Understanding How DNA Enzymes Work

2016 ◽  
Vol 55 (18) ◽  
pp. 5376-5377 ◽  
Author(s):  
Julia Wirmer-Bartoschek ◽  
Harald Schwalbe
Keyword(s):  
Dna Enzymes

Engineering DNA aptamers and DNA enzymes with fluorescence-signaling properties

2004 ◽  
Vol 76 (7-8) ◽  
pp. 1547-1561 ◽  
Author(s):  
R. Nutiu ◽  
Shirley Mei ◽  
Zhongjie Liu ◽  
Y. Li
Keyword(s):  
Dna Sequences ◽  
Rational Design ◽  
In Vitro Selection ◽  
Random Sequence ◽  
Pair Potential ◽  
Dna Aptamers ◽  
Dna Molecules ◽  
Dna Enzymes ◽  
Fluorescence Signaling

Single-stranded DNA molecules with ligand-binding ability and catalytic function, referred to as DNA aptamers and DNA enzymes, respectively, are special DNA sequences isolated from random-sequence DNA libraries by “in vitro selection”. These two new classes of artificial DNA molecules have the potential of being used as molecular tools in a variety of innovative applications ranging from biosensing to gene regulation. Our laboratory is interested in engineering fluorescence-signaling DNA aptamers and DNA enzymes that can be widely exploited for detection-directed applications. In this article, we will first discuss our recent efforts on the rational design of a new class of signaling aptamers denoted “structure- switching signaling aptamers”, which report target binding by switching structures from DNA/DNA duplex to DNA/target complex. We will then describe the in vitro selection of fluorescence-signaling DNA enzymes that exhibit a synchronized catalysis-signaling capability by cleaving a chimeric RNA/DNA substrate at the lone RNA linkage surrounded by closely spaced fluorophore-quencher pair. Potential utilities of these signaling DNA molecules will also be discussed.

scholarly journals In vitro-selected RNA cleaving DNA enzymes from a combinatorial library are potent inhibitors of HIV-1 gene expression

2000 ◽  
Vol 352 (3) ◽  
pp. 667-673 ◽  
Author(s):  
Bandi SRIRAM ◽  
Akhil C. BANERJEA
Keyword(s):  
Gene Expression ◽  
Mammalian Cell ◽  
Specific Gene ◽  
Cleavage Sites ◽  
Dna Enzymes ◽  
Biological Tool ◽  
Catalytic Motif ◽  
Target Rna ◽  
Hiv 1

Selective inactivation of a target gene by antisense mechanisms is an important biological tool to delineate specific functions of the gene product. Approaches mediated by ribozymes and RNA-cleaving DNA enzymes (DNA enzymes) are more attractive because of their ability to catalytically cleave the target RNA. DNA enzymes have recently gained a lot of importance because they are short DNA molecules with simple structures that are expected to be stable to the nucleases present inside a mammalian cell. We have designed a strategy to identify accessible cleavage sites in HIV-1 gag RNA from a pool of random DNA enzymes, and for isolation of DNA enzymes. A pool of random sequences (all 29 nucleotides long) that contained the earlier-identified 10Ő23 catalytic motif were tested for their ability to cleave the target RNA. When the pool of random DNA enzymes was targeted to cleave between any A and U nucleotides, DNA enzyme 1836 was identified. Although several DNA enzymes were identified using a pool of DNA enzymes that was completely randomized with respect to its substrate-binding properties, DNA enzyme-1810 was selected for further characterization. Both DNA enzymes showed target-specific cleavage activities in the presence of Mg2+ only. When introduced into a mammalian cell, they showed interference with HIV-1-specific gene expression. This strategy could be applied for the selection of desired target sites in any target RNA.

scholarly journals Suppression of bcr/abl chimeric gene by conjugate DNA enzymes in human cells

2005 ◽  
Vol 49 (1) ◽  
pp. 333-334 ◽  
Author(s):  
Kengo Takamori ◽  
Takanori Kubo ◽  
Zhivko Zhelev ◽  
Bakalova Rumiana ◽  
Hideki Ohba ◽  
...  
Keyword(s):  
Human Cells ◽  
Chimeric Gene ◽  
Dna Enzymes

scholarly journals Evidence for two waves of induction of DNA enzymes in stimulated human lymphocytes

1974 ◽  
Vol 1 (9) ◽  
pp. 1183-1200 ◽  
Author(s):  
Guido C.F. Pedrali Noy ◽  
Leda Dalpra' ◽  
Antonia M. Pedrini ◽  
Giovanni Ciarrocchi ◽  
Elena Giulotto ◽  
...  
Keyword(s):  
Human Lymphocytes ◽  
Dna Enzymes

scholarly journals Structural insights into DNA repair by RNase T

2014 ◽  
Vol 70 (a1) ◽  
pp. C208-C208
Author(s):  
Yu-Yuan Hsiao ◽  
Hanna Yuan
Keyword(s):  
Crystal Structure ◽  
Dna Repair ◽  
Binding Mode ◽  
Heteroduplex Dna ◽  
Dna Enzymes ◽  
Endonuclease V ◽  
Dna Damaging Agents ◽  
Bulge Dna ◽  
Repair Pathways ◽  
Structural Insights

DNA repair is generally accomplished by a coordinated effort via several types of DNA enzymes, including endonucleases, exonucleases, helicases, polymerases and ligases. Among all these DNA enzymes, the molecular functions of exonucleases, which bind at the 3′ or 5′ end of DNA and cleave one nucleotide at a time, are least understood in how they select DNA substrates for binding and trimming. Here we show that the DEDDh family exonuclease RNase T is critical for Escherichia coli resistance to various DNA damaging agents and UV radiation. RNase T specifically trims the 3′ end of structured DNA, including bulge, bubble and Y-structured DNA, and it can work with Endonuclease V to restore the deaminated base in an inosine-containing heteroduplex DNA. Our crystal structure analyses further reveal how RNase T recognizes the bulge DNA by inserting a phenylalanine into the bulge, and as a result the 3′ end of blunt-end bulge DNA can be digested by RNase T. In contrast, the homodimeric RNase T interacts with the Y-structured DNA by a different binding mode via a single protomer so that the 3′ overhang of the Y-structured DNA can be trimmed closely to the duplex region. Our data suggest that RNase T likely processes bulge and bubble DNA in the Endonuclease V-dependent DNA repair, whereas it processes Y-structured DNA in UV-induced and various other DNA repair pathways. This study thus provides mechanistic insights for RNase T and thousands of DEDDh-family exonucleases in DNA 3′-end processing.

Visual SNP genotyping using asymmetric PCR and split DNA enzymes

The Analyst ◽  
2011 ◽  
Vol 136 (8) ◽  
pp. 1569 ◽  
Author(s):  
Jia Ling Neo ◽  
Kanglie Darius Aw ◽  
Mahesh Uttamchandani
Keyword(s):  
Snp Genotyping ◽  
Asymmetric Pcr ◽  
Dna Enzymes
Sign in / Sign up

Export Citation Format

Share Document