(12) Patent Application Publication (10) Pub. No.: US 2010/013.6614 A1 Luo Et Al
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US 2010O136614A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/013.6614 A1 Luo et al. (43) Pub. Date: Jun. 3, 2010 (54) DENDRIMER-LIKE MODULAR DELIVERY Publication Classification VECTOR (51) Int. Cl. CI2P 2L/00 (2006.01) (76) Inventors: Dan Luo, Ithaca, NY (US); Yougen C08G 83/00 (2006.01) Li, Pasadena, CA (US) (52) U.S. Cl. ...…. 435/68.1: 525/54.2 (57) ABSTRACT Correspondence Address: WILSON, SONSINI, GOODRICH & ROSATI Various nucleic acid-based matrixes are provided, compris 650 PAGE MILL ROAD ing nucleic acid monomers as building blocks, as well as PALO ALTO, CA 94304-1050 (US) nucleic acids encoding proteins, so as to produce novel bio materials. The nucleic acids are used to form dendrimers that are useful as Supports, vectors, carriers or delivery vehicles (21) Appl. No.: 11/583,990 for a variety of compounds in biomedical and biotechnologi cal applications. In particular, the macromolecules may be (22) Filed: Oct. 18, 2006 used for the delivery of drugs, genetic material, imaging components or other functional molecule to which they can Related U.S. Application Data be conjugated. An additional feature of the macromolecules is their ability to be targeted for certain organs, tumors, or types (60) Provisional application No. 60/727.961, filed on Oct. of tissues. Methods of utilizing such biomaterials include 18, 2005. delivery of functional molecules to cells. Patent Application Publication Jun. 3, 2010 Sheet 1 of 13 US 2010/013.6614 A1 Patent Application Publication Jun. 3, 2010 Sheet 2 of 13 US 2010/013.6614 A1 Patent Application Publication Jun. 3, 2010 Sheet 4 of 13 US 2010/013.6614 A1 Patent Application Publication Jun. 3, 2010 Sheet 5 of 13 US 2010/013.6614 A1 Patent Application Publication Jun. 3, 2010 Sheet 6 of 13 US 2010/013.6614 A1 Patent Application Publication Jun. 3, 2010 Sheet 7 of 13 US 2010/013.6614 A1 FIG.7 SECR D NO:96 Patent Application Publication Jun. 3, 2010 Sheet 8 of 13 US 2010/013.6614 A1 FIG. 11 Patent Application Publication Jun. 3, 2010 Sheet 9 of 13 US 2010/013.6614 A1 FIG. 12 FG, 13 Patent Application Publication Jun. 3, 2010 Sheet 10 of 13 US 2010/013.6614 A1 FIG.15. J SEG ID NO:100 SEQD NO:97. P, GTGAGTAGTGA AATTGACTCATGGACTAs #élé SEO D NO:99 SEOQ ID NO:98 ? · DNA FIG. 16 SEO ID NO: 104 *woravovouvogvlowaaoauvoiejewou'257 0LLLLLLLLLSLLLLLLLLLLLLLL SEOQ ID NO: 103 <-R dumbbel-DNA. SEOQ ID NO 102 FIG. 17 SEGQD NO: 1 .....................................3????????????????????”“ **` SEOQ ID NO:3 SEO DI NO:2 ? Patent Application Publication Jun. 3, 2010 Sheet 11 of 13 US 2010/013.6614 A1 Plasmid DNA as CnC , ! Schema of viral and non-viral hybrid system Patent Application Publication Jun. 3, 2010 Sheet 12 of 13 US 2010/013.6614 A1 Patent Application Publication Jun. 3, 2010 Sheet 13 of 13 US 2010/013.6614 A1 FIG. 21. Seberinë , BOTN-spacer-DNA. (Bio-5p-SP). BioTN-spacer-DNA * GGCG---TCSACF-5° Yo-ONA . Step. Bio-5p-CCGG AAC3. tggcor-TTGACT's ... US 2010/013.6614 A1 Jun. 3, 2010 and DNA-mediated supramolecular structures (Taton et al., polynucleotide is complementary to at least a portion of the Journal of the American Chemical Society 122:6305-6306 third polynucleotide, and where the first, second, and third (2000)), DNA sensing via gold nanoparticles (Elghanian et polynucleotides are associated together to form a multimer, al., Science 277:1078-81 (1997)), Y-shape DNA molecules and at least one of the first, second and third polynucleotides (Eckardt et al., Nature 420:286 (2002)) and DNA patterning are linked to at least one bioactive agent. In some embodi via dip-pen nanolithography (Demers et al., Science 296. ments, the multimers are trimers that are Y-shape or T-shape. 1836-8 (2002)). However, the preceding prior art DNA-based In one embodiment, all the trimers are Y-shape. In another structures are are further limited to linear DNA. Linear DNA embodiment, the all the trimers are T-shape. In yet other was first used to construct an artificial nano-structure (Chenet embodiments, the trimers are Y- and T-shape. al., Nature 350,631 (1991)). Using “double crossover DNA (two crossovers connecting two helical domains), a variety of 0012. In other aspects of the invention, a multimer mol geometric objects, periodic arrays and nanoscale mechanical ecule comprises a first, a second, a third and a fourth poly devices have been constructed (Yan et al., Nature 415, 62 nucleotide, where at least a portion of the first polynucleotide (2002):Yan et al., Science 301, 1882 (2003); Seeman, Trends is complementary to at least a portion of the second poly Biochem Sci 30, 119 (2005); Pinto et al., Nano Lett 5, 2399 nucleotides, where at least a portion of the first polynucle (2005)). Recently Lin et al. used a linear DNA molecule as a otide is complementary to at least a portion of the fourth cross-linker to construct a thermal-stimulative