Studies On The Basic Electrochemical Behaviors Of Short-Chain Thiols And DNA Self-Assembled Monolayers On Gold

DNA is the carrier of genetic information and plays an important role in the life activities, such as biological growth, development and reproduction. Electron transfer through DNA can induce in the wrong reading of genetic information, lead to DNA damage, and cause cell mutations and cancer, thus studying electron transfer through DNA has important scientific significance. In 1993, Barton et al studied light-induced electron transfer through DNA by intercalated Ru metal compound and obtained that electron transfer distance can be larger than 40 A as well as electron transfer rate greater than 109 s-1. In 1997, Barton et al proposed the study of electron transfer through DNA by electrochemical method. The authors assembled thiol-modified double-stranded DNA on gold to form DNA self-assembled monolayers (Au-DNA-SAMs) and then studied electron transfer through DNA-SAMs on gold using intercalated redox probe (methylene blue). At present, three electrochemical mechanisms for the electron transfer through DNA are proposed by different groups:"π-way" mechanism, ion crystal mechanism and M-DNA transfer mechanism. However, these mechanisms are not consistent each other and there are many contradictions existing. The main reason arousing the contradictions is that surface structure of DNA-SAMs on gold is still not well understood at the molecular level until now. The thiol-modified DNA molecule is a special thiol and consists of three components,5’or 3’end of the modified thiol chain HS(CH2)6-, bases (G, C, A, T) and phosphorylated sugar ring. In order to electrochemically study the electron transfer through DNA, it is necessary to understand the basic electrochemical properties of DNA’s components. This thesis carries out the significant studies from the following three aspects:(Ⅰ) Summarizing the research progress of the electron transfer through DNA and the properties of basic components (gold substrate and thiol) of Au-DNA-SAMs; (Ⅱ) Studing the effect of some important factors on self-assembly of short-chain thiols (thioctic acid and mercaptohexanol, which have the same chains length as HS(CH2)6-) on gold and their electrochemical properties; (Ⅲ) Investigating the ion permeability and electron transfer properties through double-stranded and single-stranded DNA-SAMs on gold, establishing a simple ideal model to describing Au-DNA-SAMs, explaining the electrochemical characteristics through Au-DNA-SAMs, and discussing the practical application of the simple ideal model. Total of six chapters are included.1. Advancements of Electron Transfer Mechanism Through DNA Self-assembled Monolayers (SAMs) on Gold and the Characteristics of Basic Components of Au-DNA-SAMsInvestigation of electron transfer mechanism through the interior of DNA duplex is important in understanding DNA damage or repair and optimizing the design of DNA sensor. Studying electron transfer through DNA includes three methods:electrochemistry, photoelectrochemistry and photochemistry. Electrochemical study is an important part. Thiol-modified DNA molecules are assembled on gold to form DNA self-assembly monolayers (Au-DNA-SAMs) and a lot of redox probes (Fe(CN)63-/4-, Ru(NH3)63+, methylene blue, daunomycin or ferrocene) have been used to detect electron transfer through Au-DNA-SAMs. However, the electron transfer mechanism through Au-DNA-SAMs is still not well understood up to date. In order to discuss the mechanism of electron transfer through Au-DNA-SAMs, we must know the progress of studying electron transfer through DNA and the characteristics of basic components of Au-DNA-SAMs, e.g., the fundamental behaviors of gold electrode, factors on the preparation of self-assembled monolayers on gold, ionic permeability and electron transfer informations (diffusion, permeability and tunneling). In this chapter, we make a summary from the five aspects, including research progresses for DNA electron transfer study, fundamental behaviors of gold electrode, factors influencing the self-assembly of thiol-SAMs, interfacial parameters of thiol-SAMs and electron tunneling through thiol-SAMs.2. Direct Current Potential Control Characteristics of Short-chain Thiols of Thioctic Acid and Mercaptohexanol Self-assembled on GoldIn this chapter we systematically investigate the self-assembly of short-chain thiols of thioctic acid (TA) and mercaptohexanol (MCH) on gold under direct current potential control, Edc (-0.4,+0.4 and+0.7 V) and compared the results obtained with open circuit potential (EOCP).Effect of Edc on thiol self-asembly is inspected based on the changes in electrochemical parameters including interfacial capacitance (C), phase angle (Φ1Hz), current density difference (Δj), charge transfer resistance (Rct) through cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Experimental results show that Edc can not obtain stable short-chain self-assembled monolayers (SAMs) (TA and MCH) in a short time. Both TA and MCH have slow self-assembly dynamics and need a long time (> 24 h) to achieve adsorption equilibrium. Furthermore, the negative potential Edc (-0.4 V) does not facilitate the ordering of SAMs. The ordering of TA-SAMs is found to be the best when assembled under Edc(+0.4 V), whereas that of MCH-SAMs is almost the same when assembled under either EOCP or Edc (+0.4, +0.7 V). Furthermore, we discuss the relationships of electrochemical parameters (C,Φ1Hz,Δj and Rct) and find that C withΦ1Hz andΔj with Rct present linear relationships and CV with EIS are crosschecked. Based on our experimental results, summeries of electrochemical parameters (C,Φ1Hz,Δj and Rct) for thiols with different chain length from literature reports and comparisons with the self-assembly of long-chain thiols under potential control, we obtain that mutual interactions of adjacent chains of short-chain thiols and short-chain thiols