This work was supported by the Swiss National Science Foundation (Grants n&deg; PZ00P2_126430/1 and PZ00P2_144595). Prof. C. Leumann is gratefully acknowledged for providing the lab space and equipment, as well as for his constant support. Ms. Sue Knecht is acknowledged for fruitful discussions.

1. Synthesis of the Modified Nucleoside Triphosphates
The synthetic approach chosen follows the procedure developed by Ludwig and Eckstein since this method is generally reliable and leads to very few side-products (Figure 1A)39.
<ol>
	<li>Coevaporate the suitably 3&#8217;-OAc-protected nucleoside (&#160;typically&#160;0.1 mmol) twice with anhydrous pyridine (2 ml) and then dry under vacuum overnight. At the same time, dry tributylammonium pyrophosphate (0.13 mmol) under vacuum overnight.</li>
	<li>Dissolve the nucleoside in a minimum of dry pyridine (0.2 ml) and add dry dioxane (0.4 ml) as a cosolvent. Finally, add 2-chloro-1,3,2-benzodioxaphosphorin-4-one (0.11 mmol) and allow to react at room temperature for 45 min. 
	Note: It is noteworthy that particular care should be taken with the 2-chloro-1,3,2-benzodioxaphosphorin-4-one reagent. Indeed, even storage of this reagent under an inert gas atmosphere is not sufficient to prevent its decomposition. Thus, the white solid that is formed in this decomposition can and should be scraped off prior to use.</li>
	<li>Prepare a solution of tributylammonium pyrophosphate in dry DMF (0.17 ml) and freshly distilled tributylamine (58 &#181;l; never add molecular sieves). Add the resulting solution to the reaction mixture (a white precipitate appears but quickly disappears) and allow to react at room temperature for 45 min.</li>
	<li>Prepare a solution of iodine (0.16 mmol) in pyridine (0.98 ml) and H2O (20 &#181;l) and add to the reaction mixture in order to oxidize the P&#945;(III) center. Allow the resulting dark solution to stir at room temperature for 30 min.</li>
	<li>Use a 10% aqueous solution of NaS2O3 to quench the excess I2. Remove the solvent under vacuum (the temperature of the water bath of the rotary evaporator must be kept below 30 &#176;C). Add H2O (5 ml) and allow the mixture to stand at room temperature for 30 min to hydrolyze the cyclic triphosphate moiety.</li>
	<li>At this stage, the protecting groups are usually removed (i.e. the 3&#39;-OAc and the groups on the side chains of the nucleobase). Consequently, add NH4OH (30% in H2O, 10 ml) to the crude and stir for 1.5 hr at room temperature, and remove the solvent under vacuum.</li>
	<li>Add 2 ml of H2O and split into 2 tubes. Add 12 ml of a 2% solution of NaClO4 in acetone and centrifuge (1,000 x g) for 30 min. This procedure is repeated one more time. This precipitation allows for the separation of the solvents and reagents used in the synthesis from the triphosphate (which will precipitate), thus simplifying the ensuing RP-HPLC purification substantially.</li>
	<li>After air-drying of the oily residue, record a 31P-NMR spectrum of the crude (following standard procedures, see also List of Materials and Figure 3) and dissolve in 4 ml H2O. 
	Note: This synthetic procedure mainly focuses on the generation of modified deoxynucleoside triphosphates, but a very similar procedure can be applied for their RNA counterparts (by simply using 2&#39;,3&#39;-bis-O-acetylated precursors).</li>
</ol>
2. HPLC Purification of the Modified Nucleoside Triphosphates
<ol>
	<li>Preparation of a 1 M stock solution of triethylammonium bicarbonate (TEAB):40
	<ol>
		<li>Prepare a solution of 1 mole of triethylamine (139 ml) in &#8776; 600 ml of distilled and filtered H2O.</li>
		<li>Bubble CO2 (via dry ice and a gas bubbler) into the solution under vigorous stirring until a pH of 7.6 is reached (this will take at least 10 hr). This stock solution can be stored in the fridge for up to one month.</li>
	</ol>
	</li>
	<li>Purification:
	<ol>
		<li>Prepare two buffer solutions from the 1 M stock: 2 L of 50 mM TEAB in ultrapure water (eluent A) and 1 L of 50 mM TEAB in 50% MeCN (eluent B). Degas both eluents under vacuum and stirring for 20 min (careful attention is required so as not to alter the pH by removing CO2 during degassing).</li>
		<li>Prepare an analytical sample by dissolving 10 &#181;l of the crude triphosphate in 300 &#181;l distilled H2O and inject into an HPLC system equipped with a semi-preparative RP column (C18) and using a gradient ranging from 0-100% B in 40 min (Figure 4). Adjust the HPLC program according to the Rt of the triphosphate (which is usually the main peak on the chromatogram) and the diphosphate (which has a slightly lower Rt). Purify the crude mixture using these conditions and by removing early fractions that might contain some diphosphate.</li>
		<li>Combine all the fractions that contain the product and freeze-dry (which is preferred to evaporation on the rotary evaporator in order to minimize hydrolysis to the undesired diphosphate). Coevaporate several times with ultrapure water (to remove remnant triethylamine from the eluents). Assess the purity of the triphosphate by NMR (both 1H and 31P NMR) and MALDI-TOF by application of standard protocols (see Figure 5). Typical yields obtained by application of this protocol typically lie in the range of 30-70%, depending on the substrate.</li>
	</ol>
	</li>
</ol>
3. Primer Extension Reactions and TdT Polymerization
<ol>
	<li>5&#39;-end labeling of the primer
	<ol>
		<li>Mix 30 pmol of the appropriate primer (e.g. P1, List of Materials) with 4 &#181;l of 10x Polynucleotide kinase (PNK) buffer, 3 &#181;l of &#947;-[32P]-ATP, 1 &#181;l of PNK, and ddH2O (for a total reaction volume of 40 &#181;l). Incubate the reaction mixture at 37 &#176;C for 30 min and then heat-deactivate the kinase (10 min at 70 &#176;C).</li>
		<li>During the labeling reaction prepare a G10 Sephadex column by plugging a 1 ml pipette tip with silanized glass wool and filling the tip with G10 solution (10% in ddH2O, autoclaved). Spin down and wash three times with 500 &#181;l ddH2O and one final wash with 50 &#181;l ddH2O. Run the reaction mixture through the G10 (to remove the free radioactive label).</li>
		<li>Gel purify (PAGE 20%) the radiolabeled primer and recover by application of the crush and soak method (i.e. elution with 500 &#181;l of an aqueous solution containing 1% LiClO4 and 1 mM NEt3 (pH 8) at 72 &#176;C for 15 min). Ethanol precipitate and G10 desalt the eluted oligonucleotide.</li>
	</ol>
	</li>
	<li>Primer extension reaction
	<ol>
		<li>Anneal 1 pmol of radiolabeled primer P1, 10 pmol primer P1, and 10 pmol of template T1 (List of Materials) in 10x reaction buffer (provided by the supplier of the polymerase to be used) by placing the tube in hot (90-95 &#176;C) water and by allowing to gradually cool down to room temperature (over 45 min).</li>
		<li>Put the tube on ice and add (in turn) the dNTP cocktail (containing both the modified and the natural triphosphates, 100 &#181;M final concentration) and 1 U of the DNA polymerase (Vent (exo-), Klenow, Pwo or 9&#176;Nm) and complete with water (for a total reaction volume of 20 &#181;l). Incubate at the optimal working temperature of the enzyme (e.g. 60 &#176;C for 30 min when Vent (exo-) is being used).</li>
		<li>Add 20 &#181;l of stop solution (formamide (70%), ethylenediaminetetraacetic acid (EDTA; 50 mM), bromophenol blue (0.1%), xylene cyanol (0.1 %)), heat the samples (95 &#176;C, 5 min), cool down (0 &#176;C), and resolve by denaturing polyacrylamide gel electrophoresis. Visualize by phosphorimager.</li>
	</ol>
	</li>
	<li>TdT polymerization
	<ol>
		<li>Dilute 7 pmol of single-stranded, unlabeled primer P2 (List of Materials), 1 pmol of radiolabeled primer in 1 &#181;l TdT buffer 10x.</li>
		<li>Put the tube on ice and add (in turn) the dNTP cocktail (at an adequate concentration comprised between 10 and 200 &#181;M) and the TdT polymerase (4 U). Incubate at 37 &#176;C for 1 hr. Add 10 &#181;l of the stop solution, heat the samples (95 &#176;C, 5 min), cool down (0 &#176;C), and resolve by denaturing polyacrylamide gel electrophoresis (PAGE 15%). Visualize by phosphorimager.</li>
	</ol>
	</li>
</ol>
4. PCR with Modified Nucleoside Triphosphates
<ol>
	<li>Mix 8 pmol of both the forward and reverse primers with 0.5 pmol of the template to be amplified. Add 10x reaction buffer and the dNTP cocktail (for a 200 &#181;M final concentration) and put the tube on ice. Add 1 U of the DNA polymerase and complete with H2O to reach a final volume of 20 &#181;l. Transfer the mixture into a PCR vial and carry out 30 PCR cycles.</li>
	<li>Dilute 6 &#181;l with 6 &#181;l of 2x sucrose loading buffer and resolve by agarose 2% (stained with ethidium bromide) electrophoresis. Visualize by phosphorimager.</li>
</ol>

