Silanization of glass surfaces

Amino functionalized surfaces by silanization

The reaction mechanism of APTES with the hydroxylated mineral surface such as glass is a subject of much speculation [45]. The surface coverage and the structure depend sensitively on experimental parameters such as the reaction time, temperature, choice of solvent, water content of the solvent and silane concentration [27]. We tested, additionally to the silanization method presented in chapter 2.2.2, the silanization method presented by Heiney et al. [27] which will be explained below.

We cleaned the glass slides, in both protocols, according to the procedure presented in chapter 2.2.2. After the piranha water treatment the acid solution was washed away first few times with denatured ethanol followed by washing with ethanol (p. a.). The silanization after the protocol provided by Heiney et al. [27]

was done so that a solution of methanol 94 %, 1 % of APTES, 5 % of milli-Q water (v/v/v) and 1 mM acetic acid (end concentration) was mixed and let to incubate with the glass slides for two hours. After the incubation the slides were washed with denatured ethanol and milli-Q water and finally dried in the oven at roughly 75^◦C. The main difference here to the protocol presented in chapter 2.2.2 is that here water is added to the silanization solution.

In aqueous solvents the APTES molecules hydrolyze rapidly and these hy-drolyzed APTES molecules can either react with surface hydroxyl groups or with each other forming siloxane oligomers [18]. Structure of this polysiloxane layer on glass is by no means a monolayer when done in liquid phase – the ideal mono-layer can only be obtained by vapor phase silanization techniques [18]. In our experiments we did not see any differences between our silanization protocol and Heiney silanization protocol on the quality of the DNA carpets but we saw a difference in the wetting characteristics of the surfaces. Surfaces prepared with the protocol of Heiney were more hydrophilic which suggest that there is a higher amine density at these slides.

Carboxyl functionalized surfaces

In order to introduce carboxyl groups on glass surfaces, we chose a method where to the amino group of the APTES molecule a carboxyl group containing molecule

is complexed. This is done in a nucleophilic attack where amine compound, such as APTES, reacts with dicarboxylic acid anhydride (succinic anhydride) (23) and the amide (24) is formed (see Fig 4.8). The ring structure of anhydride opens and the APTES molecule is now terminated with carboxylic acid [19].

Experimentally we followed roughly the protocol provided by Levy et al. [46].

We dissolved 0.9 g of succinic anhydride in 666 µl of dimethylformamide. Fur-thermore 2.1 ml of APTES was mixed with 1.2 ml of ethanol (p. a.). This results in an equimolar solutions of succinic anhydride and APTES as the solu-tions are brought together. The mixture is left to react overnight while mixing.

The silanization was then done with this solution as described in chapter 2.2.2 by diluting the solution with ethanol (p. a.) (25) to 150 ml. After the silaniza-tion the washed and dried carboxyl terminated slides are ready to use. We used these slides with EDC and CDI as described above and also directly with amino-modifiedλ - DNA as will be described in chapter 5.

NH2

Figure 4.8: APTES molecules are carboxylated with succinic anhydride (23) and in the following step the glass surface is silanized (25) with carboxylated APTES (24).

Epoxy-functionalized surfaces

For a covalent end-attachment of DNA to a surface, cross-linkers are not the only possibility but silanes, for example, with epoxide end-group can provide a covalent cross-link between the surface and a amino-modified DNA. Silanes are experimentally interesting because they form direct link with end-modified DNA without any additional cross-linker.

As a direct linking possibility we tested the (3-Glycidyloxypropyl) trimethoxysilane (GOPS) which can be used to silanize glass slides with a similar

protocol as silanization with APTES. Glass slides were prepared as in chapter 2.2.2. For the remainder we adopted the silanization protocol presented by Kus-nezow [47] where GOPS was mixed as 2.5% (v/v) solution in ethanol with 10 mM of acetic acid (end-concentration) and left to react overnight (26). Afterwards the slides were sonicated for 30 minutes in ethanol and washed with ethanol and milli-Q water. After washing the slides were dried in the oven at 50^◦C. The epoxide derivative containing surface can react directly with the amino-modified DNA (27). The epoxide group will react with nucleophiles such as amino or thiol group in an ring-opening process and a stable secondary amide is formed [19]

(28). According to Hermanson the epoxide group reacts with the amino group around pH 9 and with thiol group around pH 7.5−8.5 [19]. The reaction scheme of the GOPS is shown in Fig. 4.9.

