, W. E.; Bryan, T. M.; Dinger, M. E.; Christ, D. I-Motif DNA Structures Are Formed in the Nuclei of Human Cells. Nat. Chem. 2018, 10 (6), 631–637.
(32) Benabou, S.; Avino, A.; Eritja, R.; Gonzalez, C.; Gargallo, R. Fundamental Aspects of the Nucleic Acid I-Motif Structures. RSC Adv. 2014, 4, 26956–26980.
(33) Jin, K. S.; Shin, S. R.; Ahn, B.; Rho, Y.; Kim, S. J.; Ree, M. PH-Dependent Structures of an i-Motif DNA in Solution. J. Phys. Chem. B 2009, 113 (7), 1852–1856.
(34) Cui, J.; Waltman, P.; Le, V. H.; Lewis, E. A. The Effect of Molecular Crowding on the Stability of Human C-MYC Promoter Sequence I-Motif at Neutral PH. Molecules 2013, 18, 12751–12767.
(35) Sun, D.; Hurley, L. H. The Importance of Negative Superhelicity in Inducing the Formation of G-Quadruplex and i-Motif Structures in the c-Myc Promoter: Implications for Drug Targeting and Control of Gene Expression. J. Med Chem. 2009, 52, 2863–2874.
(36) Sun, Y.; Yang, B.; Hua, Y.; Dong, Y.; Ye, J.; Wang, J.; Xu, L.; Liu, D. Construction and Characterization of a Mirror-Image L-DNA i-Motif. ChemBioChem 2020, 21 (1–2), 94–97.
(37) Saha, P.; Panda, D.; Paul, R.; Dash, J. A DNA Nanosensor for Monitoring Ligand-Induced i-Motif Formation. Org. Biomol. Chem. 2021, 19, 1965–1969.
(38) Rhodes, D.; Lipps, H. J. Survey and Summary: G-Quadruplexes and Their Regulatory Roles in Biology. Nucleic Acids Res. 2015, 43 (18), 8627–8637.
(39) Parkinson, G. N.; Lee, M. P. H.; Neidle, S. Crystal Structure of Parallel Quadruplexes from Human Telomeric DNA. Nature 2002, 417 (6891), 876–880.
(40) Lane, A. N.; Chaires, J. B.; Gray, R. D.; Trent, J. O. Stability and Kinetics of G-Quadruplex Structures. Nucleic Acids Res. 2008, 36, 5482–5515.
(41) Maizels, N.; Gray, L. T. L. T. The G4 Genome. PLoS Genet. 2013, 9 (4), e1003468.
(42) Cayrou, C.; Gregoire, D.; Coulombe, P.; Danis, E.; Mechali, M. Genome-Scale Identification of Active DNA Replication Origins. Methods 2012, 57, 158–164.
(43) Carvalho, J.; Mergny, J. L.; Salgado, G. F.; Queiroz, J. A.; Cruz, C. G-Quadruplex, Friend or Foe: The Role of the G-Quartet in Anticancer Strategies. Trends Mol. Med. 2020, 26 (9), 848–861.
(44) Moye, A. L.; Porter, K. C.; Cohen, S. B.; Phan, T.; Zyner, K. G.; Sasaki, N.; Lovrecz, G. O.; Beck, J. L.; Bryan, T. M. Telomeric G-Quadruplexes Are a Substrate and Site Localization for Human Telomerase. Nat. Commun. 2015, 6, 7643.
(45) Wang, Q.; Liu, J.; Chen, Z.; Zheng, K.; Chen, C.; Hao, Y.; Tan, Z. G-Quadruplex Formation at the 3’ End of Telomere DNA Inhibits Its Extension by Telomerase, Polymerase and Unwinding by Helicase. Nucleic Acids Res. 2011, 39 (14), 6229–6237.
(46) Prorok, P.; Artufel, M.; Aze, A.; Coulombe, P.; Peiffer, I.; Lacroix, L.; Guedin, A.; Mergny, J. L.; Damaschke, J.; Schepers, A.; Cayrou, C.; Teulade-Fichou, M.-P.; Ballester, B.; Mechali, M. Involvement of G-Quadruplex Regions in Mammalian Replication Origin Activity. Nat. Commun. 2019, 10, 3274.
(47) Bay, D. H.; Busch, A.; Lisdat, F.; Lida, K.; Ikebukuro, K.; Nagasawa, K.; Karube, I.; Yoshida, W. Identification of G-Quadruplex Structures That Possess Transcriptional Regulating Functions in the Dele and Cdc6 CpG Islands. BMC Mol. Biol. 2017, 18 (1), 17.
(48) Wu, G.; Xing, Z.; Tran, E. J.; Yang, D. DDX5 Helicase Resolves G-Quadruplex and Is Involved in MYC Gene Transcriptional Activation. Proc. Natl. Acad. Sci. U. S. A. 2019, 116 (41), 20453–20461.
(49) Jodoin, R.; Carrier, J. C.; Rivard, N.; Bisaillon, M.; Perreault, J.-P. G-Quadruplex Located in the 5’UTR of the BAG-1 MRNA Affects Both Its Cap-Dependent and Cap-Independent Translation through Global Secondary Structure Maintenance. Nucleic Acids Res. 2019, 47 (19), 10247–10266.
(50) Devi, G.; Zhou, Y.; Zhong, Z.; Toh, D. F. K.; Chen, G. RNA Triplexes: From Structural Principles to Biological and Biotech Applications. Wiley Interdiscip. Rev. RNA 2015, 6 (1), 111–128.
(51) Adams, P. L.; Stahley, M. R.; Kosek, A. B.; Wang, J.; Strobel, S. A. Crystal Structure of a Self-Splicing Group I Intron with Both Exons. Nature 2004, 430, 45–50.
(52) Toor, N.; Keating, K. S.; Taylor, S. D.; Pyle, A. M. Crystal Structure of a Self-Spliced Group II Intron. Science. 2008, 320, 77–82.
(53) Klein, D. J.; Schmeing, T. M.; Moore, P. B.; Steitz, T. A. The Kink-Turn: A New RNA Secondary Structure Motif. EMBO J. 2001, 20, 4214–4221.
(54) Ulyanov, N. B.; Shefer, K.; James, T. L.; Tzfati, Y. Pseudo- Knot Structures with Conserved Base Triples in Telom- Erase RNAs of Ciliates. Nucleic Acids Res. 2007, 35, 6150–6160.
(55) Shefer, K.; Brown, Y.; Gorkovoy, V.; Nussbaum, T.; Ulyanov, N. B.; Tzfati, Y. A Triple Helix within a Pseudo- Knot Is a Conserved and Essential Element of Telomerase RNA. Mol. Cell Biol. 2007, 27, 2130–2143.
(56) Olsthoorn, R. C. Reumerman, R.; Hilbers, C. W.; Pleij, C. W.; Heus, H. A. Functional Analysis of the SRV-1 RNA Frameshifting Pseudoknot. Nucleic Acids Res. 2010, 38, 7665–7672.
(57) Su, L.; Chen, L.; M., E.; Berger, J. M.; Rich, A. Minor Groove RNA Triplex in the Crystal Structure of a Ribosomal Frameshifting Viral Pseudoknot. Nat. Struct. Biol. 1999, 6, 285–292.
(58) Wilusz, J. E.; JnBaptiste, C. K.; Lu, L. Y.; Kuhn, C. D.; Joshua-Tor, L.; Sharp, P. A. A Triple Helix Stabilizes the 3′ Ends of Long Noncoding RNAs That Lack Poly(A) Tails. Genes Dev 2012, 26, 2392–2407.
(59) Blackburn, M. G.; Gait, M. J.; Loakes, D.; Williams, D. M. RNA Structure and Function. In Nucleic Acids in Chemistry and Biology; RSC Publishing: Cambridge, 2006; pp 253–293.