No conflicts of interest declared.

The inclusion of modifications into nucleic acids is of interest for numerous practical applications including the development of antisense and antigene agents42,43, labeling and functional tagging of oligonucleotides41, and in efforts to expand the genetic alphabet44-46. Chemical alterations and functional groups are usually introduced into nucleic acids by application of standard and automated solid-phase synthesis protocols. However, the phosphoramidite building blocks need to be resilient to the rather harsh conditions imposed by this methodology, which in turn imposes a severe restriction onto the nature of the chemical functionality47. Instead, the enzyme-mediated polymerization of modified nucleoside triphosphates allows for the introduction of a broader range of functionalities, since the sole restriction is that they act as substrates for polymerases1,2. Even though there is a noticeable lack of generally applicable methodology, reliable and robust synthetic and analytical methodologies have been developed for the synthesis of modified dNTPs. Moreover, due to their inherent nature, modified triphosphates are rather sensitive to different external conditions (e.g. pH, temperature) and thus, a detailed protocol for their synthesis and characterization is highly beneficial.
The workflow presented herein includes the chemical synthesis of modified dNTPs, RP-HPLC purification, NMR analysis, and enzymatic assays for the biochemical characterization of these nucleoside analogues. The most critical steps for a successful synthesis and characterization of modified dNTPs are the analysis of the crude product (by NMR), the thorough HPLC purification, the analysis of the purified material, and choice of an appropriate DNA (RNA) polymerase.
For the synthesis of the modified dNTPs we applied the method developed by Ludwig and Eckstein39, since fewer by-products are formed as compared to other procedures, albeit at the expense of a slightly longer synthetic route. Furthermore, the RP-HPLC purification certainly represents the pivotal step of the entire synthetic route since it will allow for the separation of the nucleoside diphosphates (dNDPs) which often strongly inhibit DNA and RNA polymerases48. After achieving the synthesis and purification, the purity of the resulting triphosphate needs to be assessed both by NMR and MALDI-TOF to ensure that no polymerase-inhibiting diphosphate is present.
The incorporation assay shown in Figure 6 clearly underscores the usefulness of this approach. Indeed, all of the dNTPs employed in this representative example reveal to be good substrates for the DNA polymerase (in this particular case Vent(exo-)) since no faster running bands corresponding to smaller fragments could be observed. Besides, the enzyme tolerates two substrates adorned with carboxylic acid residues (dUtPTP (3) and dCValTP (7)) and the polymerization of both dNTPs results in an oligonucleotide bearing not less than 39 additional negative charges. Another striking feature is that the bands resulting from the incorporation of modified dNTPs often display slower electrophoretic mobilities than the natural controls (compare e.g. lanes 11 and 12). Thus, primer extension reactions represent a powerful and yet simple way to assess the substrate acceptance of modified dNTPs.
Moreover, the TdT-mediated polymerization of triphosphates on the 3&#39;-termini of single stranded oligonucleotides is an alluring strategy for the generation of highly functionalized nucleic acids49-52.&#160;The representative example shown in Figure 7 clearly demonstrates the procedure for selecting the functionalities that are tolerated by the Co2+-dependent TdT53. Indeed, dUcPTP (1) and dUFPTP (3), which are equipped with the proteinogenic amino acid L-proline and the dipeptide &#945;-Phe-Pro, respectively, are the best substrates for the TdT and gave rise to tailing efficiencies that compare favorably to the unmodified dTTP control, even at concentrations as low as 10 &#181;M (lanes 1 and 4). Surprisingly, analogue dUtPTP (2) where the proline residue is connected to the linker arm in trans compared to the free carboxylic acid, is not as good a substrate as its cis counterpart since polydisperse longer-sized oligonucleotides are only observed at higher dNTP concentrations (&#62; 100 &#181;M, lane 2). Furthermore, the sulfonamide-modified dNTP 5 is a moderate substrate for TdT and comparable to dUtPTP (2) (lane 3). In addition, dUBpuTP (4), which bears a strong hydrogen-bond donating motif, is a rather poor substrate for TdT and the polymerization reaction seems to be indifferent to the concentration of the modified dNTP. Thus, the following order of substrate acceptance can be construed from Figure 7: dUcPTP (1), dUFPTP (3)&#62; dUtPTP (2), dUBsTP (5) &#62; dUBpuTP (4).
Finally, the procedure described for polymerization reactions under PCR conditions using the modified analogues is rather similar to that involving natural dNTPs. However, the compatibility of modified dNTPs with polymerases under these conditions is of crucial importance for the generation of high-density functionalized nucleic acids7, especially with regards to their use in in vitro selection experiments.
In summary, the method for the synthesis and characterization of modified nucleoside triphosphates was emphasized and the establishment of such a protocol will certainly help in the development and crafting of novel analogues. Concomitantly, the emergence of such novel dNTPs will facilitate the generation of functionalized oligonucleotides; particularly, catalytic nucleic acids.

