Effect of Single-Base Mutation on Activity and Folding of 10-23 Deoxyribozyme Studied by Three-Color Single-Molecule ALEX FRET

Unraveling the Kinetics of the 10-23 RNA-Cleaving DNAzyme

DNA-based enzymes, or DNAzymes, are single-stranded DNA sequences with the ability to catalyze various chemical reactions, including the cleavage of the bond between two RNA nucleotides. Lately, an increasing interest has been observed in these RNA-cleaving DNAzymes in the biosensing and therapeutic fields for signal generation and the modulation of gene expression, respectively. Additionally, multiple efforts have been made to study the effects of the reaction environment and the sequence of the catalytic core on the conversion of the substrate into product. However, most of these studies have only reported alterations of the general reaction course, but only a few have focused on how each individual reaction step is affected. In this work, we present for the first time a mathematical model that describes and predicts the reaction of the 10-23 RNA-cleaving DNAzyme. Furthermore, the model has been employed to study the effect of temperature, magnesium cations and shorter substrate-binding arms of the DNAzyme on the different kinetic rate constants, broadening the range of conditions in which the model can be exploited. In conclusion, this work depicts the prospects of such mathematical models to study and anticipate the course of a reaction given a particular environment.

Choosing the Probe for Single-Molecule Fluorescence Microscopy

Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.

Single-molecule study of the effects of temperature, pH, and RNA base on the stepwise enzyme kinetics of 10–23 deoxyribozyme

We investigated how the stepwise enzyme kinetics of 10–23 deoxyribozyme was affected by temperature, pH, and RNA residue of the substrate at the single-molecule level. A deoxyribozyme-substrate system was employed to temporally categorize a single-turnover reaction into four distinct steps: binding, cleavage, dissociation of one of the cleaved fragments, and dissociation of the other fragment. The dwell time of each step was measured as the temperature was varied from 26 to 34 °C, to which the transition state theory was applied to obtain the enthalpy and entropy of activation for individual steps. In addition, we found that only the cleavage step was significantly affected by pH, indicating that it involves deprotonation of a single proton. We also found that different RNA residues specifically affect the cleavage step and cause the dwell time to change by as much as 5 times.

We investigated how the stepwise enzyme kinetics of 10–23 deoxyribozyme was affected by temperature, pH, and RNA residue of the substrate at the single-molecule level.

Characterization of a DNA-hydrolyzing DNAzyme for generation of PCR strands of unequal length

I-R3 DNAzyme is a small, highly active catalytic DNA for DNA hydrolysis. In here, we designed two cis-structure DNAzymes (I-R3N and I-R3S) based on the different locates of the joint linker between I-R3 and its substrate. Data demonstrated that both DNAzymes were highly dependent on Zn²⁺, and worked at a narrow range around pH 7.0. They exhibited strong anti-interference with Mg²⁺ and Ca²⁺, but inhibited by Na⁺ and K⁺. Moreover, single and multiple-site mutations were generated within the catalytic core to carry out a comprehensive mutational study of I-R3 motif, in which most nucleotides were highly conserved and the nucleotides A5, T11 and T8 were identified as the mutational hotspots. Furthermore, an efficient variant A5G was obtained and its reaction condition was optimized. Finally, we constructed A5G to the 3' end of a single-stranded DNA (ssDNA) and applied it for asymmetrical PCR amplification to produce a single and double-stranded DNA mixture, in which A5G within ssDNA can self-cleave to generate a shorter desired ssDNA by denaturing gel separation. This would provide a new non-chemical modification approach for preparation of the expected ssDNA for in vitro selection of DNAzymes.

Conformational studies of 10-23 DNAzyme in solution through pyrenyl-labeled 2'-deoxyadenosine derivatives

10-23 DNAzyme is a small catalytic DNA molecule. Studies on its conformation in solution are critical for understanding its catalytic mechanism and functional optimization. Based on our previous research, two fluorescent nucleoside analogues 1 and 2 were designed for the introduction of a pyrenyl group at one of the five dA residues in the catalytic core and the unpaired adenosine residue in its full-DNA substrate, respectively. Ten pyrenyl-pyrenyl pairs are formed in the DNAzyme-substrate complexes in solution for sensing the spacial positions of the five dA residues relative to the cleavage site using fluorescence spectra. The position-dependent quenching effect of pyrene emission fluorescence by nucleobases, especially the pyrenyl-pyrenyl interaction, was observed for some positions. The adenine residues in the 3'-part of the catalytic loop seem to be closer to the cleavage site than the adenine residues in the 5'-part, which is consistent with the molecular dynamics simulation result. The catalytic activities and T_m changes also confirmed the effect of the pyrenyl-nucleobase and pyrenyl-pyrenyl pair interactions. Together with functional group mutations, catalytically relevant nucleobases will be identified for understanding the catalytic mechanism of 10-23 DNAzyme.

NAP1L1 accelerates activation and decreases pausing to enhance nucleosome remodeling by CSB

Cockayne syndrome protein B (CSB) belongs to the SWI2/SNF2 ATP-dependent chromatin remodeler family, and CSB is the only ATP-dependent chromatin remodeler essential for transcription-coupled nucleotide excision DNA repair. CSB alone remodels nucleosomes ∼10-fold slower than the ACF remodeling complex. Strikingly, NAP1-like histone chaperones interact with CSB and greatly enhance CSB-mediated chromatin remodeling. While chromatin remodeling by CSB and NAP1-like proteins is crucial for efficient transcription-coupled DNA repair, the mechanism by which NAP1-like proteins enhance chromatin remodeling by CSB remains unknown. Here we studied CSB's DNA-binding and nucleosome-remodeling activities at the single molecule level in real time. We also determined how the NAP1L1 chaperone modulates these activities. We found that CSB interacts with DNA in two principle ways: by simple binding and a more complex association that involves gross DNA distortion. Remarkably, NAP1L1 suppresses both these interactions. Additionally, we demonstrate that nucleosome remodeling by CSB consists of three distinct phases: activation, translocation and pausing, similar to ACF. Importantly, we found that NAP1L1 promotes CSB-mediated remodeling by accelerating both activation and translocation. Additionally, NAP1L1 increases CSB processivity by decreasing the pausing probability during translocation. Our study, therefore, uncovers the different steps of CSB-mediated chromatin remodeling that can be regulated by NAP1L1.

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⁺. The Ag10c was respectively labeled with 2AP at three different positions, both in the substrate strand and in the enzyme strand, one at a time. Ag⁺-induced folding was observed at the substrate cleavage junction and the A9 position of the enzyme strand, consistent with aptamer binding. The measured K_d at the A9 position was 18 μM Ag⁺ with a Hill coefficient of 2.17, similar to those obtained from the previous cleavage activity based assays. However, labeling a 2AP at the A2 position inhibited the activity and folding. Compared to other metal ions, Ag⁺ has a unique sigmoidal folding profile indicative of multiple silver binding cooperatively. This suggests that Ag⁺ can induce a local folding in the enzyme loop and this folding is important for activity. This study provides important biophysical insights into this new DNAzyme, suggesting the possibility of designing folding-based biosensors for Ag⁺.

A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing

Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na⁺ is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na⁺ aptamer using 2-aminopurine (2AP), a fluorescent adenine analog. This aptamer has two DNA strands derived from the Ce13d DNAzyme. By introducing a 2AP at the cleavage site of the substrate strand, Na⁺ induces ∼40% fluorescence increase. The signaling is improved by a series of rational mutations, reaching >600% with the C₁₀A₂₀ double mutant. This fluorescence enhancement suggests relaxed base stacking near the 2AP label upon Na⁺ binding. By replacing a non-conserved adenine in the enzyme strand by 2AP, Na⁺-dependent fluorescence quenching is observed, suggesting that the enzyme loop folds into a more compact structure upon Na⁺ binding. The fluorescence changes allow for Na⁺ detection. With an optimized sequence, a detection limit of 0.4 mM Na⁺ is achieved, reaching saturated signal in less than 10 s. The sensor response is insensitive to ionic strength, which is critical for Na⁺ detection.

A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET)

Single-molecule, protein-induced fluorescence enhancement (PIFE) serves as a molecular ruler at molecular distances inaccessible to other spectroscopic rulers such as Förster-type resonance energy transfer (FRET) or photoinduced electron transfer. In order to provide two simultaneous measurements of two distances on different molecular length scales for the analysis of macromolecular complexes, we and others recently combined measurements of PIFE and FRET (PIFE-FRET) on the single molecule level. PIFE relies on steric hindrance of the fluorophore Cy3, which is covalently attached to a biomolecule of interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate. In this work, we provide a theoretical framework that accounts for relevant photophysical and kinetic parameters of PIFE-FRET, show how this framework allows the extraction of the fold-decrease in isomerization mobility from experimental data, and show how these results provide information on changes in the accessible volume of Cy3. The utility of this model is then demonstrated for experimental results on PIFE-FRET measurement of different protein–DNA interactions. The proposed model and extracted parameters could serve as a benchmark to allow quantitative comparison of PIFE effects in different biological systems.

Spatial conservation studies of nucleobases in 10–23 DNAzyme by 2′-positioned isonucleotides and enantiomers for increased activity

d-/l-Isonucleotides were used to modify the catalytic core and recognition arms of 10–23 DNAzyme and prominently improved its bioactivity.

DNA Catalysis: The Chemical Repertoire of DNAzymes

Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.