(60) Olivas, W. M.; Maher, L. J. Overcoming Potassium-Mediated Triplex Inhibition. Nucleic Acids Res. 1995, 23 (11), 1936–1941.
(61) Hu, Y.; Cecconello, A.; Idili, A.; Ricci, F.; Willner, I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angew. Chemie - Int. Ed. 2017, 56 (48), 15210–15233.
(62) Naskar, S.; Guha, R.; Müller, J. Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads. Angew. Chemie - Int. Ed. 2020, 59 (4), 1397–1406.
(63) Megger, N.; Welte, L.; Zamora, F.; Muller, J. Metal-Mediated Aggregation of DNA Comprising 2,2’-Bipyridine Nucleoside, an Asymmetrically Substituted Chiral Bidentate Ligand. Dalt. Trans. 2011, 40 (8), 1802–1807.
(64) Su, Y.; Li, D.; Liu, B.; Xiao, M.; Wang, F.; Li, L.; Zhang, X.; Pei, H. Rational Design of Framework Nucleic Acids for Bioanalytical Applications. Chempluschem 2019, 84 (5), 512–523.
(65) Seeman, N. C. Nanomaterials Based on DNA. Annu. Rev. Biochem. 2010, 79, 65–87.
(66) Hill, A. C.; Hall, J. High-Order Structures from Nucleic Acids for Biomedical Applications. Mater. Chem. Front. 2020, 4 (4), 1074–1088.
(67) Wang, F.; Lv, H.; Li, Q.; Li, J.; Zhang, X.; Shi, J.; Wang, L.; Fan, C. Implementing Digital Computing with DNA-Based Switching Circuits. Nat. Commun. 2020, 11, 121.
(68) Corbett, K. S.; Edwards, D. K.; Leist, S. R.; Abiona, O. M.; Boyoglu-Barnum, S.; Gillespie, R. A.; Himansu, S.; Schäfer, A.; Ziwawo, C. T.; DiPiazza, A. T.; Dinnon, K. H.; Elbashir, S. M.; Shaw, C. A.; Woods, A.; Fritch, E. J.; Martinez, D. R.; Bock, K. W.; Minai, M.; Nagata, B. M.; Hutchinson, G. B.; Wu, K.; Henry, C.; Bahl, K.; Garcia-Dominguez, D.; Ma, L. Z.; Renzi, I.; Kong, W. P.; Schmidt, S. D.; Wang, L.; Zhang, Y.; Phung, E.; Chang, L. A.; Loomis, R. J.; Altaras, N. E.; Narayanan, E.; Metkar, M.; Presnyak, V.; Liu, C.; Louder, M. K.; Shi, W.; Leung, K.; Yang, E. S.; West, A.; Gully, K. L.; Stevens, L. J.; Wang, N.; Wrapp, D.; Doria-Rose, N. A.; Stewart-Jones, G.; Bennett, H.; Alvarado, G. S.; Nason, M. C.; Ruckwardt, T. J.; McLellan, J. S.; Denison, M. R.; Chappell, J. D.; Moore, I. N.; Morabito, K. M.; Mascola, J. R.; Baric, R. S.; Carfi, A.; Graham, B. S. SARS-CoV-2 MRNA Vaccine Design Enabled by Prototype Pathogen Preparedness. Nature 2020, 586 (7830), 567–571.
(69) Mulligan, M. J.; Lyke, K. E.; Kitchin, N.; Absalon, J.; Gurtman, A.; Lockhart, S.; Neuzil, K.; Raabe, V.; Bailey, R.; Swanson, K. A.; Li, P.; Koury, K.; Kalina, W.; Cooper, D.; Fontes-Garfias, C.; Shi, P. Y.; Türeci, Ö.; Tompkins, K. R.; Walsh, E. E.; Frenck, R.; Falsey, A. R.; Dormitzer, P. R.; Gruber, W. C.; Şahin, U.; Jansen, K. U. Phase I/II Study of COVID-19 RNA Vaccine BNT162b1 in Adults. Nature 2020, 586 (7830), 589–593.
(70) Noor, R. Developmental Status of the Potential Vaccines for the Mitigation of the COVID-19 Pandemic and a Focus on the Effectiveness of the Pfizer-BioNTech and Moderna MRNA Vaccines. Curr. Clin. Microbiol. Reports 2021, 8, 178-185.
(71) Plasterk, R. H. A. RNA Silencing: The Genome’s Immune System. Science 2002, 296 (5571), 1263–1265.
(72) Monia, B. P.; Lesnik, E. A.; Gonzalez, C.; Lima, W. F.; McGee, D.; Guinosso, C. J.; Kawasaki, A. M.; Cook, P. D.; Freier, S. M. Evaluation of 2’-Modified Oligonucleotides Containing 2’-Deoxy Gaps as Antisense Inhibitors of Gene Expression. J. Biol. Chem. 1993, 268 (19), 14514–14522.
(73) Liang, X. H.; Sun, H.; Nichols, J. G.; Crooke, S. T. RNase H1-Dependent Antisense Oligonucleotides Are Robustly Active in Directing RNA Cleavage in Both the Cytoplasm and the Nucleus. Mol. Ther. 2017, 25 (9), 2075–2092.
(74) Lima, J. F.; Cerqueira, L.; Figueiredo, C.; Oliveira, C.; Azevedo, N. F. Anti-MiRNA Oligonucleotides: A Comprehensive Guide for Design. RNA Biol. 2018, 15 (3), 338–352.
(75) Glazier, D. A.; Glazier, D. A.; Liao, J.; Roberts, B. L.; Li, X.; Yang, K.; Stevens, C. M.; Tang, W.; Tang, W. Chemical Synthesis and Biological Application of Modified Oligonucleotides. Bioconjug. Chem. 2020, 31 (5), 1213–1233.
(76) Singh, A.; Trivedi, P.; Jain, N. K. Advances in SiRNA Delivery in Cancer Therapy. Artif. Cells Nanomed. Biotechnol. 2018, 46 (2), 274–283.
(77) Kole, R.; Krainer, A. R.; Altman, S. RNA Therapeutics: Beyond RNA Interference and Antisense Oligonucleotides. Nat. Rev. Drug Discov. 2012, 11 (2), 125–140.
(78) Nidhi, S.; Anand, U.; Oleksak, P.; Tripathi, P.; Lal, J. A.; Thomas, G.; Kuca, K.; Tripathi, V. Novel CRISPR–Cas Systems: An Updated Review of the Current Achievements, Applications, and Future Research Perspectives. Int. J. Mol. Sci. 2021, 22 (7), 3327.
(79) Jore, M. M.; Brouns, S. J. J.; Van der Oost, J. RNA in Defense: CRISPRs Protect Prokaryotes against Mobile Genetic Elements. Cold Spring Harb. Perspect. Biol. 2012, 4, a003657.
(80) Barrangou, R.; Fremaux, C.; Deveau, H.; Richards, M.; Boyaval, P.; Moineau, S.; Romero, D. .; Horvath, P. CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes. Science 2007, 315 (5819), 1709–1712.
(81) Sapranauskas, R.; Gasiunas, G.; Fremaux, C.; Barrangou, R.; Horvath, P.; Siksnys, V. The Streptococcus Thermophilus CRISPR/Cas System Provides Immunity in Escherichia Coli. Nucleic Acids Res. 2011, 39 (21), 9275–9282.
(82) Bevacqua, R. J.; Dai, X.; Lam, J. Y.; Gu, X.; Friedlander, M. S. H.; Tellez, K.; Miguel-Escalada, I.; Bonas-Guarch, S.; Atla, G.; Zhao, W.; Kim, S. H.; Dominguez, A. A.; Qi, L. S.; Ferrer, J.; MacDonald, P. E.; Kim, S. K. CRISPR-Based Genome Editing in Primary Human Pancreatic Islet Cells. Nat. Commun. 2021, 12, 2397.