5&#39;-Nucleoside triphosphates ((d)NTPs) represent a class of vital biomolecules that are involved in countless processes and functions ranging from being the universal currency of energy to regulators of cell metabolism. In addition to their role in these fundamental biological transformations, their modified counterparts have advanced as a versatile and mild platform for the introduction of functional groups into oligonucleotides, a methodology that nicely complements the automated solid-phase synthesis that is usually applied1,2. Indeed, provided the (d)NTPs can act as substrates for RNA and DNA polymerases3, a wealth of functional groups including amino acids4-13, boronic acids14,15, nornbornene16, diamondoid-like residues17, side-chains for organocatalysis18, bile acids19, and even oligonucleotides20 can be introduced into oligonucleotides.
Beyond representing a convenient vector for the functionalization of nucleic acids, modified dNTPs can be engaged in SELEX and other related combinatorial methods of in vitro selection for the generation of modified catalytic nucleic acids21-30 and aptamers for various practical applications10,31-36. The additional side-chains that are introduced by the polymerization of the modified dNTPs are thought to increase the chemical space that can be explored during a selection experiment and supplement the rather poor functional arsenal of nucleic acids37. However, despite these attractive traits and the recent progress made in the development of both synthetic and analytical methods, no universally applicable and high-yielding procedure exists for the crafting of modified nucleoside triphosphates2,38.
The aim of this present protocol is to shed light into the (sometimes) intricate procedures leading to the synthesis and biochemical characterization of these activated building blocks (Figure 1B). Special emphasis will be given on all the synthetic details that often are difficult to find or are absent in experimental sections but are yet crucial for the successful completion of the synthetic pathway leading to the isolation of pure (d)NTPs (Figure 1).