Figure 4.9: GOPS silane is first reacted with cleaned glass (26). The GOPS-silanized surface is then left to react with amino-modified λ - DNA (27) and in the following reaction the epoxide derivative experiences a nucleophilic attack by amino group and forms a covalent secondary amine (28) [19].

The characterization of the surface chemistry was done, as always, by observ-ing the DNA carpets at the microscope. The optimal incubation conditions for homogeneous dense DNA carpets, without surface stuck molecules, were found to be in PBS at pH 6.5 with 0.5 M NaCl. These conditions are considerably different from the conditions suggested by Hermanson [19]. As a potential ex-planation to the difference in the given reaction conditions is that at neutral pH values the epoxide is more stable against hydrolysis and nucleophilic attacks [19].

This possibly means that at higher pH values hydrolysis deactivates the surface before amino-modified DNA has managed to do the nucleophilic attack.

4.3 Results and Discussion

First of all we wanted to test the effect of silanization whether the method pre-sented in chapter 2.2.2 would be better than the method of Heiney [27] (prepre-sented above) in terms of a change in the rupture length distribution. As already dis-cussed in chapter 2, independently of the silanization method, the result we got was always a broad rupture length distribution (see Fig. 2.6). This is because for the stretching experiments we had to always use biotin-streptavidin linkage in one end of the DNA molecule, as the other end-grafting possibilities presented in this chapter do not create stable end-graft in the presence of antibleaching chemicals.

This is apparently due to DTT which reduces the reactive groups before they manage to react with the end-modification of the DNA molecule. Furthermore on the basis of the fact that during these experiments we were limited to use only single biotin molecule in the end of the λ - DNA molecule, it comes clear that we cannot characterize the surface end-grafts thoroughly since we do not have a way to measure the force directly. Therefore, to give some statistics about how many molecules are really covalently end-grafted to the surface, measurements of the force are needed. With our technique we get only a positive control, meaning that when we can measure a λ - DNA molecule over 25µm, we can say that the surface chemistry is good enough (see Fig. 2.8). This assumption is only valid when there is no concatemers ofλ- DNA in the sample. We do have concatemers in our samples but the amount of them is low (see chapters 2 and 3) typically on the order of 3 % of all the molecules and therefore we expect that the concatemers do not disturb our measurements but we cannot, however, rule them completely out.

In order to characterize our end-grafting chemistries, we decided to define a chemistry ”good” when we were able to stretch few λ - DNA molecules up to 25µm (typically some 5 out of 20 molecules) and we leave the more qualitative measurements for later time. The end-grafting chemistries, where the previously mentioned criterion was fulfilled, are collected to a Table 4.1 with some remarks.

Another criterion for successful surface chemistry is that with it must be possible to create dense DNA carpets. Up to now we have characterized all the DNA carpets by observing them with microscopy (see Fig. 4.2)). This is naturally rather inaccurate when the carpets are very dense (see Fig. 4.2 (b)) but gives us anyway a qualitative picture of the homogeneity of the carpets. Furthermore in order to optimize the parameters to produce the DNA carpets the use of microscopy provided accurate enough tool since there were considerable variations in the end-grafting densities.

In conclusion here as a result came out that the carpets done with sulfo-SIAB and GOPS silanization were the densest: they were on the same level as the carpets done with techniques presented in chapter 2. Other surface chemistries are at the moment less efficient but this can partly be also due to the fact that the optimal reaction conditions have not been found yet.

Table 4.1: Summary of the grafting protocols: At the first column is the name of the cross-linker (first four ones) or the surface which reacts directly with modified DNA (two last ones). The type of cross-linker is presented at the second column.

At the third column is presented the functional groups with which the cross-linker/surface reacts. The columns four and five show the optimal conditions on which the cross-linker/ functionalized surface reacts. On column four is the surface side of the cross-linker and on column five is the DNA or streptavidin side. Finally on column six is the surface end-graft density commented.