(83) Langner, T.; Kamoun, S.; Belhaj, K. CRISPR Crops: Plant Genome Editing Towards Disease Resistance. Annu. Rev. Phytopathol. 2018, 56, 479–512.
(84) Deltcheva, E.; Chylinski, K.; Sharma, C. M.; Gonzales, K.; Chao, Y.; Pirzada, Z. A.; Eckert, M. R.; Vogel, V.; Charpentier, E. CRISPR RNA Maturation by Trans-Encoded Small RNA and Host Factor RNase III. Nature 2011, 471, 602–607.
(85) Jinek, M.; Chylinski, K.; Fonfara, I.; Hauer, M.; Doudna, J. A.; Charpentier, E. A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science 2012, 337 (6096), 816–821.
(86) Shu, D.; Shu, Y.; Haque, F.; Abdelmawla, S.; Guo, P. Thermodynamically Stable RNA Three-Way Junction for Constructing Multifunctional Nanoparticles for Delivery of Therapeutics. Nat. Nanotechnol. 2011, 6, 658–667.
(87) Chen, J. H.; Seeman, N. C. The Synthesis from DNA of a Molecule with the Connectivity of a Cube. Nature 1991, 350, 631–633.
(88) Chen, J. H.; Kallenbach, N. R.; Seeman, N. C. A Specific Quadrilateral Synthesized from DNA Branched Junctions. J. Am. Chem. Soc. 1989, 111, 6402–6407.
(89) Zhang, Y.; Seeman, N. C. The Construction of a DNA Truncated Octahedron. J. Am. Chem. Soc. 1994, 116, 1661–1669.
(90) Rothemund, P. M. K. Folding DNA to Create Nanoscale Shapes and Patterns. Nature 2006, 440, 297–302.
(91) Li, H.; Zhang, K.; Pi, F.; Guo, S.; Shlyakhtenko, L.; Chiu, W.; Shu, D.; Guo, P. Controllable Self-Assembly of RNA Tetrahedrons with Precise Shape and Size for Cancer Targeting. Adv. Mater. 2016, 28 (34), 7501–7507.
(92) Mela, I.; Vallejo‐Ramirez, P. P.; Makarchuk, S.; Christie, G.; Bailey, D.; Henderson, R. M.; Sugiyama, H.; Endo, M.; Kaminski, C. F. DNA Nanostructures for Targeted Antimicrobial Delivery. Angew. Chemie 2020, 132 (31), 12798–12802.
(93) Ijäs, H.; Hakaste, I.; Shen, B.; Kostiainen, M. A.; Linko, V. Reconfigurable DNA Origami Nanocapsule for PH-Controlled Encapsulation and Display of Cargo. ACS Nano 2019, 13 (5), 5959–5967.
(94) Xu, C.; Li, H.; Zhang, K.; Binzel, D. W.; Yin, H.; Chiu, W.; Guo, P.; Chemistry, P.; Heart, D. M. D.; Comprehensive, J.; State, T. O.; Park, M. Photo-Controlled Release of Paclitaxel and Model Drugs from RNA Pyramids. Nano Res. 2019, 12 (1), 41–48.
(95) Tan, X.; Lu, X.; Jia, F.; Liu, X.; Sun, Y.; Logan, J. K.; Zhang, K. Blurring the Role of Oligonucleotides: Spherical Nucleic Acids as a Drug Delivery Vehicle. J. Am. Chem. Soc. 2016, 138 (34), 10834–10837.
(96) Choi, C. H. J.; Hao, L.; Narayan, S. P.; Auyeung, E.; Mirkin, C. A. Mechanism for the Endocytosis of Spherical Nucleic Acid Nanoparticle Conjugates. Proc. Natl. Acad. Sci. U. S. A. 2013, 110 (19), 7625–7630.
(97) Cutler, J. I.; Auyeung, E.; Mirkin, C. A. Spherical Nucleic Acids. J. Am. Chem. Soc. 2012, 134 (3), 1376–1391.
(98) Shi, B.; Zheng, M.; Tao, W.; Chung, R.; Jin, D.; Ghaffari, D.; Farokhzad, O. C. Challenges in DNA Delivery and Recent Advances in Multifunctional Polymeric DNA Delivery Systems. Biomacromolecules 2017, 18 (8), 2231–2246.
(99) Ho, W.; Gao, M.; Li, F.; Li, Z.; Zhang, X.-Q.; Xu, X. Next-Generation Vaccines: Nanoparticle-Mediated DNA and MRNA Delivery. Adv. Healthc. Mater. 2021, 10 (8), 2001812.
(100) Fong, F. Y.; Oh, S. S.; Hawker, C. J.; Soh, H. T. In Vitro Selection of PH-Activated DNA Nanostructures. Angew. Chemie - Int. Ed. 2016, 55 (49), 15258–15262.
(101) Knutson, S. D.; Sanford, A. A.; Swenson, C. S.; Korn, M. M.; Manuel, B. A.; Heemstra, J. M. Thermoreversible Control of Nucleic Acid Structure and Function with Glyoxal Caging. J. Am. Chem. Soc. 2020, 142 (41), 17766–17781.
(102) Huang, F.; Liao, W.-C.; Sohn, Y. S.; Nechushtai, R.; Lu, C.-H.; Willner, I. Light-Responsive and PH-Responsive DNA Microcapsules for Controlled Release of Loads. J. Am. Chem. Soc. 2016, 138 (28), 8936–8945.
(103) Jeong, M.-J.; Shim, C.-K.; Lee, J.-O.; Kwon, H.-B.; Kim, Y.-H.; Lee, S.-K.; Byun, M.-O.; Park, S.-C. Plant Gene Responses to Frequency-Specific Sound Signals. Mol. Breed. 2008, 21, 217–226.
(104) Wang, Y.; Li, J.; Wang, H.; Jin, J.; Liu, J.; Wang, K.; Tan, W.; Yang, R. Silver Ions-Mediated Conformational Switch: Facile Design of Structure-Controllable Nucleic Acid Probes. Anal. Chem. 2010, 82 (15), 6607–6612.
(105) Riemann, A.; Schneider, B.; Ihling, A.; Nowak, M.; Sauvant, C.; Thews, O.; Gekle, M. Acidic Environment Leads to ROS-Induced MAPK Signaling in Cancer Cells. PLoS One 2011, 6 (7), e22445.
(106) Vaupel, P.; Kallinowski, F.; Okunieff, P. Blood Flow, Oxygen and Nutrient Supply, and Metabolic Microenvironment of Human Tumors: A Review. Cancer Res. 1989, 49 (23), 6449–6465.
(107) Cheng, E.; Xing, Y.; Chen, P.; Yang; Sun, Y.; Zhou, D.; Xu, T.; Fan, Q.; Liu, D. A PH-Triggered, Fast-Responding DNA Hydrogel. Angew. Chemie - Int. Ed. 2009, 48 (41), 7660–7663.
(108) Chen, W. H.; Yu, X.; Cecconello, A.; Sohn, Y. S.; Nechushtai, R.; Willner, I. Stimuli-Responsive Nucleic Acid-Functionalized Metal-Organic Framework Nanoparticles Using PH- and Metal-Ion-Dependent DNAzymes as Locks. Chem. Sci. 2017, 8 (8), 5769–5780.
(109) Ochoa, S.; Milam, V. T. Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides. Molecules 2020, 25 (20), 4659.
(110) Prakash, T. P. An Overview of Sugar-Modified Oligonucleotides for Antisense Therapeutics. Chem. Biodivers. 2011, 8 (9), 1616–1641.
(111) Fresco, J. R.; Doty, P. Polynucleotides. I. Molecular Properties and Configurations of Polyriboadenylic Acid in Solution. J. Am. Chem. Soc. 1957, 79 (14), 3928–3929.
(112) Fresco, J. R.; Klemperer, E. Polyriboadenylic Acid, A Molecular Analogue of Ribonucleic Acid and Desoxyribonucleic Acid. Ann. N. Y. Acad. Sci. 1959, 81, 730–741.