<table border="0" cellpadding="0" cellspacing="0" width="799">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">tributylammonium pyrophosphate&#160;</td>
			<td style="width:109px;">Sigma Aldrich</td>
			<td style="width:143px;">P8533</td>
			<td style="width:215px;">Hygroscopic solid, keep under Ar</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">2-chloro-1,3,2-benzodioxaphosphorin-4-one&#160;</td>
			<td style="width:109px;">Sigma Aldrich</td>
			<td align="right" style="width:143px;">324124</td>
			<td>Moisture sensitive</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Pyridine</td>
			<td style="width:109px;">Sigma Aldrich</td>
			<td align="right" style="width:143px;">82704</td>
			<td>Under molecular sieves</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Dioxane</td>
			<td style="width:109px;">Sigma Aldrich</td>
			<td align="right" style="width:143px;">296309</td>
			<td>Under molecular sieves</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">dimethylformamide (DMF)</td>
			<td style="width:109px;">Sigma Aldrich</td>
			<td align="right" style="width:143px;">40248</td>
			<td>Under molecular sieves</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:333px;">Acetonitrile&#160;</td>
			<td style="width:109px;">Fisher Scientific</td>
			<td style="width:143px;"></td>
			<td>HPLC grade</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Triethylamine</td>
			<td style="width:109px;">Sigma Aldrich</td>
			<td align="right" style="width:143px;">90342</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Tributylamine</td>
			<td style="width:109px;">Sigma Aldrich</td>
			<td align="right" style="width:143px;">90781</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:333px;">ddH2O</td>
			<td style="width:109px;">Milli-Q</td>
			<td style="width:143px;"></td>
			<td>deionized and purified water, autoclaved in the presence of Diethylpyrocarbonate (DEPC)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Diethylpyrocarbonate (DEPC)</td>
			<td style="width:109px;">Sigma Aldrich</td>
			<td align="right" style="width:143px;">159220</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="86">
			<td height="86" style="height:86px;width:333px;">D2O</td>
			<td style="width:109px;">Cambridge Isotope Laboratories, Inc.</td>
			<td style="width:143px;">DLM-4-25</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Biochemical reagents</td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:333px;">g-[32P]-ATP</td>
			<td style="width:109px;">Hartmann Analytics</td>
			<td style="width:143px;">FP-301</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Natural dNTPs</td>
			<td style="width:109px;">Promega</td>
			<td style="width:143px;">U1420</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:333px;">Vent (exo-) DNA polymerase</td>
			<td style="width:109px;">NEB</td>
			<td style="width:143px;">M0257S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">DNA polymerase I, Large (Klenow) Fragment</td>
			<td style="width:109px;">NEB</td>
			<td style="width:143px;">MO210S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:333px;">9&#176;Nm DNA polymerase</td>
			<td style="width:109px;">NEB</td>
			<td style="width:143px;">MO260S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Terminal deoxynucleotidyl Transferase (TdT)</td>
			<td style="width:109px;">Promega</td>
			<td style="width:143px;">M828A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Pwo DNA polymerase</td>
			<td style="width:109px;">Peqlab</td>
			<td style="width:143px;">01 01 5010</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:333px;">T4 PNK</td>
			<td style="width:109px;">Thermo Scientific</td>
			<td>EK0032</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Acrylamide/bisacrylamide (19:1, 40%)</td>
			<td style="width:109px;">Serva</td>
			<td align="right" style="width:143px;">10679.01</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:333px;">Agarose</td>
			<td style="width:109px;">Apollo Scientific</td>
			<td style="width:143px;">BIA1177</td>
			<td></td>
		</tr>
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			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">G10 Sephadex</td>
			<td style="width:109px;">Sigma</td>
			<td style="width:143px;">G10120</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:333px;">Urea</td>
			<td style="width:109px;">Apollo Scientific</td>
			<td style="width:143px;">BIU4110</td>
			<td></td>
		</tr>
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			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Equipment</td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
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			<td height="21" style="height:21px;width:333px;"></td>
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			<td style="width:143px;"></td>
			<td></td>
		</tr>
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			<td height="42" style="height:42px;width:333px;">Jupiter semi-preparative RP-HPLC column (5m C18 300&#197;)</td>
			<td style="width:109px;">Phenomenex</td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
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			<td height="21" style="height:21px;width:333px;"></td>
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			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Gene Q Thermal Cycler</td>
			<td style="width:109px;">Bioconcept</td>
			<td style="width:143px;">BYQ6042E</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">PCR vials</td>
			<td style="width:109px;">Bioconcept</td>
			<td style="width:143px;">3220-00</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:333px;">HPLC system</td>
			<td style="width:109px;">Amersham Pharmacia Biotech</td>
			<td style="width:143px;"></td>
			<td>&#196;kta basic 10/100</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
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			<td height="21" style="height:21px;width:333px;">Oligonucleotides</td>
			<td style="width:109px;"></td>
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		</tr>
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		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:333px;">All oligonucleotides were purchased from Microsynth and purified by PAGE</td>
			<td style="width:109px;"></td>
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			<td></td>
		</tr>
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			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">5&#39;-CAAGGACAAAATACCTGTATTCCTT P1</td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:333px;">5&#39;-GACATCATGAGAGACATCGCCTCTGGGCTAAT-AGGACTACTTCTAATCTGTAAGAGCAGATCCCTGG-ACAGGCAAGGAATACAGGTATTTTGTCCTTG T1</td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">5&#39;-GAATTCGATATCAAG P2</td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;"></td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:333px;">More information on experimental procedures and equipment can be found in the following articles:</td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:333px;">Chem. Eur. J. 2012, 18, 13320 &#8211; 13330</td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:333px;">Org. Biomol. Chem. 2013, DOI: 10.1039/C3OB40842F.</td>
			<td style="width:109px;"></td>
			<td style="width:143px;"></td>
			<td></td>
		</tr>
	</tbody>
</table>

nucleoside triphosphates - from synthesis to biochemical characterization

The traditional strategy for the introduction of chemical functionalities is the use of solid-phase synthesis by appending suitably modified phosphoramidite precursors to the nascent chain. However, the conditions used during the synthesis and the restriction to rather short sequences hamper the applicability of this methodology. On the other hand, modified nucleoside triphosphates are activated building blocks that have been employed for the mild introduction of numerous functional groups into nucleic acids, a strategy that paves the way for the use of modified nucleic acids in a wide-ranging palette of practical applications such as functional tagging and generation of ribozymes and DNAzymes. One of the major challenges resides in the intricacy of the methodology leading to the isolation and characterization of these nucleoside analogues.
	
	In this video article, we present a detailed protocol for the synthesis of these modified analogues using phosphorous(III)-based reagents. In addition, the procedure for their biochemical characterization is divulged, with a special emphasis on primer extension reactions and TdT tailing polymerization. This detailed protocol will be of use for the crafting of modified dNTPs and their further use in chemical biology.

