Thymine Base Research Articles

Ultrafast Cycloreversion of Thymine-Toluene [2 + 2] Cycloadducts by DNA Photolyase.

DNA photolyases use blue light and fully reduced flavin cofactor to repair UV-induced cyclobutane pyrimidine dimers (CPD) formed between two adjacent thymine bases in DNA. Thymine can form [2 + 2] cyclobutane adducts with its biological isosteres like toluene upon UV irradiation, resulting in chemically different analogues of CPD. Here, we investigated the cycloreversion reactions of two such adducts formed between thymine and toluene, T<>Tol, catalyzed by a class-I CPD photolyase. The photolyase can bind to the T<>Tol adducts efficiently and restore the constituent bases upon excitation. Using femtosecond spectroscopy, we systematically characterized all the elementary steps involved in the enzymatic cycloreversion of the T<>Tol adducts and comprehensively analyzed the key intermolecular electron-transfer (ET) reactions and cyclobutane bond splitting steps. The initial electron injection to the bound adducts happens primarily through a two-step electron hopping mechanism, unlike in CPD repair where direct electron tunneling is dominant. After electron injection and ultrafast first-bond splitting, the delicate competition between the second bond splitting and a futile back ET dictates the overall reaction quantum yields of the adducts, influenced by the stability of adduct intermediates and steric crowding around the constituent bases. The final electron return for the cycloreversion reactions adopts a different pathway compared to CPD repair. The photolyase utilizes its conserved photorepair mechanism and allows ET pathway flexibility to reverse the [2 + 2] cycloaddition reaction of non-natural analogues of CPD.

Oligonucleotides Containing 8,1′‐Ethano‐2′‐deoxyadenosine: Synthesis and Properties

AbstractOligonucleotides containing 8,1′‐ethano‐2′‐deoxyadenosine (ethano‐dA) were synthesized in which the adenine base (ethA) is fixed in the syn conformation. Ethano‐dA phosphoramidite was synthesized by using a 1,5‐hydrogen‐atom transfer/radical cyclization process and introduced into oligonucleotides, which were successfully obtained by employing the 4,4′‐dimethoxytrityl‐off synthesis mode. The duplex‐forming ability of the oligonucleotides containing ethano‐dA was evaluated. In the antiparallel Watson–Crick duplex, the ethA formed stable base pairs with thymine and guanine, in which two Hoogsteen‐type hydrogen bonds could be formed. By contrast, the parallel Hoogsteen duplex containing the ethA:thymine base pair showed thermal stability comparable to that containing a natural adenine:thymine base pair because ethA and thymine can form two Watson–Crick‐type hydrogen bonds. These results indicated that ethano‐dA may be helpful for elucidating the function of adenine bases through the syn conformation in DNA.

Uracil base PCR implemented for reliable DNA walking

PCR-based DNA walking is of efficacy for capturing unknown flanking genomic sequences. Here, an uracil base PCR (UB-PCR) with satisfying specificity has been devised for DNA walking. Primary UB-PCR replaces thymine base with uracil base, resulting in a primary PCR product composed of U-DNAs. A single-primer (primary nested sequence-specific primer) single-cycle amplification, using the four normal bases (adenine, thymine, cytosine, and guanine) as substrate, is then performed on the primary PCR product. Clearly, only those U-DNAs, ended by the primary nested sequence-specific primer at least at one side, will produce the corresponding normal single strands. Next, the single-cycle product undergoes uracil-DNA glycosylase treatment to destroy the U-DNAs, while the normal single strands are unaffected. Afterward, secondary even tertiary PCR is performed to exclusively enrich the target product. The feasibility of UB-PCR has been checked by obtaining unknown sequences bordering the three selected genetic sites.