(113) Rich, A.; Davies, D. R.; Crick, F.; Watson, J. D. The Molecular Structure of Polyadenylic Acid. J. Mol. Biol. 1961, 3 (1), 71–86.
(114) Safaee, N.; Noronha, A. M.; Rodionov, D.; Kozlov, G.; Wilds, C. J.; Sheldrick, G. M.; Gehring, K. Structure of the Parallel Duplex of Poly(A) RNA: Evaluation of a 50 Year-Old Prediction. Angew. Chemie - Int. Ed. 2013, 52 (39), 10370–10373.
(115) Copp, W.; Denisov, A. Y.; Xie, J.; Noronha, A. M.; Liczner, C.; Safaee, N.; Wilds, C. J.; Gehring, K. Influence of Nucleotide Modifications at the C2′ Position on the Hoogsteen Base-Paired Parallel-Stranded Duplex of Poly(A) RNA. Nucleic Acids Res. 2017, 45 (17), 10321–10331.
(116) Gleghorn, M. L.; Zhao, J.; Turner, D. H.; Maquat, L. E. Crystal Structure of a Poly(RA) Staggered Zipper at Acidic PH: Evidence That Adenine N1 Protonation Mediates Parallel Double Helix Formation. Nucleic Acids Res. 2016, 44 (17), 8417–8424.
(117) Zarudnaya, M. I.; Hovorun, D. M. Hypothetical Double-Helical Poly (A) Formation in a Cell and Its Possible Biological Significance. IUBMB Life 1999, 48, 581–584.
(118) Pickard, M. A. G.; Brylow, K. B.; Cisco, L. A.; Anecelle, M. R.; Pershun, M. L.; Chandrasekaran, A. R.; Halvorsen, K.; Gleghorn, M. L. Parallel Poly(A) Homo- And Hetero-Duplex Formation Detection with an Adapted DNA Nanoswitch Technique. RNA 2020, 26 (9), 1118–1130.
(119) Chakraborty, S.; Sharma, S.; Maiti, P. K.; Krishnan, Y. The Poly DA Helix: A New Structural Motif for High Performance DNA-Based Molecular Switches. Nucleic Acids Res. 2009, 37 (9), 2810–2817.
(120) Huang, Z.; Liu, B.; Liu, J. Parallel Polyadenine Duplex Formation at Low PH Facilitates DNA Conjugation onto Gold Nanoparticles. Langmuir 2016, 32 (45), 11986–11992.
(121) Kolb, H. C.; Finn, M. G.; Sharpless, K. B. Click Chemistry: Diverse Chemical Function from a Few Good Reactions. Angew. Chemie - Int. Ed. 2001, 40 (11), 2004–2021.
(122) Rostovtsev, V. V.; Green, L. G.; Fokin, V. V.; Sharpless, B. K. A Stepwise Huisgen Cycloaddition Process: Copper(I)-Catalyzed Regioselective “Ligation” of Azides and Terminal Alkynes. Angew. Chemie - Int. Ed. 2002, 41 (14), 2596–2599.
(123) Tornøe, C. W.; Christensen, C.; Meldal, M. Peptidotriazoles on Solid Phase: [1,2,3]-Triazoles by Regiospecific Copper(I)-Catalyzed 1,3-Dipolar Cycloadditions of Terminal Alkynes to Azides. J. Org. Chem. 2002, 67 (9), 3057–3064.
(124) Agard, N. J.; Baskin, J. M.; Prescher, J. A.; Lo, A.; Bertozzi, C. R. A Comparative Study of Bioorthogonal Reactions with Azides. ACS Chem. Biol. 2006, 1 (10), 644–648.
(125) Johansson, J. R.; Beke-Somfai, T.; Said Stålsmeden, A.; Kann, N. Ruthenium-Catalyzed Azide Alkyne Cycloaddition Reaction: Scope, Mechanism, and Applications. Chem. Rev. 2016, 116 (23), 14726–14768.
(126) El-Sagheer, A. H.; Brown, T. A Triazole Linkage That Mimics the DNA Phosphodiester Group in Living Systems. Q. Rev. Biophys. 2015, 48 (4), 429–436.
(127) Baker, Y. R.; Traoré, D.; Wanat, P.; Tyburn, A.; El-Sagheer, A. H.; Brown, T. Searching for the Ideal Triazole: Investigating the 1,5-Triazole as a Charge Neutral DNA Backbone Mimic. Tetrahedron 2020, 76 (7), 130914.
(128) George, J. T.; Srivatsan, S. G. Posttranscriptional Chemical Labeling of RNA by Using Bioorthogonal Chemistry. Methods 2017, 120, 28–38.
(129) Ren, X.; El-Sagheer, A. H.; Brown, T. Efficient Enzymatic Synthesis and Dual-Colour Fluorescent Labelling of DNA Probes Using Long Chain Azido-DUTP and BCN Dyes. Nucleic Acids Res. 2016, 44 (8), e79.
(130) Pujari, S. S.; Seela, F. Cross-Linked DNA: Propargylated Ribonucleosides as “Click” Ligation Sites for Bifunctional Azides. J. Org. Chem. 2012, 77 (9), 4460–4465.
(131) Pujari, S. S.; Seela, F. Parallel Stranded DNA Stabilized with Internal Sugar Cross-Links: Synthesis and Click Ligation of Oligonucleotides Containing 2′-Propargylated Isoguanosine. J. Org. Chem. 2013, 78 (17), 8545–8561.
(132) El-Sagheer, A. H.; Brown, T. Click Nucleic Acid Ligation: Applications in Biology and Nanotechnology. Acc. Chem. Res. 2012, 45 (8), 1258–1267.
(133) Paredes, E.; Das, S. R. Click Chemistry for Rapid Labeling and Ligation of RNA. ChemBioChem 2011, 12 (1), 125–131.
(134) Mack, S.; Fouz, M. F.; Dey, S. K.; Das, S. R. Pseudo-Ligandless Click Chemistry for Oligonucleotide Conjugation. Curr. Protoc. Chem. Biol. 2016, 8 (2), 83–95.
(135) Liu, L.; Fang, Z.; Zheng, X.; Xi, D. Nanopore-Based Strategy for Sensing of Copper(II) Ion and Real-Time Monitoring of a Click Reaction. ACS Sensors 2019, 4 (5), 1323–1328.
(136) Winz, M. L.; Samanta, A.; Benzinger, D.; Jäschke, A. Site-Specific Terminal and Internal Labeling of RNA by Poly(A) Polymerase Tailing and Copper-Catalyzed or Copper-Free Strain-Promoted Click Chemistry. Nucleic Acids Res. 2012, 40 (10), e78.
(137) Balintová, J.; Špaček, J.; Pohl, R.; Brázdová, M.; Havran, L.; Fojta, M.; Hocek, M. Azidophenyl as a Click-Transformable Redox Label of DNA Suitable for Electrochemical Detection of DNA-Protein Interactions. Chem. Sci. 2015, 6 (1), 575–587.
(138) Chen, J.; Baker, Y. R.; Brown, A.; El-Sagheer, A. H.; Brown, T. Enzyme-Free Synthesis of Cyclic Single-Stranded DNA Constructs Containing a Single Triazole, Amide or Phosphoramidate Backbone Linkage and Their Use as Templates for Rolling Circle Amplification and Nanoflower Formation. Chem. Sci. 2018, 9 (42), 8110–8120.
(139) Pujari, S. S.; Leonard, P.; Seela, F. Oligonucleotides with “Clickable” Sugar Residues: Synthesis, Duplex Stability, and Terminal versus Central Interstrand Cross-Linking of 2′-O-Propargylated 2-Aminoadenosine with a Bifunctional Azide. J. Org. Chem. 2014, 79 (10), 4423–4437.