Modified nucleoside triphosphates are alluring synthetic targets since they allow for the facile introduction of an vast array of functional groups into nucleic acids41. However, the isolation and characterization of these activated building blocks is often revealed to be arduous. Consequently, the results shown herein are thought to provide a helping hand to follow the various steps within the aforementioned synthetic and biochemical procedures (Figure 1B).
In particular, Figure 3 shows a typical crude 31P-NMR spectrum of a modified dNTP (in this particular case, dUBpuTP (4)18, Figure 2), where the characteristic signals of the phosphorous centers can be observed (i.e. a doublet at -5.02 (P&#947;), a doublet at -10.44 (P&#945;), and a triplet at -20.55 (P&#946;) ppm). In addition, signals stemming for the diphosphate (two doublets at -4.84 and -10.63 ppm) and monophosphate (singlet at -0.18 ppm) side-products along with higher phosphates (signals at -21.02 and -23.19 ppm) are always observed at this stage. A first RP-HPLC analysis of the crude mixture is shown on Figure 4 (for dUBpuTP (4)) where the main peak (Rt = 30.78 min) corresponds to the 5&#39;-triphosphate, while the main byproduct, the 5&#39;-diphosphate, displays a slightly lower retention time (Rt = 30.03 min). Finally, after a thorough RP-HPLC purification, the modified dNTP needs to be characterized by NMR and MALDI-TOF (Figure 5). Both the 1H-NMR and 31P-NMR spectra are crucial for assessing the purity of the modified dNTPs, since the presence of undesired di- and mono-phosphates gives distinctive signals.
After establishing the purity of the nucleoside analogue and assessing the concentration of the stock solution either by mass or by UV-spectroscopy, the modified dNTP can be used in primer extension reactions in order to assess its substrate acceptance capacity by various polymerases. Figure 6 illustrates the outcome of primer extension reactions with dUtPTP (2), dAHsTP (6), and dCValTP (7) used either as lone modifications (lanes 5-7), as combinations of two modified dNTPs (lanes 8-10), or together along with the lone natural dGTP (lane 11).
Finally, Figure 7 shows representative TdT-mediated polymerization reactions with different modified dUTP analogues. In this context, dUcPTP (1) and dUFPTP (3) are the best substrates for TdT (lanes 1 and 4) since the tailing efficiencies are comparable or exceed those of the natural dTTP (lane 6). Instead, dUBpuTP (4) (lane 5) is a rather poor substrate in this context since little polydisperse longer-sized oligonucleotides can be observed.
<img alt="Figure 1" fo:content-width="5in" fo:src="/files/ftp_upload/51385/51385fig1highres.jpg" src="/files/ftp_upload/51385/51385fig1.jpg" width="600px" /> 
Figure 1. A) Ludwig-Eckstein approach for the synthesis of (base) modified nucleoside triphosphates39. B) Schematic representation of all the steps required for the synthesis and biochemical characterization of modified dNTPs prior to their use in applications such as SELEX. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/51385/51385fig1highres.jpg" target="_blank">Click here to view larger image</a>.
<img alt="Figure 2" fo:content-width="5in" fo:src="/files/ftp_upload/51385/51385fig2highres.jpg" src="/files/ftp_upload/51385/51385fig2.jpg" width="600px" /> 
Figure 2. Chemical structures of the modified nucleoside triphosphates: dUcPTP (1), dUtPTP (2), dUFPTP (3), dUBpuTP (4), dUBsTP (5),18 dAHsTP (6), and dCValTP (7)&#160;13. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/51385/51385fig2highres.jpg" target="_blank">Click here to view larger image</a>.
<img alt="Figure 3" fo:content-width="5in" fo:src="/files/ftp_upload/51385/51385fig3highres.jpg" src="/files/ftp_upload/51385/51385fig3.jpg" width="600px" /> 
Figure 3. 31P-NMR spectrum (121.4 MHz, D2O) of the crude reaction mixture of dUBpuTP (4). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/51385/51385fig3highres.jpg" target="_blank">Click here to view larger image</a>.
<img alt="Figure 4" fo:content-width="5in" fo:src="/files/ftp_upload/51385/51385fig4highres.jpg" src="/files/ftp_upload/51385/51385fig4.jpg" width="600px" /> 
Figure 4. RP-HPLC profile of crude dUBpuTP (4): 0-100% eluent B in 40 min, flow rate: 3.5 ml/min&#160;(eluent A: 50 mM TEAB in H2O; eluent B: 50 mM TEAB in H2O/CH3CN (1/1)). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/51385/51385fig4highres.jpg" target="_blank">Click here to view larger image</a>.
<img alt="Figure 5" fo:content-width="5in" fo:src="/files/ftp_upload/51385/51385fig5highres.jpg" src="/files/ftp_upload/51385/51385fig5.jpg" width="600px" /> 
Figure 5. Characterization of the modified nucleoside triphosphate dUBsTP (5): A) 31P-NMR spectrum (121.4 MHz, D2O, 128 scans);18 B) 1H-NMR spectrum (300 MHz, D2O, 128 scans); C) MALDI-TOF spectrum. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/51385/51385fig5highres.jpg" target="_blank">Click here to view larger image</a>.
<img alt="Figure 6" fo:content-width="5in" fo:src="/files/ftp_upload/51385/51385fig6highres.jpg" src="/files/ftp_upload/51385/51385fig6.jpg" width="600px" /> 
Figure 6. Representative gel image (PAGE 15%) of primer extension reactions with various base modified dNTP analogues. Lane 1: primer; lane 2: natural dNTPs without dUTP; lane 3: natural dNTPs without dATP; lane 4: natural dNTPs without dCTP; lane 5: dUtPTP (2); lane 6: dAHsTP (6); lane 7: dCValTP (7); lane 8: dAHsTP (6) and dUtPTP (2); lane 9: dAHsTP (6) and dCValTP (7); lane 10: dUtPTP (2) and dCValTP (7); lane 11: dUtPTP (2), dAHsTP (6), and dCValTP (7); lane 12: natural dNTPs. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/51385/51385fig6highres.jpg" target="_blank">Click here to view larger image</a>.
<img alt="Figure 7" fo:content-width="5in" fo:src="/files/ftp_upload/51385/51385fig7highres.jpg" src="/files/ftp_upload/51385/51385fig7.jpg" width="600px" /> 
Figure 7. Gel image (PAGE 20%) of the TdT polymerization reactions with various base modified dUTP analogues. Lane 1: dUcPTP (1); lane 2: dUtPTP (2); lane 3: dUBsTP (5); lane 4: dUFPTP (3); lane 5: dUBpuTP (4); lane 6: dTTP; lane 7: primer. Concentrations: 10 &#181;M, 25 &#181;M, 50 &#181;M, 75 &#181;M, and 100 &#181;M. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/51385/51385fig7highres.jpg" target="_blank">Click here to view larger image</a>.

Watch this Scientific Journal Video about Nucleoside Triphosphates - From Synthesis to Biochemical Characterization at JoVE.com

Nucleoside Triphosphates - From Synthesis to Biochemical Characterization

The protocol described herein aims to explain and abridge the numerous obstacles in the way of the intricate route leading to modified nucleoside triphosphates. Consequently, this protocol facilitates both the synthesis of these activated building-blocks and their availability for practical applications.