polyacryla polynucleotide, where at least a portion of the third poly mide hydrogel, creating a DNA-polymer hybrid hydrogel nucleotide is complementary to at least a portion of second system (Lin et al., J Biomech Eng 126, 104 (2004)). polynucleotide and where at least a porting of the third poly 0009. However, dendrimer-like nucleic acid compositions nucleotide is complementary to at least a portion of the fourth have not been utilized to effect delivery of bioactive agents to polynucleotides, and where at least one of the first, second, cells (either in a targeted or nonspecific manner). Therefore third and fourth polynucleotides are linked to at least one there is a need for new biomaterials that have applications in bioactive agent. In some embodiments, the multimers are diverse areas of biotechnology and medicine, and which pro tetramers that are X-shape or dumbbell shape. For dumbbell vide more effecient modular delivery, sufficient release and shapes, the second polynucleotide comprises at least portions effective cellular/tissue targeting. The present invention pro vides compositions and methods that provide dendrimer-like that are complementary to the first, third and fourth nucle nucleic acid-based products useful in biotechnology and otides. Similarly, the fourth polynucleotide comprises at least medicine as modular delivery vectors for a multitidue of Some portions that are complementary to the first, second and compounds. third polynucleotides. In one embodiment, all the tetramers are X-shape. In another embodiment, the all the tetramers are SUMMARY OF THE INVENTION dumbbell-shape. In yet other embodiments, the tetramers are X- and dumbbell-shape. 0010 Certain aspects of the present invention provide a 0013. In some aspects of the invention also provide a multivalent vector capable of providing a plurality of attach method of making a nucleic acid assembly by associating at ment points for a plurality of the same or distinct bioactive least two mutlimers together. In some embodiments, the mul agents. Such bioactive agents include without limitation, timers so assembled are all of one shape (i.e., Y, T, X- or therapeutics (e.g., drugs, nucleic acids, Small organic mol dumbbell shape). In yet, other embodiments, the multimers so ecules, inorganic molecules), targeting or delivery moieties assembled are of one or more different shape. Such Y, T, X (e.g., signal peptides, nucleic acid condensing peptides, anti or dumbbell-shape molecules are building blocks which form bodies, one or more receptor/ligand or other binding pair an assembled structure. In some embodiments, a multimer members, biotin or nucleic acids), labeling/staining moieties building block comprises at least one polynucleotide having a (e.g., quantum dots, dyes, stains, selection markers), as well Sticky end. In other embodiments, a multimer comprises as Solid Substrates (e.g., agarose beads, magnetic beads, etc.). polynucleotides, each of which comprises a sticky end. Therefore, a key feature of a multivalent vector is that any number of different chemical/biochemical entities can be 0014. In some embodiments, a nucleic acid assembly is linked directly or indirectly to the multivalent vector. Den produced by associating a plurality of multimers together. In drimers as described herein provide a multivalent and/or Some embodiments, such associations produce Dendrimer monodisperse structure that provides multiple sites for addi Like-Nucleic Acid Molecules (DL-NAMs). In yet other tion of one or more molecules of interest, including without embodiments, DL-NAMs comprise at least some linear linker limitation bioactive agents, targeting agents, selection mark nucleic acid molecules. In various embodiments, DL-NAMs ers, antibiotics, detection signals/labels, drugs ora combina are comprised of a single shape or at least two different shape tion thereof. In various embodiments, such vectors can be building block molecules. utilized to deliver one or more bioactive agents to a cell or [0015] In certain embodiments, the DL-NAMs are pro animal. In other embodiments, such Vectors can also be uti duced in a controlled fashion, by adding multimer building lized in diagnostics by targeting specific cells related to dis blocks in Successive rounds to producea highly branched, ease (e.g., pathogens, cancer, etc.). Moreover, such multiva tree-shape DL-NAMs. In some embodiments, DL-NAMs are lent vectors are utilized in vivo as well as in vitro. produced that are either isotropic or anisotropic, providing 0011. In some aspects of the invention a composition com molecules that are linked to various other biochemical/ prises a multimer molecule, including a first, a second, and a chemical entities (e.g., therapeutics, targeting/delivery third polynucleotide, where at least a portion of the first agents, labeling/staining agents, binding pair members, etc.). polynucleotide is complementary to at least a portion of the 0016.