(140) Ibarra-Soza, J. M.; Morris, A. A.; Jayalath, P.; Peacock, H.; Conrad, W. E.; Donald, M. B.; Kurth, M. J.; Beal, P. A. 7-Substituted 8-Aza-7-Deazaadenosines for Modification of the SiRNA Major Groove. Org. Biomol. Chem. 2012, 10, 6491–6497.
(141) Phelps, K. J.; Ibarra-Soza, J. M.; Tran, K.; Fisher, A. J.; Beal, P. A. Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-Aza-7-Deazaadenosine in RNA. ACS Chem. Biol. 2014, 9 (8), 1780–1787.
(142) Kopcial, M.; Wojtczak, B. A.; Kasprzyk, R.; Kowalska, J.; Jemielity, J. N1-Propargylguanosine Modified MRNA Cap Analogs: Synthesis, Reactivity, and Applications to the Study of Cap-Binding Proteins. Molecules 2019, 24 (10), 1899.
(143) Domingo, O.; Hellmuth, I.; Jäschke, A.; Kreutz, C.; Helm, M. Intermolecular “Cross-Torque”: The N4-Cytosine Propargyl Residue Is Rotated to the ’CH’-Edge as a Result of Watson-Crick Interaction. Nucleic Acids Res. 2015, 43 (11), 5275–5283.
(144) Grøtli, M.; Douglas, M.; Eritja, R.; Sproat, B. S. 2’-O-Propargyl Oligoribonucleotides: Synthesis and Hybridisation. Tetrahedron 1998, 54 (22), 5899–5914.
(145) Egli, M.; Minasov, G.; Tereshko, V.; Pallan, P. S.; Teplova, M.; Inamati, G. B.; Lesnik, E. A.; Owens, S. R.; Ross, B. S.; Prakash, T. P.; Manoharan, M. Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2′-O-Ribonucleic Acid Modifications. Biochemistry 2005, 44 (25), 9045–9057.
(146) Jana, S. K.; Leonard, P.; Ingale, S. A.; Seela, F. 2′-: O -Methyl- and 2′- O -Propargyl-5-Methylisocytidine: Synthesis, Properties and Impact on the IsoCd-DG and the IsoCd-IsoGd Base Pairing in Nucleic Acids with Parallel and Antiparallel Strand Orientation. Org. Biomol. Chem. 2016, 14 (21), 4927–4942.
(147) Puglisi, J. D.; Tinoco, I. Absorbance Melting Curves of RNA. Methods Enzymol. 1989, 180, 304–325.
(148) Mergny, J. L.; Lacroix, L. Analysis of Thermal Melting Curves. Oligonucleotides 2003, 13 (6), 515–537.
(149) Harp, J. M.; Coates, L.; Sullivan, B.; Egli, M. Water Structure around a Left-Handed Z-DNA Fragment Analyzed by Cryo Neutron Crystallography. Nucleic Acids Res. 2021, gkab264.
(150) Woody, R. W. Circular Dichroism. Methods Enzymol. 1995, 246, 34–71.
(151) Noe, C. R.; Winkler, J.; Urban, E.; Gilbert, M.; Haberhauer, G.; Brunar, H. Zwitterionic Oligonucleotides: A Study on Binding Properties of 2′-O-Aminohexyl Modifications. Nucleosides, Nucleotides and Nucleic Acids 2005, 24 (8), 1167–1185.
(152) Hashimoto, H.; Nelson, M. G.; Switzer, C. Formation of Chimeric Duplexes between Zwitterionic and Natural DNA. J. Org. Chem. 1993, 58 (16), 4194–4195.
(153) Hashimoto, H.; Nelson, M. G.; Switzer, C. Zwitterionic DNA. J. Am. Chem. Soc. 1993, 115 (16), 7128–7134.
(154) Noe, C. R.; Brunar, H. Preparation of Modified Oligonucleotides as Active Substances, 1995.
(155) Brunar, H.; Haberhauer, G.; Werner, D.; Noe, C. R. 2’-O-Modified Oligonucleotides: Synthesis and Biophysical Analysis. Eur. J. Pharm. Sci. 1994, 2 (1–2), 150.
(156) Biscans, A.; Rouanet, S.; Bertrand, J. R.; Vasseur, J. J.; Dupouy, C.; Debart, F. Synthesis, Binding, Nuclease Resistance and Cellular Uptake Properties of 2′-O-Acetalester-Modified Oligonucleotides Containing Cationic Groups. Bioorganic Med. Chem. 2015, 23 (17), 5360–5368.
(157) Griffey, R. H.; Monia, B. P.; Cummins, L. L.; Freier, S.; Greig, M. J.; Guinosso, C. J.; Lesnik, E.; Manalili, S. M.; Mohan, V.; Owens, S.; Ross, B. R.; Sasmor, H.; Wancewicz, E.; Weiler, K.; Wheeler, P. D.; Cook, P. D. 2′-O-Aminopropyl Ribonucleotides: A Zwitterionic Modification That Enhances the Exonuclease Resistance and Biological Activity of Antisense Oligonucleotides. J. Med. Chem. 1996, 39 (26), 5100–5109.
(158) Milton, S.; Honcharenko, D.; Rocha, C. S. J.; Moreno, P. M. D.; Edvard Smith, C. I.; Strömberg, R. Nuclease Resistant Oligonucleotides with Cell Penetrating Properties. Chem. Commun. 2015, 51 (19), 4044–4047.
(159) Seio, K.; Tokugawa, M.; Kanamori, T.; Tsunoda, H.; Ohkubo, A.; Sekine, M. Synthesis and Properties of Cationic 2′-O-[N-(4-Aminobutyl)Carbamoyl] Modified Oligonucleotides. Bioorganic Med. Chem. Lett. 2012, 22 (7), 2470–2473.
(160) Teplova, M.; Wallace, S. T.; Tereshko, V.; Minasov, G.; Symons, A. M.; Cook, P. D.; Manoharan, M.; Egli, M. Structural Origins of the Exonuclease Resistance of a Zwitterionic RNA. Proc. Natl. Acad. Sci. U. S. A. 1999, 96 (25), 14240–14245.
(161) Nawale, G. N.; Bahadorikhalili, S.; Sengupta, P.; Kadekar, S.; Chatterjee, S.; Varghese, O. P. 4′-Guanidinium-Modified SiRNA: A Molecular Tool to Control RNAi Activity through RISC Priming and Selective Antisense Strand Loading. Chem. Commun. 2019, 55 (62), 9112–9115.
(162) Cullis, P. R.; Hope, M. J. Lipid Nanoparticle Systems for Enabling Gene Therapies. Mol. Ther. 2017, 25 (7), 1467–1475.
(163) Piotrowski-Daspit, A. S.; Kauffman, A. C.; Bracaglia, L. G.; Saltzman, M. W. Polymeric Vehicles for Nucleic Acid Delivery. Adv. Drug Deliv. Rev. 2020, 156, 119–132.
(164) Hall, H. K. Correlation of the Base Strengths of Amines. J. Am. Chem. Soc. 1957, 79, 5441–5444.
(165) Woodson, S. A.; Koculi, E. Analysis of RNA Folding by Native Polyacrylamide Gel Electrophoresis. Methods Enzymol. 2009, 469, 189–208.
(166) Steely Jr., T. H.; Gray, D. M.; Ratliff, R. L. CD of Homopolymer DNA/RNA Hybrid Duplexes and Triplexes Containing A/T and A/U Base Pairs. Nucleic Acids Res. 1986, 14, 10071–10090.
(167) Prakash, T. P.; Püschl, A.; Lesnik, E.; Mohan, V.; Tereshko, V.; Egli, M.; Manoharan, M. 2′-O-[2-(Guanidinium)Ethyl]-Modified Oligonucleotides: Stabilizing Effect on Duplex and Triplex Structures. Org. Lett. 2004, 6 (12), 1971–1974.