Theoretical Investigation of the structure and Raman scattering properties of Hoogsteen- and Watson-Crick-type Adenine-Thymine base pair

Hoogsteen (HG) and Watson-Crick (WC) adenine–thymine (A-T) base pairs are fundamental to gene expression and genomic stability. Our research applied density functional theory (DFT) calculations to analyze these base pairs, demonstrating that linking them with ribose or deoxyribose and their immersion in solvents markedly enhances the distinctions in their optical properties. DFT results reveal that N···HN hydrogen bonds in both HG and WC pairs exhibit characteristics of both ionic and covalent bonds, playing a crucial role in their stability. While WC base pairs demonstrate stronger orbital interactions, they also experience greater repulsion than HG pairs. This repulsion offsets the positive interactions to a degree, making the interaction energy of WC pairs slightly lower than that of HG pairs. Furthermore, the distinct conformations of these base pairs result in different vibrational modes, suggesting Raman spectroscopy as an effective method for distinguishing between WC and HG base pairs.

Programmable DNA pyrimidine base editing via engineered uracil-DNA glycosylase

DNA base editing technologies predominantly utilize engineered deaminases, limiting their ability to edit thymine and guanine directly. In this study, we successfully achieve base editing of both cytidine and thymine by leveraging the translesion DNA synthesis pathway through the engineering of uracil-DNA glycosylase (UNG). Employing structure-based rational design, exploration of homologous proteins, and mutation screening, we identify a Deinococcus radiodurans UNG mutant capable of effectively editing thymine. When fused with the nickase Cas9, the engineered DrUNG protein facilitates efficient thymine base editing at endogenous sites, achieving editing efficiencies up to 55% without enrichment and exhibiting minimal cellular toxicity. This thymine base editor (TBE) exhibits high editing specificity and significantly restores IDUA enzyme activity in cells derived from patients with Hurler syndrome. TBEs represent efficient, specific, and low-toxicity approaches to base editing with potential applications in treating relevant diseases.

Synthesis and characterization of oligonucleotides containing 2′-O,4′-C-methyleneoxy-bridged 5-methyluridine with an unsubstituted bridge

In this study, a 2′-O,4′-C-methyleneoxy-bridged 5-methyluridine with three consecutive acetal groups (TaNA with a thymine base) was synthesized. The synthesized TaNA was incorporated into oligonucleotides (ONs), and their properties were compared with those of ONs containing the 7′-methylated analog (Me-TaNA) modifications previously reported by us. The duplex stability of TaNA with single-stranded RNA was comparable to that of Me-TaNA. However, the triplex stability of TaNA-modified ONs with double-stranded DNA was slightly lower than that of Me-TaNA-modified ONs. Additionally, the enzymatic stability of TaNA-modified ONs was lower than that of Me-TaNA-modified ONs. These results suggest that the 7′-methyl substitution on the TaNA structure is crucial for enhancing the properties of modified ONs.

Proofreading exonuclease activity of replicative polymerase epsilon promotes cellular tolerance to arabinosides in CTF18-dependent and -independent manner

Ara-A, Ara-C, Ara-G, and Ara-T are arabinose sugars combined with adenine, cytosine, guanine, and thymine bases, respectively. These drugs are clinically important as these drugs are commonly used as anti-viral and anti-cancer drugs. Ara-C, an arabinoside, serves as a chain terminator of deoxyribonucleic acid (DNA) replication by interfering with replication after it is incorporated at the 3′ end of nascent DNA, thereby restricting the proliferation of viruses and cancer cells. The incorporated Ara-CMP is efficiently removed by the proofreading exonuclease activity of polymerase epsilon (Polε), in which the alternative clamp loader CTF18 plays a pivotal role. However, the requirement of CTF18 for the removal of the other arabinosides from the 3′ end of nascent DNA remains unclear. Here, we explored DNA repair pathways responsible for the cellular tolerance to Ara-A and found that cells deficient in the proofreading exonuclease activity of Polε (POLE1exo−/−) showed the highest sensitivity to Ara-A. This activity was also required for cellular tolerance to Ara-G and Ara-T. CTF18−/− cells showed higher Ara-A sensitivity than wild-type cells, though it was critically lower than that of POLE1exo−/− cells. Similar trends were observed for the sensitivity to Ara-G and Ara-T. These results indicate that these arabinosides are removed by Polε proofreading exonuclease activity, and CTF18 is pivotal for Polε-mediated Ara-C removal but does not play critical roles for Polε-mediated removal of Ara-A, Ara-G, and Ara-T. In this study, we unveiled a difference between Ara-C and the other arabinosides (Ara-A, Ara-G, and Ara-T) in the removal from the 3′ end of nascent DNA.

