4-Cyanoindole-2'-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics

Decoupling Global and Local Structural Changes in Self-aminoacylating Ribozymes Reveals the Critical Role of Local Structural Dynamics in Ribozyme Activity

Self-aminoacylating ribozymes catalyze the attachment of amino acids to RNA, serving as pivotal models to investigate the catalytic roles of RNA in prebiotic evolution. In this study, we investigated how divalent metal ions (Mg2+ and Ca2+) modulate local and global structures in two such ribozymes, S-1A.1-a and S-2.1-a, using 4-cyanotryptophan (4CNW) fluorescence and native gel electrophoresis. By tracking 4CNW fluorescence changes at varying concentrations of Mg2+ and Ca2+ and temperatures, we determined how these ions influence the catalytic sites and overall conformations of the ribozymes. Our findings reveal that Mg2+ specifically binds to S-1A.1-a at low concentrations, stabilizing the local structure around the aminoacylation site and causing the site to become more buried, which is essential for catalytic activity. Although higher Mg2+ and Ca2+ concentrations induce global structural rearrangements, these shifts have minimal impact on the local environment of the aminoacylation site, underscoring the dominance of local structural stability in sustaining ribozyme function. In contrast, the activity of S-2.1-a effectively adapts to both Mg2+ and Ca2+, and its fluorescence results indicate a more solvent-exposed aminoacylation site. Overall, these data highlight that local structural changes in the ribozyme's catalytic core are more critical for its function than global conformational shifts. Our study highlights the importance of local environmental changes in ion-dependent ribozyme catalysis and provides insights into the molecular mechanisms of self-aminoacylating ribozymes.

Photophysics of a Nucleoside Analogue: 4-Cyanoindole-2'-deoxyribonucleoside

It has been shown that 4-cyanoindole-2'-deoxyribonucleoside (4CNI-NS) is a versatile spectroscopic probe of DNA structure and dynamics, as it can pair with all four natural DNA bases. However, its photophysics have not been examined in detail. Herein, we employed multiple techniques, including static fluorescence spectroscopy, time-resolved fluorescence spectroscopy, transient infrared spectroscopy, and theoretical calculations, to assess the photophysical properties of this nucleoside analogue in a series of solvents. We found that (1) its fluorescence has a large quantum yield (0.85 ± 0.10) and a relatively long decay lifetime (10.3 ± 1.0 ns) in H2O, both of which become smaller in other solvents examined, (2) its maximum fluorescence emission frequency exhibits a linear dependence on the relative polarity index of the solvent, (3) the oscillator strength of its C≡N stretching vibration is increased by a factor of >10 upon transition to its excited electronic state (S1), (4) besides solvent relaxation, a rotational motion around the single bond connecting the pentose group and the indole ring is also present in the S1 state, and (5) in aprotic solvents both processes lead the C≡N stretching frequency (νESA) to shift toward higher frequencies, whereas in protic solvents the effects of these processes are more complex. Taken together, these findings provide a molecular basis for interpreting the spectroscopic signals of this nucleoside analogue in practical applications.

Probing DNA G-Quadruplex and I-Motif Structures Via a Fluorescent Nucleoside Analogue: 4-Cyanoindole-2'-Deoxyribonucleoside

Since the building blocks of DNA are nonfluorescent, various external fluorescence reporters have been employed to investigate the structure, dynamics, and function of DNA G-quadruplexes (GQs) and i-motifs (iMs), which play an important role in gene regulation and expression. However, most of those fluorescence reporters lack the ability to provide site-specific structural information of interest. Therefore, it is necessary to develop fluorescent nucleoside analogues that can be covalently inserted into oligonucleotides, which not only serve this purpose, but minimize any potential perturbation towards the native structure of the DNA systems in question. Herein, we characterize the spectroscopic utility of a high quantum yield fluorescent nucleoside analogue, 4-cyanoindole-2'-deoxyribonucleoside (4CNI-NS). We show that (1) incorporation of 4CNI-NS into various oligonucleotides does not alter their ability to fold into their respective native structures, nor does it affect the overall stability of those structures and (2) the fluorescence property of 4CNI-NS is sensitive to its local environment, and the fluorescence intensity and decay kinetics of the 4CNI-NS-containing oligonucleotides exhibit a clear dependence on their secondary structure formation. Collectively, our results demonstrate that 4CNI-NS can be used as a sensitive, isomorphic probe in the study of noncanonical DNA structures.