(168) Dirks, R. W.; Tanke, Hans, J. Advances in Fluorescent Tracking of Nucleic Acids in Living Cell. Biotechniques 2018, 40 (4), 489–495.
(169) Jett, J. H.; A., K. R.; Martin, J. C.; Marrone, B. L.; Moyzis, R. K.; Ratliff, R. L.; Seitzinger, N. K.; Shera, E. B.; Stewart, C. C. High-Speed DNA Sequencing: An Approach Based upon Fluorescence Detection of Single Molecules. J. Biomol. Struct. Dyn. 1989, 7 (2), 301–309.
(170) Rieder, M. J.; Taylor, S. L.; Tobe, V. O.; Nickerson, D. A. Automating the Identification of DNA Variations Using Quality-Based Fluorescence Re-Sequencing: Analysis of the Human Mitochondrial Genome. Nucleic Acids Res. 1998, 26 (4), 967–973.
(171) Tang, X.; Wang, Y.; Li, H. O.; Sakatsume, O.; Sarai, A.; Yokoyama, K. DNA Fingerprinting Involving Fluorescence-Labeled Termini of Any Enzymatically Generated Fragments of DNA. Jpn. J. Hum. Genet. 1994, 39 (4), 379–391.
(172) Prasad, A.; Mohammad Abid Hasan, S.; Grouchy, S.; Gartia, M. R. DNA Microarray Analysis Using a Smartphone to Detect the BRCA-1 Gene. Analyst 2018, 144 (1), 197–205.
(173) Østergaard, M. E.; Hrdlicka, P. J. Pyrene-Functionalized Oligonucleotides and Locked Nucleic Acids (LNAs): Tools for Fundamental Research, Diagnostics, and Nanotechnology. Chem. Soc. Rev. 2011, 40 (12), 5771–5788.
(174) Yamana, K.; Iwase, R.; Furutani, S.; Tsuchida, H.; Zako, H.; Yamaoka, T.; Murakami, A. 2’-Pyrene Modified Oligonucleotide Provides a Highly Sensitive Fluorescent Probe of RNA. Nucleic Acids Res. 1999, 27 (11), 2387–2392.
(175) Christensen, U. B.; Pedersen, E. B. Intercalating Nucleic Acids Containing Insertions of 1-O-(1-Pyrenylmethyl)Glycerol: Stabilisation of DsDNA and Discrimination of DNA over RNA. Nucleic Acids Res. 2002, 30 (22), 4918–4925.
(176) Korshun, V. A.; Stetsenko, D. A.; Gait, M. J. Novel Uridin-2′-Yl Carbamates: Synthesis, Incorporation into Oligodeoxyribonucleotides, and Remarkable Fluorescence Properties of 2′-Pyren-1-Ylmethylcarbamate. J. Chem. Soc. Perkin 1 2002, 2 (8), 1092–1104.
(177) Nakamura, M.; Fukunaga, Y.; Sasa, K.; Ohtoshi, Y.; Kanaori, K.; Hayashi, H.; Nakano, H.; Yamana, K. Pyrene Is Highly Emissive When Attached to the RNA Duplex but Not to the DNA Duplex: The Structural Basis of This Difference. Nucleic Acids Res. 2005, 33 (18), 5887–5895.
(178) Kalyanasundaram, K.; Thomas, J. K. Environmental Effects on Vibronic Band Intensities in Pyrene Monomer Fluorescence and Their Application in Studies of Micellar Systems. J. Am. Chem. Soc. 1977, 99, 2039–2044.
(179) Dougherty, G.; Pilbrow, J. R. Physico-Chemical Probes of Intercalation. Int. J. Biochem. 1984, 16 (12), 1179–1192.
(180) Hrdlicka, P. J.; Karmakar, S. 25 Years and Still Going Strong: 2′-O-(Pyren-1-Yl)Methylribonucleotides-Versatile Building Blocks for Applications in Molecular Biology, Diagnostics and Materials Science. Org. Biomol. Chem. 2017, 15 (46), 9760–9774.
(181) Förster, U.; Lommel, K.; Sauter, D.; Grünewald, C.; Engels, J. W.; Wachtveitl, J. 2-(1-Ethynylpyrene)-Adenosine as a Folding Probe for RNA - Pyrene in or Out. ChemBioChem 2010, 11 (5), 664–672.
(182) Kumar, P.; Shaikh, K. I.; Jørgensen, A. S.; Kumar, S.; Nielsen, P. Three Pyrene-Modified Nucleotides: Synthesis and Effects in Secondary Nucleic Acid Structures. J. Org. Chem. 2012, 77 (21), 9562–9573.
(183) Ueda, T.; Kobori, A.; Yamayoshi, A.; Yoshia, H.; Yamaguchi, M.; Murakami, A. RNA-Based Diagnosis in a Multicellular Specimen by Whole Mount in Situ Hybridization Using an RNA-Specific Probe. Bioorganic Med. Chem. 2012, 20 (20), 6034–6039.
(184) Liao, X.; Pan, J.; Zhang, X.; Tang, Q. Sensitive Detection of Argonaute 2 by Triple-Helix Molecular Switch Reaction and Pyrene Excimer Switching. Aust. J. Chem. 2020, 73 (11), 1074–1079.
(185) Kovacic, M.; Podbevsek, P.; Tateishi-Karimata, H.; Takahashi, S.; Sugimoto, N.; Plavec, J. Thrombin Binding Aptamer G-Quadruplex Stabilized by Pyrene-Modified Nucleotides. Nucleic Acids Res. 2020, 48 (7), 3975–3986.
(186) Semikolenova, O. A.; Golyshev, V. M.; Kim, B. H.; Venyaminova, A. G.; Novopashina, D. S. New Two-Component Pyrene Probes Based on Oligo(2’-O-Methylribonucleotides) for MicroRNA Detection. Russ. J. Bioorganic Chem. 2021, 47, 432–440.
(187) Masuko, M.; Ohtani, H.; Ebata, K.; Shimadzu, A. Optimization of Excimer-Forming Two-Probe Nucleic Acid Hybridization Method with Pyrene as a Fluorophore. Nucleic Acids Res. 1998, 26 (23), 5409–5416.
(188) Copp, W. Influence of Modifications of the Ribose Sugar on the Parallel Stranded Adenosine Duplex. MSc Thesis, Concordia University, QC. 2016.
(189) Cho, N.; Asher, S. A. UV Resonance Raman Studies of DNA-Pyrene Interactions: Optical Decoupling Raman Spectroscopy Selectively Examines External Site Bound Pyrene. J. Am. Chem. Soc. 1993, 115 (14), 6349–6356.
(190) Young, J. S.; Rhee, H.; Joo, T.; Byeang, H. K. Self-Duplex Formation of an A(Py)-Substituted Oligodeoxyadenylate and Its Unique Fluorescence. J. Am. Chem. Soc. 2007, 129 (16), 5244–5247.
(191) Bains, G.; Patel, A. B.; Narayanaswami, V. Pyrene: A Probe to Study Protein Conformation and Conformational Changes. Molecules 2011, 16 (9), 7909–7935.
(192) Yao, C.; Kraatz, H.-B.; Steer, R. P. Photophysics of Pyrene-Labelled Compounds of Biophysical Interest. Photochem. Photobiol. Sci. 2005, 4, 191–199.
(193) Nakajima, A. Solvent Effect on the Vibrational Structures of the Fluorescence and Absorption Spectra of Pyrene. Bull. Chem. Soc. Jpn. 1971, 44, 3272–3277.
(194) Winnik, F. M. Photophysics of Preassociated Pyrenes in Aqueous Polymer Solutions and in Other Organized Media. Chem. Rev. 1993, 93 (2), 587–614.
(195) Dioubankova, N. N.; Malakhov, A. D.; Stetsenko, D. A.; Gait, M. J.; Volynsky, P. E.; Efremov, R. G.; Korshun, V. A. Pyrenemethyl Ara-Uridine-2′-Carbamate: A Strong Interstrand Excimer in the Major Groove of a DNA Duplex. ChemBioChem 2003, 4 (9), 841–847.