with gold substrate play an important role in the ordering of SAMs and permeation of ions and water molecules perhaps dominates the slow self-assembly dynamics of short-chain thiols (TA and MCH) under Edc.3. Studies on the Effect of Solvents on Self-assembly of Thioctic Acid and Mercaptohexanol on Gold In this chapter we investigate the effect of solvents (CC14, CH3CN, DMF, ethanol, ethanol-H2O and H2O) on self-assembly of Thioctic acid (TA) and Mercaptohexanol (MCH) on gold by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Electrochemical characteristics of TA and MCH self-assembled monolayers (SAMs) formed in different solvents are evaluated by inspecting the ions permeability (interfacial capacitance C and phase angleΦ1Hz) and electron transfer capability (current density differenceΔj and charge transfer resistance Rct). Experimental results indicate that the ability of solvents availing the ordering of SAMs is:for TA, CC14> ethanol> CH3CN> ethanol-H2O> DMF; for MCH, H2O> ethanol-H2O≈CC14> ethanol≈CH3CN> DMF. Through relating the C,Φ1Hz,Δj and Rct of SAMs (TA and MCH) with parameters of solvent (polarity ETN, solubility parameter 8 and octanol/water partition coefficients logPow), it is found that solvents with bigger logPow (smaller ETN andδ) availed the ordering of TA-SAMs but the effect of solvents on MCH self-assembly is complex and MCH-SAMs formed in H2O (the biggest ETN,δand the smallest logPow) and CCl4 (the smallest ETN,δand the biggest logPow) are more ordered than in other solvents.4. Electrochemical Studies on the Permeable Characteristics of Thiol-modified Double-stranded DNA Self-assembled Monolayers on GoldIn this chapter we study the permeable characteristics of thiol-modified double-stranded DNA (ds-DNA) self-assembled monolayers (SAMs) on gold substrate assembled under different NaCl concentrations by electrochemical methods. It is based on the inspection of six important parameters including interfacial capacitance (C), phase angle (Φ1Hz), ions transfer resistance (Rit*), current density difference (Δj), charge transfer resistance (Rct) and surface coverage (Γm) through cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and chronocoulometry (CC). Three sections are included:(1) Investigation of the relationships of C,Φ1Hz,Rit*,Δj,Rct andΓm with NaCl concentrations and comparison with the reports from literature. Experimental results show that ds-DNA-SAMs are permeable films; (2) Construction of a simple model for exploring the permeable characteristics of ds-DNA-SAMs on gold; (3) Confirmation of the simple model and its application to explain our experimental phenomena and literature reports. This study is significant for exploring the mechanism of electron transfer through the interior of ds-DNA duplex helix.5. Electrochemical Exploration of the Specific Structural Characteristics of Thiol-modified Single-stranded DNA Self-assembled Monolayers on GoldSpecific structural characteristics of thiol-modified single-stranded DNA (ss-DNA) self-assembled monolayers (SAMs) on gold substrate assembled under different NaCl concentrations are explored in this chapter based on the reports from Chapter four about double-stranded DNA (ds-DNA) SAMs. The ss-DNA molecules are flexible and the flexibility is related to ionic strength of solution. The configuration of ss-DNA molecules on Au is different from that in solution due to thiol-Au restriction and other interactions. We propose that ss-DNA configuration on gold can be quantified using the calibrated gyration diameter dg’ (dg’=rdg) by introducing a calibrating factor r, where dg is ss-DNA gyration diameter in solution. Six important electrochemical parameters including surface coverage (Γm), interfacial capacitance (C), phase angle (Φ1Hz), ions transfer resistance (Rit*), current density difference (Δj) and charge transfer resistance (Rct) from chronocoulometry (CC), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) are used to investigate the specific structural characteristics of ss-DNA-SAMs on gold. Three main aspects are included:(1) Discussion of the relationships of parameters (Tm, C,Φ1Hz,Rit*,Δj and Rct) with NaCl concentrations; (2) Construction of a simple model using dg’ through introducing the calibrating factor r (0.627) to describe the configuration of ss-DNA-SAMs on gold assembled under different NaCl concentration; (3) Confirmation of the simple model and discussion of its application to optimize DNA sensor for achieving the maximal hybridization efficiency and density.6. Effect of Monovalent Cations (Li+,Na+,K+,Cs+) on Self-assembly of Thiol-modified Double-stranded and Single-stranded DNA on Gold ElectrodeIn this chapter we investigate the effect of monovalent cations (Li+, Na+, K+, Cs+) on self-assembly of thiol-modified double-stranded DNA (ds-DNA) and single-stranded DNA (ss-DNA) on gold electrode. Electrochemical characteristics (surface coverage, ions penetration and charge transfer) of ds-DNA-SAMs and ss-DNA-SAMs formed with different monovalent cations are inspected based on six important interfacial parameters including surface coverage (Γm), interfacial capacitance (C), phase angle (Φ1Hz), ions transfer resistance (Rit*), current density difference (Δj) and charge transfer resistance (Rct) from chronocoulometry (CC), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Three sections are included:(1) Investigation of the relationships of parameters (Fm, C,Φ1Hz, Rit*,Δj and Rct) for ds-DNA-SAMs with cations’types and concentrations; (2) Investigation of the relationships of parameters (Γm, C,Φ1Hz,Rit*,Δj and Rct) for ss-DNA-SAMs with cations’types and concentrations; (3) Discussion of the different effect of monovalent cations on self-assembly of ds-DNA and ss-DNA molecules on gold. This work further confirms our recently proposed simple model of DNA-SAMs on gold and might provide a useful reference for understanding interactional mechanism of cations with DNA molecules.