Enhanced sampling strategies for molecular simulation of DNA

AbstractMolecular dynamics (MD) simulations can provide detailed insights into complex molecular systems, such as DNA, at high resolution in space and time. Using current computer architectures, time scales of tens of microseconds are feasible with contemporary all‐atom force fields. However, these timescales are insufficient to accurately characterize large conformational transitions in DNA and compare calculations to experimental data. This review discusses the advantages and drawbacks of two simulation approaches to overcome the timescale challenge. The first approach is based on adding biasing potentials to the system to drive transitions. Umbrella sampling, steered MD, and metadynamics are examples of these methods. A key challenge of such methods is the necessity of selecting one or a few efficient coordinates, commonly referred to as collective variables (CVs), along which to apply the biasing potential. The path‐metadynamics methodology addresses this issue by finding the optimal route(s) between states in a multi‐dimensional CV space. The second strategy is path sampling, which focuses MD simulations on the transitions. The assumption is that even though transitions between states are rare, they are generally fast. Stopping the simulations as soon as they reach a stable state can significantly increase simulation efficiency. We introduce these methods on the two‐dimensional Müller–Brown potential. DNA applications are featured for two different processes: the Watson–Crick–Franklin to Hoogsteen transition in adenine–thymine base pairs and the binding of a DNA‐binding protein domain to DNA.This article is categorized under: Molecular and Statistical Mechanics Molecular Dynamics and Monte‐Carlo Methods Molecular and Statistical Mechanics Free Energy Methods Software Simulation Methods

Photochemical processes to cellular DNA damage by UV radiation of different wavelengths: biological consequences

UV radiation of sunlight induces in cellular DNA of different organisms photochemical reactions, which may lead to the development of series biological responses to arising lesions, including apoptosis, mutagenesis, and carcinogenesis. The chemical nature and the amount of DNA lesions depend on the wavelength of UV radiation. Photons of UV radiation in the region B (UVB, 290–320 nm) cause the production of two main defects, namely, cyclobutane pyrimidine dimers and, with a less yield, pyrimidine (6-4) pyrimidone photoproducts; their formation is the result of the direct UVB photon absorption by DNA bases. Photons of UV radiation in the region A (UVA, 320–400 nm) induce only cyclobutane dimers that can be formed by triplet-triplet energy transfer from cellular chromophores, absorbing photons of this UV region, to DNA thymine bases. UVA is much more effective than UVB in the sensitized oxidatively lesion formation in DNA such as single strand breaks and oxidized bases; among those, 8-oxo-dihydroguanine is the most frequent since it can be produced from several oxidation processes. In recent years, multiple papers, reporting novel, more detailed information about molecular mechanisms of photochemical reactions underlying the formation of different lesions in DNA were published. The present review mainly aims at summarizing and analyzing data contained in these publications, particularly regarding oxidative reactions that are initiated by reactive oxygen species and radicals generated by potential endogenous photosensitizers such as pterins, riboflavin, protoporphyrin IX, NADH, and melanin. The role of specific DNA photoproducts in genotoxic processes induced in living systems by UV radiation of different wavelengths, including human skin carcinogenesis, is discussed.

Copper(II) coordination compounds based on bis-hydrazones of 2,6-diacetylpyridine: synthesis, structure, and cytotoxic activity.

By reacting a series of 2,6-diacetylpyridine bis-hydrazones containing pyrimidine (H2L1), benzimidazole (H2L2) and phthalazine (H2L3) heterocyclic fragments with copper(II) chloride and bromide, a variety of pentacoordinated complexes of the composition [Cu(H2L1)X]X, [Cu(HL2)X] and [Cu(HL3)X], where X = Cl-, Br-, are formed. The properties and structure of the compounds were studied by means of NMR, IR, UV-vis, ESR, and X-ray absorption spectroscopy, cyclic voltammetry and X-Ray single crystal diffraction methods. It was shown that complexes of the cationic type [Cu(H2L1)X]X have an asymmetric structure with a distorted square-pyramidal geometry of the coordination unit. The coordination polyhedron of metal chelates [Cu(HL2)X] and [Cu(HL3)X] is an almost ideal square pyramid. Investigations of the cytotoxic activity of the obtained compounds in vitro on human hepatocellular carcinoma (HepG2) and non-tumor human lung fibroblast (MRC-5) cell lines demonstrated that complexes show higher activity compared with the well-known anticancer agent cisplatin. In addition, metal chelates [Cu(H2L1)Cl]Cl, [Cu(HL2)Cl], [Cu(HL2)Br] and [Cu(HL3)Cl] were less toxic to non-tumor cells MRC-5. A study of the binding of complexes to bovine serum albumin (BSA) protein using fluorescence spectroscopy showed that copper complexes are strongly bound to BSA. To study the mechanism of interaction of the complexes with the DNA of cancer cells, molecular dynamics simulation of the compound [Cu(HL3)Cl] was carried out. It was shown that the complex enters into π-stacking interactions predominantly with adenine and thymine bases.