(196) Croonen, Y.; Geladé, E.; Van Der Zegel, M.; Van Der Auweraer, M.; Vandendriessche, H.; De Schryver, F. C.; Almgren, M. Influence of Salt, Detergent Concentration, and Temperature on the Fluorescence Quenching of 1-Methylpyrene in Sodium Dodecyl Sulfate with m-Dicyanobenzene. J. Phys. Chem. 1983, 87 (8), 1426–1431.
(197) Neidle, S. Nucleic Acid Structure and Recognition; Oxford University Press: Oxford, 2002.
(198) Rao, S. N.; Kollman, P. A. Molecular Mechanical Simulations on Double Intercalation of 9-Amino Acridine into d(CGCGCGC) X d(GCGCGCG): Analysis of the Physical Basis for the Neighbor-Exclusion Principle. Proc. Natl. Acad. Sci. U. S. A. 1987, 84 (16), 5735–5739.
(199) Gray, D. M.; Ratliff, R. L. Circular Dichroism Spectra of Poly[d(AC):D(GT)], Poly[r(AC):R(GU)], and Hybrids Poly[d(AC):R(GU)] and Poly[r(AC):D(GT)] in the Presence of Ethanol. Biopolymers 1975, 14 (3), 487–498.
(200) Struther Arnott, R.; Chandrasekaran, R. P.; Millane, H.-S. P. DNA-RNA Hybrid Secondary Structures. J. Mol. Biol. 1986, 188 (4), 631–640.
(201) Zimmerman, S. B.; Pheiffer, B. H. A RNA.DNA Hybrid That Can Adopt Two Conformations: An x-Ray Diffraction Study of Poly(RA).Poly(DT) in Concentrated Solution or in Fibers. Proc. Natl. Acad. Sci. U. S. A. 1981, 78 (1), 78–82.
(202) Kypr, J.; Kejnovska, I.; Renciuk, D.; Vorlickova, M. Circular Dichroism and Conformational Polymorphism of DNA. Nucleic Acids Res. 2009, 37 (6), 1713–1725.
(203) Obika, S.; Sekine, M. Synthesis of Therapeutic Oligonucleotides; Springer Nature Singapore: Singapore, 2018.
(204) Liczner, C.; Duke, K.; Juneau, G.; Egli, M.; Wilds, C. J. Beyond Ribose and Phosphate: Selected Nucleic Acid Modifications for Structure-Function Investigations and Therapeutic Applications. Beilstein J. Org. Chem. 2021, 17, 908–931.
(205) Eckstein, F. Nucleoside Phosphorothioates. J. Am. Chem. Soc. 1966, 88 (18), 4292–4294.
(206) Clavé, G.; Reverte, M.; Vasseur, J.-J.; Smietana, M. Modified Internucleoside Linkages for Nuclease-Resistant Oligonucleotides. RSC Chem. Biol. 2021, No. 1.
(207) Pallan, P. S.; Lybrand, T. P.; Schlegel, M. K.; Harp, J. M.; Jahns, H.; Manoharan, M.; Egli, M. Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost. Biochemistry 2020, 59 (49), 4627–4637.
(208) Mori, K.; Boiziau, C.; Cazenave, C.; Matsukura, M.; Subasinghe, C.; Cohen, J. S.; Broder, S.; Toulme, J. J.; Stein, C. A. Phosphoroselenoate Oligodeoxynucleotides: Synthesis, Physico-Chemical Characterization, Anti-Sense Inhibitory Properties and Anti-HIV Activity. Nucleic Acids Res. 1989, 17 (20), 8207–8219.
(209) Wilds, C. J.; Pattanayek, R.; Pan, C.; Wawrzak, Z.; Egli, M. Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure. J. Am. Chem. Soc. 2002, 124 (50), 14910–14916.
(210) Hara, R. I.; Saito, T.; Kogure, T.; Hamamura, Y.; Uchiyama, N.; Nukaga, Y.; Iwamoto, N.; Wada, T. Stereocontrolled Synthesis of Boranophosphate DNA by an Oxazaphospholidine Approach and Evaluation of Its Properties. J. Org. Chem. 2019, 84 (12), 7971–7983.
(211) Eckstein, F. A Dinucleoside Phosphorothioate. Tetrahedron Lett. 1967, 8 (13), 1157–1160.
(212) Tang, J. Y.; Temsamani, J.; Agrawal, S. Self-Stabilized Antisense Oligonucleotide Phosphorothioates: Properties and Anti-HIV Activity. Nucleic Acids Res. 1993, 21 (11), 2729–2735.
(213) Koziolkiewicz, M.; Krakowiak, A.; Kwinkowski, M.; Boczkowska, M.; Stec, W. J. Stereodifferentiation--the Effect of P Chirality of Oligo(Nucleoside Phosphorothioates) on the Activity of Bacterial RNase H. Nucleic Acids Res. 1995, 23 (24), 5000–5005.
(214) Koziolkiewicz, M.; Wojcik, M.; Kobylanska, A.; Karwowski, B.; Rebowska, B.; Guga, P.; Stec, W. J. Stability of Stereoregular Oligo(Nucleoside Phosphorothioate)s in Human Plasma: Diastereoselectivity of Plasma 3’-Exonuclease. Antisense Nucleic Acid Drug Dev. 2009, 7 (1), 43–48.
(215) Roberts, T. C.; Langer, R.; Wood, M. J. A. Advances in Oligonucleotide Drug Delivery. Nat. Rev. Drug Discov. 2020, 19 (10), 673–694.
(216) Crooke, S. T.; Witztum, J. L.; Bennett, C. F.; Baker, B. F. RNA-Targeted Therapeutics. Cell Metab. 2018, 27 (4), 714–739.
(217) Shen, X.; Corey, D. R. Chemistry, Mechanism and Clinical Status of Antisense Oligonucleotides and Duplex RNAs. Nucleic Acids Res. 2018, 46 (4), 1584–1600.
(218) Ali, M. M.; Li, F.; Zhang, Z.; Zhang, K.; Kang, D.-K.; Ankrum, J. A.; Le, C. X.; Zhao, W. Rolling Circle Amplification: A Versatile Tool for Chemical Biology, Materials Science and Medicine. Chem. Soc. Rev. 2014, 43, 3324–3341.
(219) An, R.; Li, Q.; Fan, Y.; Li, J.; Pan, X.; Komiyama, M.; Liang, X. Highly Efficient Preparation of Single-Stranded DNA Rings by T4 Ligase at Abnormally Low Mg(II) Concentration. Nucleic Acids Res. 2017, 45, e139.
(220) Cui, Y.; Han, X.; An, R.; Zhou, G.; Komiyama, M.; Liang, X. Cyclization of Secondarily Structured Oligonucleotides to Single-Stranded Rings by Using Taq DNA Ligase at High Temperatures. RSC Adv. 2018, 8 (34), 18972–18979.
(221) Kalinowski, M.; Haug, R.; Said, H.; Piasecka, S.; Kramer, M.; Richert, C. Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures. ChemBioChem 2016, 17 (12), 1150–1155.
(222) El-Sagheer, A. H.; Brown, T. Single Tube Gene Synthesis by Phosphoramidate Chemical Ligation. Chem. Commun. 2017, 53 (77), 10700–10702.
(223) Gryaznov, S. M.; Letsinger, R. L. Synthesis and Properties of Oligonucleotides Containing Aminodeoxythymidine Units. Nucleic Acids Res. 1992, 20 (13), 3403–3409.
(224) De Mesmaeker, A.; Waldner, A.; Lebreton, J.; Hoffmann, P.; Fritsch, V.; Wolf, R. M.; Freier, S. M. Amides as a New Type of Backbone Modification in Oligonucleotides. Angew Chem Int Ed Engl. 1994, 33 (2), 226–229.