The  traditional strategy for the introduction of chemical functionalities is the  use of solid-phase synthesis by appending suitably modified ...

nucleoside-triphosphates-from-synthesis-to-biochemical

Nanyang Technological University

Research

JoVE Journal

Chemistry

17.0K Views.  University of Bern. The protocol described herein aims to explain and abridge the numerous obstacles in the way of the intricate route leading to modified nucleoside triphosphates. Consequently, this protocol facilitates both the synthesis of these activated building-blocks and their availability for practical applications.

Video: Nucleoside Triphosphates - From Synthesis to Biochemical Characterization

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid phase by using combinatorial chemistry. One of the most well studied classes of peptidomimetics is peptoids. Peptoids are easy to synthesize and have been shown to be proteolysis-resistant and cell-permeable. Over the past decade, many useful protein ligands have been identified through screening of peptoid libraries. However, most of the ligands identified from peptoid libraries do not display high affinity, with rare exceptions. This may be due, in part, to the lack of chiral centers and conformational constraints in peptoid molecules. Recently, we described a new synthetic route to access peptide tertiary amides (PTAs). PTAs are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. With side chains on both &#945;-carbon and main chain nitrogen atoms, the conformation of these molecules are greatly constrained by sterical hindrance and allylic 1,3 strain. (Figure 1) Our study suggests that these PTA molecules are highly structured in solution and can be used to identify protein ligands. We believe that these molecules can be a future source of high-affinity protein ligands. Here we describe the synthetic method combining the power of both split-and-pool and sub-monomer strategies to synthesize a sample one-bead one-compound (OBOC) library of PTAs.

Peptide tertiary amides (PTAs) are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. Here we describe a synthetic method which combines&#160;both split-and-pool and sub-monomer strategies to synthesize a one-bead one-compound library of PTAs.

Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid ...

Synthesis and Characterization of Functionalized Metal-organic Frameworks

Metal-organic frameworks have attracted extraordinary amounts of research attention, as they are attractive candidates for numerous industrial and technological applications. Their signature property is their ultrahigh porosity, which however imparts a series of challenges when it comes to both constructing them and working with them. Securing desired MOF chemical and physical functionality by linker/node assembly into a highly porous framework of choice can pose difficulties, as less porous and more thermodynamically stable congeners (e.g., other crystalline polymorphs, catenated analogues) are often preferentially obtained by conventional synthesis methods. Once the desired product is obtained, its characterization often requires specialized techniques that address complications potentially arising from, for example, guest-molecule loss or preferential orientation of microcrystallites. Finally, accessing the large voids inside the MOFs for use in applications that involve gases can be problematic, as frameworks may be subject to collapse during removal of solvent molecules (remnants of solvothermal synthesis). In this paper, we describe synthesis and characterization methods routinely utilized in our lab either to solve or circumvent these issues. The methods include solvent-assisted linker exchange, powder X-ray diffraction in capillaries, and materials activation (cavity evacuation) by supercritical CO2 drying. Finally, we provide a protocol for determining a suitable pressure region for applying the Brunauer-Emmett-Teller analysis to nitrogen isotherms, so as to estimate surface area of MOFs with good accuracy.

Synthesis, activation, and characterization of intentionally designed metal-organic framework materials is challenging, especially when building blocks are incompatible or unwanted polymorphs are thermodynamically favored over desired forms. We describe how applications of solvent-assisted linker exchange, powder X-ray diffraction in capillaries and activation via supercritical CO2 drying, can address some of these challenges.

Metal-organic frameworks have attracted extraordinary amounts of research attention, as they are attractive candidates for numerous industrial and ...

Metal-free Synthesis of Ynones from Acyl Chlorides and Potassium Alkynyltrifluoroborate Salts

Ynones are a valuable functional group and building block in organic synthesis. Ynones serve as a precursor to many important organic functional groups and scaffolds. Traditional methods for the preparation of ynones are associated with drawbacks including harsh conditions, multiple purification steps, and the presence of unwanted byproducts. An alternative method for the straightforward preparation of ynones from acyl chlorides and potassium alkynyltrifluoroborate salts is described herein. The adoption of organotrifluoroborate salts as an alternative to organometallic reagents for the formation of new carbon-carbon bonds has a number of advantages. Potassium organotrifluoroborate salts are shelf stable, have good functional group tolerance, low toxicity, and a wide variety are straightforward to prepare. The title reaction proceeds rapidly at ambient temperature in the presence of a Lewis acid without the exclusion of air and moisture. Fair to excellent yields may be obtained via reaction of various aryl and alkyl acid chlorides with alkynyltrifluoroborate salts in the presence of boron trichloride.

The goal of this manuscript is to demonstrate a straightforward method for the preparation of ynones from acyl chloride and potassium alkynyltrifluoroborate salt starting materials. The one-pot reaction proceeds rapidly in the presence of boron trichloride without exclusion of air and moisture.

Ynones are a valuable functional group and building block in organic synthesis. Ynones serve as a precursor to many important organic functional groups ...

The Synthesis, Characterization and Reactivity of a Series of Ruthenium N-triphosPh Complexes

Herein we report the synthesis of a tridentate phosphine ligand N(CH2PPh2)3 (N-triphosPh) (1) via a phosphorus based Mannich reaction of the hydroxylmethylene phosphine precursor with ammonia in methanol under a nitrogen atmosphere. The N-triphosPh ligand precipitates from the solution after approximately 1 hr of reflux and can be isolated analytically pure via simple cannula filtration procedure under nitrogen. Reaction of the N-triphosPh ligand with [Ru3(CO)12] under reflux affords a deep red solution that show evolution of CO gas on ligand complexation. Orange crystals of the complex [Ru(CO)2{N(CH2PPh2)3}-&#954;3P] (2) were isolated on cooling to RT. The 31P{1H} NMR spectrum showed a characteristic single peak at lower frequency compared to the free ligand. Reaction of a toluene solution of complex 2 with oxygen resulted in the instantaneous precipitation of the carbonate complex [Ru(CO3)(CO){N(CH2PPh2)3}-&#954;3P] (3) as an air stable orange solid. Subsequent hydrogenation of 3 under 15 bar of hydrogen in a high-pressure reactor gave the dihydride complex [RuH2(CO){N(CH2PPh2)3}-&#954;3P] (4), which was fully characterized by X-ray crystallography and NMR spectroscopy. Complexes 3 and 4 are potentially useful catalyst precursors for a range of hydrogenation reactions, including biomass-derived products such as levulinic acid (LA). Complex 4 was found to cleanly react with LA in the presence of the proton source additive NH4PF6 to give [Ru(CO){N(CH2PPh2)3}-&#954;3P{CH3CO(CH2)2CO2H}-&#954;2O](PF6) (6).

