DNAmoreDB - A Database of Deoxyribozymes

Abstract:

The selection of modified DNAzymes represents an important endeavor in expanding the chemical and catalytic properties of catalytic nucleic acids. Few examples of such exist and to date, there is no example where three different modified bases have been simultaneously incorporated for catalytic activity. Herein, dCTP, dATP and dUTP bearing, respectively, a cationic amine, an imidazole and a cationic guanidine, were enzymatically polymerized on a DNA template for the selection of a highly functionalized DNAzyme, called DNAzyme 9-86, that catalyzed (M 2+ )-independent self-cleavage under physiological conditions at a single ribo(cytosine)phosphodiester linkage with a rate constant of (0.134 ± 0.026) min −1 . A pH rate profile analysis revealed p Ka 's of 7.4 and 8.1, consistent with both general acid and base catalysis. The presence of guanidinium cations permits cleavage at significantly higher temperatures than previously observed for DNAzymes with only amines and imidazoles. Qualitatively, DNAzyme 9-86 presents an unprecedented ensemble of synthetic functionalities while quantitatively it expresses one of the highest reported values for any self-cleaving nucleic acid when investigated under M 2+ -free conditions at 37°C.

DNAzymes linked to this article:

Name	Isolated sequence	Length	Reaction
Dz9-3	ACCAACACTGCGTGTGTCTTGTGTGCG	27	RNA cleavage
Dz9-4	ACCAACACTAGCAGCGCCAGTGAGGCTCGCGTT	33	RNA cleavage
Dz9-5	ACCAACAGAGAGTGTACTGTGGGTGTA	27	RNA cleavage
Dz9-9	ACCAACATTGTTGCATCGCATGTGATG	27	RNA cleavage
Dz9-11	ACCACATGGTGAGTGTGGACGGTGTTT	27	RNA cleavage
Dz9-12	ACCAACACCGTGTGTGTGTCGTGTGTA	27	RNA cleavage
Dz9-13	ACCAACAGAGAGTGTATCGTGGTGGGTC	28	RNA cleavage
Dz9-17	ACCAACAGAGAGTGTACCATGTGTGTA	27	RNA cleavage
Dz9-18	ACCAACAATGGAGCGCTAGTGATGTTTC	28	RNA cleavage
Dz9-28	ACCAACATTGCCAGCGGTAGTGTCGCTCGCT	31	RNA cleavage
Dz9-29	ACCAACATTGCCAGCGGCAGTGAGGCTTC	29	RNA cleavage
Dz9-33	ACCAACATCGCCAGCGGCAGTGAGGTTCGCA	31	RNA cleavage
Dz9-36	ACCAACATTCCCAGCGGGAGTGTCGCC	27	RNA cleavage
Dz9-40	ACCAACAGGATTGCAGTAGGTTGTGCCG	28	RNA cleavage
Dz9-43	ACCAACAGTGTTTGCTTGGCTATGGCTC	28	RNA cleavage
Dz9-52	ACCAACACCATACAGCGCTAGTGTC	25	RNA cleavage
Dz9-53	ACCAACAACGCATCGTTAGTGAGGGTGC	28	RNA cleavage
Dz9-54	ACCAACATGGTGTGTCTGGGTGGGGTGT	28	RNA cleavage
Dz9-55	ACCAACAGGCACAGGGGGAGTGGTGTTG	28	RNA cleavage
Dz9-56	ACCAACATTGCCAGCGGCAGTGAGTGCAC	29	RNA cleavage
Dz9-57	ACCAACATGTGCACAGTGGTTCGGTG	26	RNA cleavage
Dz9-59	ACCAACAAAGCAGCGTTAGTGAGGCGC	27	RNA cleavage
Dz9-60	ACCAACAGCCTACTAGCGGGAGTGAG	26	RNA cleavage
Dz9-61	ACCAACAGAGAGTGTTTGATGGGTGTG	27	RNA cleavage
Dz9-63	ACCAACAGAGAGTGTTTTATGGGTGTC	27	RNA cleavage
Dz9-64	ACCAACATTAGCAGCGCATGTGGTGGCTTG	30	RNA cleavage
Dz9-67	ACCAACACAGTGTGTCACAGCGGTGTA	27	RNA cleavage
Dz9-77	ACCACCCTGGAGTGGACTATGTGGGTA	27	RNA cleavage
Dz9-81	ACCAACATGTCGCGTACGGTTGGTGTTG	28	RNA cleavage
Dz9-82	ACCAACATGAGAGCTTCGTACGGGAGGT	28	RNA cleavage
Dz9-83	ACCAACAGCACGTATCGGGTTTTGTT	26	RNA cleavage
Dz9-86	ACCAACATCATGCAGCGCGTAGTGTC	26	RNA cleavage
Dz9-92	ACCAACATTAGCAGTGCATGTGATGGCTGC	30	RNA cleavage
Dz9-96	ACCAACAGTGAGTGTACTATGTTGTGTC	28	RNA cleavage

Menu: