Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.

The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it.

Reselection Yielding a Smaller and More Active Silver-Specific DNAzyme.

Ag10c is a recently reported RNA-cleaving DNAzyme obtained from in vitro selection. Its cleavage activity selectively requires Ag ions, and thus it has been used as a sensor for Ag detection. However, the previous selection yielded very limited information regarding its sequence requirement, since only ∼0.

Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence.

The RNA-cleaving Ag10c DNAzyme was recently isolated via in vitro selection and it can bind two Ag ions for activity. The Ag10c contains a well-defined Ag binding aptamer as indicated by DMS footprinting. Since aptamer binding is often accompanied with conformational changes, we herein used 2-aminopurine (2AP) to probe its folding in the presence of Ag.

Two Completely Different Mechanisms for Highly Specific Na Recognition by DNAzymes.

Our view of the interaction between Na and nucleic acids was changed by a few recently discovered Na -specific RNA-cleaving DNAzymes. In addition to nonspecific electrostatic interactions, highly specific recognition is also possible. Herein, two such DNAzymes, named EtNa and Ce13d, are compared to elucidate their mechanisms of Na binding.

Metal Sensing by DNA.

Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main biological role of DNA is to store genetic information, its chemical structure is ideal for metal binding via both the phosphate backbone and nucleobases.

A Silver-Specific DNAzyme with a New Silver Aptamer and Salt-Promoted Activity.

Most RNA-cleaving DNAzymes require a metal ion to interact with the scissile phosphate for activity. Therefore, few unmodified DNAzymes work with thiophilic metals because of their low affinity for phosphate. Recently, an Ag-specific Ag10c DNAzyme was reported via in vitro selection.

An Exceptionally Selective DNA Cooperatively Binding Two Ca Ions.

Ca is a highly important metal ion in biology and in the environment, and thus there is extensive work in developing sensors for Ca detection. Although many Ca -binding proteins are known, few nucleic acids can selectively bind Ca . DNA-based biosensors are attractive for their high stability and excellent programmability.

Label-Free Ag⁺ Detection by Enhancing DNA Sensitized Tb(3+) Luminescence.

In this work, the effect of Ag⁺ on DNA sensitized Tb(3+) luminescence was studied initially using the Ag⁺-specific RNA-cleaving DNAzyme, Ag10c. While we expected to observe luminescence quenching by Ag⁺, a significant enhancement was produced. Based on this observation, simple DNA oligonucleotide homopolymers were used with systematically varied sequence and length.

A Silver DNAzyme.

Silver is a very common heavy metal, and its detection is of significant analytical importance. DNAzymes are DNA-based catalysts; they typically recruit divalent and trivalent metal ions for catalysis. Herein, we report a silver-specific RNA-cleaving DNAzyme named Ag10c obtained after six rounds of in vitro selection.

Deciphering the role of Atg5 in nucleotide dependent interaction of Rab33B with the dimeric complex, Atg5-Atg16L1.

Autophagy is a lysosomal degradation pathway that degrades cytosolic constituents, including whole organelles and intracellular pathogens. Previous studies on various autophagy related genes revealed the importance of the Atg12-Atg5-Atg16 complex in autophagy. Atg16L1 is an effector of Golgi-resident Rab33B and the molecular mechanism of the interaction of Rab33B with either Atg16L1 or in complex with Atg5 is still elusive.

A New Na(+)-Dependent RNA-Cleaving DNAzyme with over 1000-fold Rate Acceleration by Ethanol.

Enzymes working in organic solvents are important for analytical chemistry, catalysis, and mechanistic studies. Although a few protein enzymes are highly active in organic solvents, little is known regarding nucleic acid-based enzymes. Herein, we report the first RNA-cleaving DNAzyme, named EtNa, that works optimally in concentrated organic solvents containing only monovalent Na(+).

Searching for a DNAzyme Version of the Leadzyme.

The leadzyme refers to a small ribozyme that cleaves a RNA substrate in the presence of Pb(2+). In an optimized form, the enzyme strand contains only two unpaired nucleotides. Most RNA-cleaving DNAzymes are much longer.

Tandem DNAzymes for mRNA cleavage: choice of enzyme, metal ions and the antisense effect.

The concept of DNAzyme-based gene silencing via mRNA cleavage was proposed over twenty years ago. A number of studies regarding intracellular gene silencing have been reported as well. However, questions have been raised regarding the lack of enzyme activity in physiological buffer conditions and it is being doubted that in the previously reported studies, gene silencing might be simply due to an antisense effect.