The Synthesis, Characterization and Reactivity of a Series of Ruthenium N-triphosPh Complexes

Ruthenium phosphine complexes are widely used for homogeneous catalytic reactions such as hydrogenations. The synthesis of a series of novel tridentate ruthenium complexes bearing the N-triphos ligand N(CH2PPh2)3 is reported. Additionally, the stoichiometric reaction of a dihydride Ru&#8211;N-triphos complex with levulinic acid is described.

Herein we report the synthesis of a tridentate phosphine ligand N(CH2PPh2)3 (N-triphosPh) (1) via a phosphorus based Mannich reaction of the ...

Synthesis, Characterization, and Functionalization of Hybrid Au/CdS and Au/ZnS Core/Shell Nanoparticles

Plasmonic nanoparticles are an attractive material for light harvesting applications due to their easily modified surface, high surface area and large extinction coefficients which can be tuned across the visible spectrum. Research into the plasmonic enhancement of optical transitions has become popular, due to the possibility of altering and in some cases improving photo-absorption or emission properties of nearby chromophores such as molecular dyes or quantum dots. The electric field of the plasmon can couple with the excitation dipole of a chromophore, perturbing the electronic states involved in the transition and leading to increased absorption and emission rates. These enhancements can also be negated at close distances by energy transfer mechanism, making the spatial arrangement of the two species critical. Ultimately, enhancement of light harvesting efficiency in plasmonic solar cells could lead to thinner and, therefore, lower cost devices. The development of hybrid core/shell particles could offer a solution to this issue. The addition of a dielectric spacer between a gold nanoparticles and a chromophore is the proposed method to control the exciton plasmon coupling strength and thereby balance losses with the plasmonic gains. A detailed procedure for the coating of gold nanoparticles with CdS and ZnS semiconductor shells is presented. The nanoparticles show high uniformity with size control in both the core gold particles and shell species allowing for a more accurate investigation into the plasmonic enhancement of external chromophores.

The synthesis of uniform gold nanoparticles coated with semiconductor shells of CdS or ZnS is performed. The semiconductor coating is conducted by first depositing a silver sulfide shell and exchanging the silver cations for zinc or cadmium cations.

Plasmonic nanoparticles are an attractive material for light harvesting applications due to their easily modified surface, high surface area and large ...

Synthesis and Characterization of Supramolecular Colloids

Control over colloidal assembly is of utmost importance for the development of functional colloidal materials with tailored structural and mechanical properties for applications in photonics, drug delivery and coating technology. Here we present a new family of colloidal building blocks, coined supramolecular colloids, whose self-assembly is controlled through surface-functionalization with a benzene-1,3,5-tricarboxamide (BTA) derived supramolecular moiety. Such BTAs interact via directional, strong, yet reversible hydrogen-bonds with other identical BTAs. Herein, a protocol is presented that describes how to couple these BTAs to colloids and how to quantify the number of coupling sites, which determines the multivalency of the supramolecular colloids. Light scattering measurements show that the refractive index of the colloids is almost matched with that of the solvent, which strongly reduces the van der Waals forces between the colloids. Before photo-activation, the colloids remain well dispersed, as the BTAs are equipped with a photo-labile group that blocks the formation of hydrogen-bonds. Controlled deprotection with UV-light activates the short-range hydrogen-bonds between the BTAs, which triggers the colloidal self-assembly. The evolution from the dispersed state to the clustered state is monitored by confocal microscopy. These results are further quantified by image analysis with simple routines using ImageJ and Matlab. This merger of supramolecular chemistry and colloidal science offers a direct route towards light- and thermo-responsive colloidal assembly encoded in the surface-grafted monolayer.

A protocol for the synthesis and characterization of colloids coated with supramolecular moieties is described. These supramolecular colloids undergo self-assembly upon the activation of the hydrogen-bonds between the surface-anchored molecules by UV-light.

Control over colloidal assembly is of utmost importance for the development of functional colloidal materials with tailored structural and mechanical ...

HPLC-based Assay to Monitor Extracellular Nucleotide/Nucleoside Metabolism in Human Chronic Lymphocytic Leukemia Cells

This method describes a sensitive, specific, reliable and reproducible reverse phase high-performance liquid chromatography (RP-HPLC) assay developed and validated for the quantification of extracellular purine nucleotides and nucleosides produced by purified chronic lymphocytic leukemia (CLL) cells under different culture conditions. The chromatographic separation of adenosine 5&#39;-monophosphate (AMP), adenosine (ADO) and inosine (INO) is performed at RT on a silica-based, reversed-phase column that is used for polar compound retention. The method includes a binary mobile phase, which consists of 7 mM ammonium acetate and acetonitrile with a flow rate of 1.00 ml/min. The eluates are monitored using a Photodiode Array UV detector set at 260 nm. A standard calibration curve is generated to calculate the equation for the analytical quantification of each purine compound. System control, data acquisition and analysis are then performed. Applying this protocol, AMP, INO and ADO elute at 7, 11 and 11.9 min, respectively, and the total run time for each sample is 20 min. This protocol may be applied to different cell types and cell lines (both suspension and adherent), using culture media as matrix. The advantages are easy and fast sample preparation and the requirement of a small amount of supernatant for analysis. Furthermore, the use of a serum-free medium allows skipping the protein precipitation step with acetonitrile that impacts the final concentration of purine compounds. One of the limitations of the method is the requirement of the equilibration column run before each single sample run, making the total run time of the experiment longer and preventing high throughput screening applications.