Triple-Bond Vibrations: Emerging Applications in Energy and Biological Sciences

Triple bonds, such as that formed between two carbon atoms (i.e., C≡C) or that formed between one carbon atom and one nitrogen atom (i.e., C≡N), afford unique chemical bonding and hence vibrational characteristics. As such, they are not only frequently used to construct molecules with tailored chemical and/or physical properties but also employed as vibrational probes to provide site-specific chemical and/or physical information at the molecular level. Herein, we offer our perspective on the emerging applications of various triple-bond vibrations in energy and biological sciences with a focus on C≡C and C≡N triple bonds.

Synthesis and photophysical characterization of fluorescent indole nucleoside analogues

Fluorescent nucleosides are useful chemical tools for biochemical research and are frequently incorporated into nucleic acids for a variety of applications. The most widely utilized fluorescent nucleoside is 2-aminopurine-2'-deoxyribonucleoside (2APN). However, 2APN is limited by a moderate Stokes shift, molar extinction coefficient, and quantum yield. We recently reported 4-cyanoindole-2'-deoxyribonucleoside (4CIN), which offers superior photophysical characteristics in comparison to 2APN. To further improve upon 4CIN, a focused library of additional analogues combining the structural features of 2APN and 4CIN were synthesized and their photophysical properties were quantified. Nucleosides 2-6 were found to possess diverse photophysical properties with some features superior to 4CIN. In addition, the structure-function relationship data gained from 1-6 can inform the design of next-generation fluorescent indole nucleosides.

The photophysics of 2-cyanoindole probed by femtosecond spectroscopy

The photophysics of 2-cyanoindole (2-CI) in solution (water, 2,2,2-trifluoroethanol, acetonitrile‚ and tetrahydrofuran) was investigated by steady-state as well as time resolved fluorescence and absorption spectroscopy. The fluorescence quantum yield of 2-cyanoindole is strongly sensitive to the solvent. In water the quantum yield is as low as 4.4 × 10–4. In tetrahydrofuran, it amounts to a yield of 0.057. For 2-CI dissolved in water, a bi-exponential fluorescence decay with time constants of ∼1 ps and ∼8 ps is observed. For short wavelength excitation (266 nm) the initial fluorescence anisotropy is close to zero. For excitation with 310 nm it amounts to 0.2. In water, femtosecond transient absorption reveals that the fluorescence decay is solely due to internal conversion to the ground state. In aprotic solvents, the fluorescence decay takes much longer (acetonitrile: ∼900 ps, tetrahydrofuran: ∼2.6 ns) and intersystem crossing contributes.

Graphical abstract

Visualization of Platelet Integrins via Two-Photon Microscopy Using Anti-transmembrane Domain Peptides Containing a Blue Fluorescent Amino Acid

The fluorescent reporters commonly used to visualize proteins can perturb both protein structure and function. Recently, we found that 4-cyanotryptophan (4CN-Trp), a blue fluorescent amino acid, is suitable for one-photon imaging applications. Here, we demonstrate its utility in two-photon fluorescence microscopy by using it to image integrins on cell surfaces. Specifically, we used solid-phase peptide synthesis to generate CHAMP peptides labeled with 4-cyanoindole (4CNI) at their N-termini to image integrins on cell surfaces. CHAMP (computed helical anti-membrane protein) peptides spontaneously insert into membrane bilayers to target integrin transmembrane domains and cause integrin activation. We found that 4CNI labeling did not perturb the ability of CHAMP peptides to insert into membranes, bind to integrins, or cause integrin activation. We then used two-photon fluorescence microscopy to image 4CNI-containing integrins on the surface of platelets. Compared to a 4CNI-labeled scrambled peptide that uniformly decorated cell surfaces, 4CNI-labeled CHAMP peptides were present in discrete blue foci. To confirm that these foci represented CN peptide-containing integrins, we co-stained platelets with integrin-specific fluorescent monoclonal antibodies and found that CN peptide and antibody fluorescence coincided. Because 4CNI can readily be biosynthetically incorporated into proteins with little if any effect on protein structure and function, it provides a facile way to directly monitor protein behavior and protein-protein interactions in cellular environments. In addition, these results clearly demonstrate that the two-photon excitation cross section of 4CN-Trp is sufficiently large to make it a useful two-photon fluorescence reporter for biological applications.