Electrochemiluminescence Sensor Based on CeO2 Nanocrystalline for Hg2+ Detection in Environmental Samples.

The excessive concentration of heavy-metal mercury ions (Hg2+) in the environment seriously affects the ecological environment and even threatens human health. Therefore, it is necessary to develop rapid and low-cost determination methods to achieve trace detection of Hg2+. In this paper, an Electrochemiluminescence (ECL) sensing platform using a functionalized rare-earth material (cerium oxide, CeO2) as the luminescent unit and an aptamer as a capture unit was designed and constructed. Using the specific asymmetric matching between Hg2+ and thymine (T) base pairs in the deoxyribonucleic acid (DNA) single strand, the "T-Hg-T" structure was formed to change the ECL signal, leading to a direct and sensitive response to Hg2+. The results show a good linear relationship between the concentration and the response signal within the range of 10 pM-100 µM for Hg2+, with a detection limit as low as 0.35 pM. In addition, the ECL probe exhibits a stable ECL performance and excellent specificity for identifying target Hg2+. It was then successfully used for spiked recovery tests of actual samples in the environment. The analytical method solves the problem of poor Hg2+ recognition specificity, provides a new idea for the efficient and low-cost detection of heavy-metal pollutant Hg2+ in the environment, and broadens the prospects for the development and application of rare-earth materials.

Visualizing the DNA repair process by a photolyase at atomic resolution.

Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.

Discotic Star Mesogen with Thymine Nucleobases Exhibiting a Rare Gyroid Cubic Mesophase with 3D Conductivity.

A unique gyroid cubic phase has been discovered for a discotic star mesogen with three covalently attached DNA bases. In this cubic phase, the conjugated core of the mesogens and the thymine pseudo guests self-assemble in mirror image continuous networks, representing a semiconducting material with three-dimensional transport pathways. The hole carrier mobilities are found to be in the typical range of poly(phenylenevinylene) scaffolds. This structure is stabilized by a weak hydrogen bonding between the thymine bases and can be switched to a columnar liquid crystal - thermally and by the addition of complementary adenine guests.

Mapping electronic decoherence pathways in molecules.

Establishing the fundamental chemical principles that govern molecular electronic quantum decoherence has remained an outstanding challenge. Fundamental questions such as how solvent and intramolecular vibrations or chemical functionalization contribute to the decoherence remain unanswered and are beyond the reach of state-of-the-art theoretical and experimental approaches. Here we address this challenge by developing a strategy to isolate electronic decoherence pathways for molecular chromophores immersed in condensed phase environments that enables elucidating how electronic quantum coherence is lost. For this, we first identify resonance Raman spectroscopy as a general experimental method to reconstruct molecular spectral densities with full chemical complexity at room temperature, in solvent, and for fluorescent and non-fluorescent molecules. We then show how to quantitatively capture the decoherence dynamics from the spectral density and identify decoherence pathways by decomposing the overall coherence loss into contributions due to individual molecular vibrations and solvent modes. We illustrate the utility of the strategy by analyzing the electronic decoherence pathways of the DNA base thymine in water. Its electronic coherences decay in [Formula: see text]30 fs. The early-time decoherence is determined by intramolecular vibrations while the overall decay by solvent. Chemical substitution of thymine modulates the decoherence with hydrogen-bond interactions of the thymine ring with water leading to the fastest decoherence. Increasing temperature leads to faster decoherence as it enhances the importance of solvent contributions but leaves the early-time decoherence dynamics intact. The developed strategy opens key opportunities to establish the connection between molecular structure and quantum decoherence as needed to develop chemical strategies to rationally modulate it.