Name Type Reacts with Optimal Optimal Carpet

conditions conditions Density Sulfo- Hetero- Amines, PBS: pH 7.2, PBS: pH 8.3, Good

SIAB bifunctional thiols 10mM EDTA 0.5 M NaCl

Glutar- Homo- Amines 8% PBS: pH 8 See

aldehyde bifunctional solution chapter 2

EDC + Zero-length Carboxyls, MES: pH 5.5 PBS: pH 7.2, Poor

sulfo-NHS amines 0.5 M NaCl

Thiolated Hetero- Thiols, PBS: pH 7.2, TBE: pH 9, Good streptavidin bifunctional biotins 10mM EDTA 0.5 M NaCl

Gold No Thiols TBE at pH 9 - Good

cross-linker

GOPS No amines See PBS: pH 6.5, Good

cross-linker silanization 0.5 M NaCl

4.4 Conclusions

In this chapter we studied ways to circumvent the problem of biotin-streptavidin linkage weakness. Here we study several possibilities to end-graft λ - DNA onto a surface. The methods were optimized in order to maximize to the end-grafting carpet density and minimize the sticking of DNA to the surface. The stability of the end-grafts were tested by end-graftingλ - DNA between two surfaces and observing the rupture length of the molecule. The measured rupture lengths show that the developed end-grafting methods are working but since we had to use single streptavidin-biotin linkage to establish double-sided end-graft quantitative results cannot be obtained from this. However on a single molecule level the methods are successful. In summary the best methods we found were: (i) sulfo-SIAB which provides a simple and reliable method to end-graft covalently thiol-modified DNA on the surface, (ii) epoxy silanized surfaces provide a method with which amino-modified DNA can be covalently end-grafted directly without using any additional cross-linker. The problem here, however, was that epoxy group is not specific against amino-group. Finally, (iii) thiolation of streptavidins provides an interesting method to end-graft biotin-modified DNA molecules on a gold surface. Here as a problem remains the non-covalent character of biotin-streptavidin linkage.

Characterization and density enhancement of DNA carpets

Abstract

In order to characterize the DNA carpets presented in chapters 2 and 4, we used confocal fluorescence microscopy and microarray reader. Confocal fluorescence microscopy was used to estimate the density of YOYO-1 loaded DNA carpets directly or from combed carpets. Microarray reader was used to measure the intensity of flu-orescence emitted by Cy3-modified DNA carpets and the measured intensity was later related to end-grafting density by fluorescence microscopy. The results from these three methods vary between 0.08−0.3 molecules/µm² showing roughly the limits of the carpet density. Furthermore we tested several methods to enhance the surface end-graft density over the above mentioned limit. Using conducting transparent substrates and electrophoresis, we reached surface densities of roughly 0.3 molecules/µm². Additionally the method of repeated combing on streptavidin surfaces shows also promising results though this has to be further verified in coming experiments.

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5.1 Introduction

Polymers tethered to a solid substrate play an important role in wide range of technical applications, such as biocompatible surfaces [48], colloidal stabiliza-tion [49] and lubricastabiliza-tion [50]. There are two limiting regimes when the polymers are end-grafted to the surface: (i) The polymers are packed on a surface so densely that the distance between grafting sites (d) is much smaller than the radius of gyration (R_g) of the polymer coils. In this case the polymer carpet is in so called

”brush” regime where individual polymers interact and stretch away from the surface by entropic repulsion. (ii) The polymers are attached to the surface so that the distance between adjacent grafting sites is more than the radius of gy-ration (d > R_g) and then the polymer carpet is in so called ”mushroom” regime.

The snapshots what we have shown in chapter 4 were all taken from carpets in the mushroom regime since we were able to distinct individual molecules. Our goal here is to go beyond this regime and achieve high density end-grafted λ -DNA carpets for the experiment presented in the general introduction 1.

In chapters 2 and 4 we have developed ways to create end-grafted polymer carpets and in this chapter we concentrate on characterization of them and on enhancing the surface end-grafting density. For the characterizations we use confocal fluorescence microscopy and microarray reader. Furthermore we will study the effect of electrophoresis, depletion forces and combing to enhance the end-grafting densities.

5.2 Materials and methods