Niche Genetic Algorithms are better than traditional Genetic Algorithms for de novo Protein Folding

Here we demonstrate that Niche Genetic Algorithms (NGA) are better at computing de novo protein folding than traditional Genetic Algorithms (GA). Previous research has shown that proteins can fold into their active forms in a limited number of ways; however, predicting how a set of amino acids will fold starting from the primary structure is still a mystery.  GAs have a unique ability to solve these types of scientific problems because of their computational efficiency. Unfortunately, GAs are generally quite poor at solving problems with multiple optima.  However, there is a special group of GAs called Niche Genetic Algorithms (NGA) that are quite good at solving problems with multiple optima.  In this study, we use a specific NGA: the Dynamic-radius Species-conserving Genetic Algorithm (DSGA), and show that DSGA is very adept at predicting the folded state of proteins, and that DSGA is better than a traditional GA in deriving the correct folding pattern of a protein.

Maximizing information content of single-molecule FRET experiments: multi-color FRET and FRET combined with force or torque

Since its first demonstration about twenty years ago, single-molecule fluorescence resonance energy transfer (FRET) has undergone remarkable technical advances. In this tutorial review, we will discuss two technical advances that increase the information content of the single-molecule FRET measurements: single-molecule multi-color FRET and single-molecule FRET combined with force or torque. Our expectations for future developments will be briefly discussed at the end.

The bright future of single-molecule fluorescence imaging

Single-molecule Förster resonance energy transfer (smFRET) is an essential and maturing tool to probe biomolecular interactions and conformational dynamics in vitro and, increasingly, in living cells. Multi-color smFRET enables the correlation of multiple such events and the precise dissection of their order and timing. However, the requirements for good spectral separation, high time resolution, and extended observation times place extraordinary demands on the fluorescent labels used in such experiments. Together with advanced experimental designs and data analysis, the development of long-lasting, non-fluctuating fluorophores is therefore proving key to progress in the field. Recently developed strategies for obtaining ultra-stable organic fluorophores spanning the visible spectrum are underway that will enable multi-color smFRET studies to deliver on their promise of previously unachievable biological insights.

DNA as sensors and imaging agents for metal ions

Increasing interest in detecting metal ions in many chemical and biomedical fields has created demands for developing sensors and imaging agents for metal ions with high sensitivity and selectivity. This review covers recent progress in DNA-based sensors and imaging agents for metal ions. Through both combinatorial selection and rational design, a number of metal-ion-dependent DNAzymes and metal-ion-binding DNA structures that can selectively recognize specific metal ions have been obtained. By attachment of these DNA molecules with signal reporters such as fluorophores, chromophores, electrochemical tags, and Raman tags, a number of DNA-based sensors for both diamagnetic and paramagnetic metal ions have been developed for fluorescent, colorimetric, electrochemical, and surface Raman detection. These sensors are highly sensitive (with a detection limit down to 11 ppt) and selective (with selectivity up to millions-fold) toward specific metal ions. In addition, through further development to simplify the operation, such as the use of "dipstick tests", portable fluorometers, computer-readable disks, and widely available glucose meters, these sensors have been applied for on-site and real-time environmental monitoring and point-of-care medical diagnostics. The use of these sensors for in situ cellular imaging has also been reported. The generality of the combinatorial selection to obtain DNAzymes for almost any metal ion in any oxidation state and the ease of modification of the DNA with different signal reporters make DNA an emerging and promising class of molecules for metal-ion sensing and imaging in many fields of applications.

SOLVING SINGLE BIOMOLECULES BY ADVANCED FRET-BASED SINGLE-MOLECULE FLUORESCENCE TECHNIQUES

The use of Förster resonance energy transfer (FRET) has undergone a renaissance in the last two decades, especially in the study of structure of biomolecules, biomolecular interactions, and dynamics. Thanks to powerful advances in single-molecule fluorescence (SMF) techniques, seeing molecules at work is a reality, which has helped to build up the mindset of molecular machines. In the last few years, many technical developments have broadened the applications of SMF-FRET, expanding the amount of information that can be recovered from individual molecules. Here, we focus on the non-standard SMF-FRET techniques, such as two-color coincidence detection (TCCD), alternating laser excitation (ALEX), multiparameter fluorescence detection (MFD); the addition of fluorescence lifetime as an orthogonal dimension in single-molecule experiments; or the development of novel and improved methods of analysis constituting to a set of advanced methodologies that may become routine tools in a close future.

[Formula: see text]Special Issue Comment: This review about advanced single-molecule FRET techniques is specially related to the review by Jørgensen and Hatzakis,6 who detail experimetal strategies to solve the activity of single enzymes. The advanced techniques described in our paper may serve as interesting alternatives when applied to enzyme studies. Our manuscript is also related to the reviews in this Special Issue that deal with model solving.22,130