Synthesis of 4-Cyanoindole Nucleosides, 4-Cyanoindole-2'-Deoxyribonucleoside-5'-Triphosphate (4CIN-TP), and Enzymatic Incorporation of 4CIN-TP into DNA

4-Cyanoindole-2'-deoxyribonucleoside (4CIN) is a fluorescent isomorphic nucleoside analogue with superior spectroscopic properties in terms of Stokes shift and quantum yield in comparison to the widely utilized isomorphic nucleoside analogue, 2-aminopurine-2'-deoxyribonucleoside (2APN). Notably, when inserted into single- or double-stranded DNA, 4CIN experiences substantially less in-strand fluorescence quenching compared to 2APN. Given the utility of these properties for a spectrum of research applications involving oligonucleotides and oligonucleotide-protein interactions (e.g., enzymatic processes, DNA hybridization, DNA damage), we envision that additional reagents based on 4-cyanoindole nucleosides may be widely utilized. This protocol expands on the previously published synthesis of 4CIN to include synthetic routes to both 4-cyanoindole-ribonucleoside (4CINr) and 4-cyanoindole-2'-deoxyribonucleoside-5'-triphosphate (4CIN-TP), as well as a method for the enzymatic incorporation of 4CIN-TP into DNA by a polymerase. These methods are anticipated to further enable the utilization of 4CIN in diverse applications involving DNA and RNA oligonucleotides. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Synthesis of 4-cyanoindole-2'-deoxyribonucleoside (4CIN) and 4CIN phosphoramidite 4 Basic Protocol 2: Synthesis of 4-cyanoindole-ribonucleoside (4CINr) Basic Protocol 3: Synthesis of 4-cyanoindole-2'-deoxyribonucleoside-5'-triphosphate (4CIN-TP) Basic Protocol 4: Steady state incorporation kinetics of 2AP-TP and 4CIN-TP by a DNA polymerase.

4-Cyanoindole-based fluorophores for biological spectroscopy and microscopy

Most biological molecules are intrinsically non- or weakly-fluorescent, hence requiring labeling with an external fluorophore(s) to be studied via fluorescence-based techniques. However, such labeling could perturb the native property of the system in question. One effective strategy to minimize such undesirable perturbation is to use fluorophores that are simple analogs of natural amino acids. In this chapter, we describe the synthesis and spectroscopic utility of two indole-based fluorophores, 4-cynaotryprophan (4CN-Trp) and 4-cyanoindole-2'-deoxyribonucleoside (4CNI-NS), with a focus on 4CN-Trp. This unnatural amino acid, which is only slightly larger than its natural counterpart, tryptophan (Trp), exhibits unique photophysical properties, making it a versatile fluorophore in biological spectroscopic and imaging applications. Through several specific examples, we highlight its broad utility in the study of various biological problems and processes.

PET and FRET utility of an amino acid pair: tryptophan and 4-cyanotryptophan

Methods based on fluorescence resonance energy transfer (FRET) and photo-induced electron transfer (PET) are widely used in the biological sciences, employing mostly dye-based FRET and PET pairs. While very useful and important, dye-based reporters are not always applicable without concern, for example, in cases where the fluorophore size needs to be minimized. Therefore, development and characterization of smaller, ideally amino acid-based PET and FRET pairs will expand the biological spectroscopy toolbox to enable new applications. Herein, we show that, depending on the excitation wavelength, tryptophan and 4-cyanotrptophan can interact with each other via the mechanism of either energy or electron transfer, hence constituting a dual FRET and PET pair. The biological utility of this amino acid pair is further demonstrated by applying it to study the end-to-end collision rate of a short peptide, the mode of interaction between a ligand and BSA, and the activity of a protease.