Label-free identification of DNA single-base mutation for clinical diagnostics based on plasmonic SiNW@AgNP arrays

Surface-enhanced Raman spectroscopy (SERS) has exhibited great potential in deoxyribonucleic acid (DNA) analysis. Rapid and label-free identification of single-base mutation in DNA is still limited by the sensitivity and reproducibility of SERS substrates. In this work, we develope plasmonic SiNW arrays decorated with Ag nanoparticles (SiNW@AgNP arrays) via hexadecyltrimethylammonium bromide (CTAB)-assisted galvanic reaction to address these challenges, which show excellent sensitivity and reproducibility. Under optimized experimental conditions, plasmonic SiNW@AgNP arrays enable detection of DNA bases of adenine (A), guanine (G), cytosine (C), and thymine (T) in solution at concentration down to pM-μM range, and multiple detection ability with mixture of DNA bases. More significantly, our study demonstrates the SiNW@AgNP arrays may serve as excellent SERS substrates in discriminating DNA single-base mutation between sickle cell anemia gene and normal hemoglobin gene in serum samples, which can be exploited in a wide range of plasmonic enhanced sensing applications for a fast, real-time, label-free and cost-effective clinical diagnosis.

Interactions of adenine–thymine base pair with potassium cation and water clusters

The structures of Ade-Thy-K+(H2O)n (n = 0–6) clusters were determined, and the interaction mechanism of K+-base pair (A-T) in water clusters was elucidated. The non-hydrated Ade-Thy-K+ shows a planar structure, while the complex transforms into a stacked form when the water molecules are involved. It is noted that K+ no longer connects to adenine but is tricoordinated with thymine and the adjacent water from n = 3, and then forms a tetracoordinate ion from n = 4. The RDG, AIM, and EDA combined with interaction energy analyses show that the interaction between K+ and base pair weakens gradually when the first four water molecules are involved successively, and then strengthens for n = 5, 6. The interaction between K+ and the A-T base pair is dominated by an electrostatic power, followed by dispersion, whereas the interactions between adenine and thymine are always dominated by dispersion from n = 1 to 6.

DNA i‐motif formation at physiological pH revealed by Raman spectroscopy

AbstractThe intercalated motif (iM) is a four‐stranded structure consisting of two parallel homoduplexes formed by hemiprotonated C.C+ pairs and intercalated antiparallel to each other. iM is generally formed at acidic pH, as cytosine protonation is required for its formation. However, sequences with long cytosine tracts can form iM at physiological pH conditions. Here, we use both off‐resonant Raman and UV‐resonant Raman (using synchrotron radiation) spectroscopy (RS) to study the sequence (C9T3)3C9, which has been recently thoroughly analysed by other spectroscopic methods (CD, 1H NMR). In line with these methods, RS has shown that (C9T3)3C9 adopts iM at neutral pH and the iM forms with slow kinetics, melts in multiple steps and exhibits a large thermal hysteresis between the folding and refolding processes. The presence of isosbestic points in the temperature‐dependent Raman spectra (in line with the SVD analysis indicating just two independent spectral components) suggests that the (C9T3)3C9 is found as a mixture of disordered and ordered structures, the proportion of which is temperature dependent. The ordered iM species are believed to be composed of the same type of C.C+ pairs but differing in their number and arrangement along the cytosine tracts. The related sequence (C9A3)3C9 shows the same behaviour as (C9T3)3C9, indicating that the substitution of adenine bases for thymine bases has little effect.