The protocol described here represents an easy and reproducible method that employs reverse phase high-performance liquid chromatography (RP-HPLC) to measure purine metabolism on chronic lymphocytic leukemia (CLL) cells cultured under different conditions.

This method describes a sensitive, specific, reliable and reproducible reverse phase high-performance liquid chromatography (RP-HPLC) assay developed and ...

Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level

We demonstrate a method for the synthesis of cyclic polymers and a protocol for characterizing their diffusive motion in a melt state at the single molecule level. An electrostatic self-assembly and covalent fixation (ESA-CF) process is used for the synthesis of the cyclic poly(tetrahydrofuran) (poly(THF)). The diffusive motion of individual cyclic polymer chains in a melt state is visualized using single molecule fluorescence imaging by incorporating a fluorophore unit in the cyclic chains. The diffusive motion of the chains is quantitatively characterized by means of a combination of mean-squared displacement (MSD) analysis and a cumulative distribution function (CDF) analysis. The cyclic polymer exhibits multiple-mode diffusion which is distinct from its linear counterpart. The results demonstrate that the diffusional heterogeneity of polymers that is often hidden behind ensemble averaging can be revealed by the efficient synthesis of the cyclic polymers using the ESA-CF process and the quantitative analysis of the diffusive motion at the single molecule level using the MSD and CDF analyses.

A protocol for the synthesis and characterization of diffusive motion of cyclic polymers at the single molecule level is presented.

We demonstrate a method for the synthesis of cyclic polymers and a protocol for characterizing their diffusive motion in a melt state at the single ...

Synthesis and Characterization of Fe-doped Aluminosilicate Nanotubes with Enhanced Electron Conductive Properties

The goal of the protocol is to synthesize Fe-doped aluminosilicate nanotubes of the imogolite type with the formula (OH)3Al2-xFexO3SiOH. Doping with Fe aims at lowering the band gap of imogolite, an insulator with the chemical formula (OH)3Al2O3SiOH, and at modifying its adsorption properties towards azo-dyes, an important class of organic pollutants of both wastewater and groundwater.
Fe-doped nanotubes are obtained in two ways: by direct synthesis, where FeCl3 is added to an aqueous mixture of the Si and Al precursors, and by post-synthesis loading, where preformed nanotubes are put in contact with a FeCl3&#8226;6H2O aqueous solution. In both synthesis methods, isomorphic substitution of Al3+ by Fe3+ occurs, preserving the nanotube structure. Isomorphic substitution is indeed limited to a mass fraction of ~1.0% Fe, since at a higher Fe content (i.e., a mass fraction of 1.4% Fe), Fe2O3 clusters form, especially when the loading procedure is adopted. The physicochemical properties of the materials are studied by means of X-ray powder diffraction (XRD), N2 sorption isotherms at -196 &#176;C, high resolution transmission electron microscopy (HRTEM), diffuse reflectance (DR) UV-Vis spectroscopy, and &#950;-potential measurements. The most relevant result is the possibility to replace Al3+ ions (located on the outer surface of the nanotubes) by post-synthesis loading on preformed imogolite without perturbing the delicate hydrolysis equilibria occurring during nanotube formation. During the loading procedure, an anionic exchange occurs, where Al3+ ions on the outer surface of the nanotubes are replaced by Fe3+ ions. In Fe-doped aluminosilicate nanotubes, isomorphic substitution of Al3+ by Fe3+ is found to affect the band gap of doped imogolite. Nonetheless, Fe3+ sites on the outer surface of nanotubes are able to coordinate organic moieties, like the azo-dye Acid Orange 7, through a ligand-displacement mechanism occurring in an aqueous solution.

Here, we present a protocol to synthesize and characterize Fe-doped aluminosilicate nanotubes. The materials are obtained by either sol-gel synthesis upon addition of FeCl3&#8226;6H2O to the mixture containing the Si and Al precursors or by post-synthesis ionic exchange of preformed aluminosilicate nanotubes.

The goal of the protocol is to synthesize Fe-doped aluminosilicate nanotubes of the imogolite type with the formula (OH)3Al2-xFexO3SiOH. Doping with Fe ...

Enzymatic Cascade Reactions for the Synthesis of Chiral Amino Alcohols from L-lysine

Amino alcohols are versatile compounds with a wide range of applications. For instance, they have been used as chiral scaffolds in organic synthesis. Their synthesis by conventional organic chemistry often requires tedious multi-step synthesis processes, with difficult control of the stereochemical outcome. We present a protocol to enzymatically synthetize amino alcohols starting from the readily available L-lysine in 48 h. This protocol combines two chemical reactions that are very difficult to conduct by conventional organic synthesis. In the first step, the regio- and diastereoselective oxidation of an unactivated C-H bond of the lysine side-chain is catalyzed by a dioxygenase; a second regio- and diastereoselective oxidation catalyzed by a regiodivergent dioxygenase can lead to the formation of the 1,2-diols. In the last step, the carboxylic group of the alpha amino acid is cleaved by a pyridoxal-phosphate (PLP) decarboxylase (DC). This decarboxylative step only affects the alpha carbon of the amino acid, retaining the hydroxy-substituted stereogenic center in a beta/gamma position. The resulting amino alcohols are therefore optically enriched. The protocol was successfully applied to the semipreparative-scale synthesis of four amino alcohols. Monitoring of the reactions was conducted by high performance liquid chromatography (HPLC) after derivatization by 1-fluoro-2,4-dinitrobenzene. Straightforward purification by solid-phase extraction (SPE) afforded the amino alcohols with excellent yields (93% to &#62;95%).

Chiral amino alcohols are versatile molecules for use as scaffolds in organic synthesis. Starting from L-lysine, we synthesize amino alcohols by an enzymatic cascade reaction combining diastereoselective C-H oxidation catalyzed by dioxygenase followed by cleavage of the carboxylic acid moiety of the corresponding hydroxyl amino acid by a decarboxylase.

Amino alcohols are versatile compounds with a wide range of applications. For instance, they have been used as chiral scaffolds in organic synthesis. ...