(225) Kuwahara, M.; Takeshima, H.; Nagashima, J.; Minezaki, S.; Ozaki, H.; Sawai, H. Transcription and Reverse Transcription of Artificial Nucleic Acids Involving Backbone Modification by Template-Directed DNA Polymerase Reactions. Bioorganic Med. Chem. 2009, 17 (11), 3782–3788.
(226) Obika, S.; Nanbu, D.; Hari, Y.; Morio, K. I.; In, Y.; Ishida, T.; Imanishi, T. Synthesis of 2’-O,4’-C-Methyleneuridine and -Cytidine. Novel Bicyclic Nucleosides Having a Fixed C3-Endo Sugar Puckering. Tetrahedron Lett. 1997, 38 (50), 8735–8738.
(227) Singh, S. K.; Nielsen, P.; Koshkin, A. A.; Wengel, J. LNA ( Locked Nucleic Acids ): Synthesis and High-Affinity Nucleic Acid Recognition. Chem. Commun. 1998, No. 4, 455–456.
(228) Koshkin, A.; Singh, S. K.; Nielsen, P.; Meldgaard, M.; Rajwanshi, V. K.; Kumar, R.; Skouv, J.; Nielsen, C. B.; Jacobsen, J. P.; Jacobsen, N.; Olsen, C. E.; Wengel, J. LNA (Locked Nucleic Acids): Synthesis of the Adenine, Cytosine, Guanine, 5-Methylcytosine, Thymine, and Uracil Bicyclonucleoside Monomers, Oligomerisation, and Unprecedented Nucleic Acid Recognition. Tetrahedron 1998, 54, 3607–3630.
(229) Bondensgaard, K.; Petersen, M.; Singh, S. K.; Rajwanshi, V. K.; Kumar, R.; Wengel, J.; Jacobsen, J. P. Structural Studies of LNA:RNA Duplexes by NMR: Conformations and Implications for RNase H Activity. Chem. - A Eur. J. 2000, 6 (15), 2687–2695.
(230) Petersen, M.; Bondensgaard, K.; Wengel, J.; Jacobsen, J. P. Locked Nucleic Acid (LNA) Recognition of RNA: NMR Solution Structures of LNA:RNA Hybrids. J. Am. Chem. Soc. 2002, 124 (21), 5974–5982.
(231) Platts, J. A.; Howard, S. T.; Bracke, B. R. F. Directionality of Hydrogen Bonds to Sulfur and Oxygen. J. Am. Chem. Soc. 1996, 118 (11), 2726–2733.
(232) Oka, N.; Kondo, T.; Fujiwara, S.; Maizuru, Y.; Wada, T. Stereocontrolled Synthesis of Oligoribonucleoside Phosphorothioates by an Oxazaphospholidine Approach. Org. Lett. 2009, 11 (4), 967–970.
(233) Østergaard, M. E.; De Hoyos, C. L.; Wan, W. B.; Shen, W.; Low, A.; Berdeja, A.; Vasquez, G.; Murray, S.; Migawa, M. T.; Liang, X. H.; Swayze, E. E.; Crooke, S. T.; Seth, P. P. Understanding the Effect of Controlling Phosphorothioate Chirality in the DNA Gap on the Potency and Safety of Gapmer Antisense Oligonucleotides. Nucleic Acids Res. 2020, 48 (4), 1691–1700.
(234) Astakhova, I. K.; Wengel, J. Scaffolding along Nucleic Acid Duplexes Using 2’-Amino-Locked Nucleic Acids. Acc. Chem. Res. 2014, 47 (6), 1768–1777.
(235) Egli, M.; Pallan, P. S. Insights from Crystallographic Studies into the Structural and Pairing Properties of Nucleic Acid Analogs and Chemically Modified DNA and RNA Oligonucleotides. Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 281–305.
(236) Conlon, P. F.; Eguaogie, O.; Wilson, J. J.; Sweet, J. S. T.; Steinhoegl, J.; Englert, K.; Hancox, O. G. A.; Law, C. J.; Allman, S. A.; Tucker, J. H. R.; Hall, J. P.; Vyle, J. S. Solid-Phase Synthesis and Structural Characterisation of Phosphoroselenolate-Modified DNA: A Backbone Analogue Which Does Not Impose Conformational Bias and Facilitates SAD X-Ray Crystallography. Chem. Sci. 2019, 10 (47), 10948–10957.
(237) Sood, A.; Shaw, B. R.; Spielvogel, B. F. Boron-Containing Nucleic Acids: Synthesis of Oligodeoxynucleoside Boranophosphates. J. Am. Chem. Soc. 1990, 112, 9000–9001.
(238) Hall, A. H. S.; Wan, J.; Shaughnessy, E. E.; Shaw, B. R.; Alexander, K. A. RNA Interference Using Boranophosphate SiRNAs: Structure-Activity Relationships. Nucleic Acids Res. 2004, 32 (20), 5991–6000.
(239) Bartosik, K.; Debiec, K.; Czarnecka, A.; Sochacka, E.; Leszczynska, G. Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach. Molecules 2020, 25 (15).
(240) Eckhardt, M.; Fu, G. C. The First Applications of Carbene Ligands in Cross-Couplings of Alkyl Electrophiles: Sonogashira Reactions of Unactivated Alkyl Bromides and Iodides. J. Am. Chem. Soc. 2003, 125 (45), 13642–13643.
(241) Kwon, T.; Piton, N.; Grünewald, C.; Engels, J. W. Synthesis of Pyrene Labeled RNA for Fluorescence Measurements. Nucleosides, Nucleotides and Nucleic Acids 2007, 26 (10–12), 1381–1386.
(242) Grünewald, C.; Kwon, T.; Piton, N.; Förster, U.; Wachtveitl, J.; Engels, J. W. RNA as Scaffold for Pyrene Excited Complexes. Bioorganic Med. Chem. 2008, 16 (1), 19–26.
(243) Kauffman, G. B.; Teter, L. A.; Rhoda, R. N. Recovery of Platinum from Laboratory Residues. In Inorganic Syntheses; Kleinberg, J., Ed.; McGraw-Hill, 1963; Vol. 7, pp 232–236.
(244) Tataurov, A. V.; You, Y.; Owczarzy, R. Predicting Ultraviolet Spectrum of Single Stranded and Double Stranded Deoxyribonucleic Acids. Biophys. Chem. 2008, 133 (1–3), 66–70.
(245) Ma, Q.; Yang, H.; Hao, J.; Tan, Y. Synthesis and Aggregation Behavior of Copolymer of Acrylamide with Pseudorotaxane Monomer by Threading Cucurbit[6]Uril onto N′-(4-Vinylbenzyl)-1,4-Diaminobutane Dihydrochloride. J. Dispers. Sci. Technol. 2012, 33 (5), 639–646.
(246) Ju, Y.; Kumar, D.; Varma, R. S. Revisiting Nucleophilic Substitution Reactions: Microwave-Assisted Synthesis of Azides , Thiocyanates , and Sulfones in an Aqueous Medium. J. Org. Chem. 2006, 71, 6697–6700.
(247) Zhang, Y.; Duan, D.; Zhong, Y.; Guo, X.; Guo, J.; Gou, J. Fe ( III ) -Catalyzed Aerobic Intramolecular N − N Coupling of Aliphatic Azides with Amines. Org. Lett. 2019, 21 (13), 4960–4965.
(248) Bartels, J. L.; Lu, P.; Walker, A.; Maurer, K.; Moeller, K. D. Building Addressable Libraries: A Site-Selective Click-Reaction Strategy for Rapidly Assembling Mass Spectrometry Cleavable Linkers. Chem. Commun. 2009, 37, 5573–5575.
(249) Burrows, C. J.; Muller, J. G. Oxidative Nucleobase Modifications Leading to Strand Scission. Chem. Rev. 1998, 98 (3), 1109–1151.