DNA BARCODING UNTUK VALIDASI SPESIES PAUS SPERMA (Physeter macrocephalus LINNAEUS, 1758) DARI PERAIRAN LAUT SAWU, NUSA TENGGARA TIMUR, INDONESIA

The sperm whale (Physeter macrocephalus) is a protected marine biota in Indonesia. Molecular identification of sperm whales from the Sawu Sea (East Nusa Tenggara, Indonesia) was carried out using the 16S rRNA gene. This study aims to validate the species of the sperm whale (Physeter macrocephalus) in Indonesia using the partial cytochrome oxidase subunit I (COI) gene. The specimens used were tissue specimens from laboratory collections taken from Sawu Sea waters in 2014. The three samples were validated as Physeter microcephalus with 100% similarity. The base composition is dominated by the base thymine (31.7–31.8%) with a GC content of 42.7–42.8%. The genetic distance for the same species was 0.0015, while the highest genetic distance for Orcaella brevirostris was 0.2128. Molecular identification using the 16S rRNA gene and COI has validated the species of a sperm whale (Physeter macrocephalus) in Indonesia so that this genetic data can be used as a basis for sperm whale resource management and conservation.

Genetic development of Stx phage

Abstract. Sjahriani T, Kurniati M, Arivo D, Syukri DM, Tyasningsih W. 2023. Genetic development of Stx phage. Biodiversitas 24: 4334-4341. Stx phages have been studied and described due to their involvement in shigatoxin. The variety, evolution, dispersion, and molecular mechanisms of STEC and Stx phages have all been widely studied, but the further research is still required. The objective of this study was to investigate the unique sequences of bacteriophage DNA from the NCBI database and to identify the changes in the DNA sequence of both regular and stx-carrying bacteriophages. It was first reported in 2001, but studies have not been carried out. The stx-carrying bacteriophage DNA sequence, similarity of identity, e-value, and gaps were analyzed using PCR and DNA sequencing. The number of bacteriophage that used in this study was eight. The results revealed the similarity of bacteriophage to stx-carrying bacteriophages by 82.67% to 88.5%, and exhibited notable variations in comparison to each phage 1 to 8 (Eco157 phage WASJ/2022) (p&lt;0.001). Moreover, results exhibited an e-value ranging from 7e-85 to 3e-44. In addition, results showed gaps between 1-2% in comparison to other stx-carrying bacteriophages in NCBI with bacteriophage alterations on the bases of Cytosine and Thymine in 184th and 263rd. Therefore, this work provided the potency of bacteriophage as an alternative pharmaceuticals in controlling foodborne diseases.

(Invited) Kinetics of SWCNT Coating Displacement By ssDNA Depends on SWCNT Structure

Non-covalent hybrids formed by suspending single-wall carbon nanotubes (SWCNTs) in single-stranded DNA (ssDNA) present novel phenomena and suggest potential applications in biomedicine and nanotube sorting. Although the structures of these hybrids have been simulated using molecular dynamics calculations, much more experimental research is needed to understand their properties. In this study, selective interactions between SWCNTs and ssDNA are probed by measuring the kinetics by which ssDNA displaces SDS (sodium dodecyl sulfate) coatings on the nanotube surfaces. We used samples initially suspended in a low concentration of SDS to allow the coating displacement to occur and to suppress formation of free SDS micelles. The displacement process was monitored by time-dependent measurements of SWCNT fluorescence intensities and wavelengths. Our experiments showed very smooth decreases in fluorescence intensity and red-shifts in fluorescence wavelengths during the displacement process. Through a series of measurements, we found that ssDNA sequences with repeated guanine (G) and thymine (T) bases showed systematic patterns in the coating displacement kinetics. One result is that SDS displacement depends strongly on oligo length, with (GT)3 showing an initial rate constant 500 times greater than that of (GT)20. For shorter oligos in the (GT) n series, we observe an inverse dependence of initial rate constant on SWCNT diameter, with SDS displacement from (6,5) more than twice as fast as from (8,7). However, this diameter dependence is not present for (GT) n oligos with n greater than 6. We also find a distinct and systematic dependence of initial rate constant on nanotube chiral angle for (GT)5 and (GT)6. This effect gives a factor of ~3 difference between (9,1) and (6,5) despite their identical diameters. We empirically find these initial rate constants to vary as (SWCNT diameter)-4(cos 3θ)-y with y = -1/2 for (GT)5 and -1 for (GT)6. In addition, the full displacement kinetic traces are well fitted by double exponential kinetics, with rate constants and amplitudes dependent on SWCNT diameter. A two-step kinetic model for the displacement process will be presented to account for these findings.