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Related Topics: High Resolution Melting, Real-Time PCR Data Analysis, and Real-Time PCR Troubleshooting. A number of free online resources are available to help you with primer design (see the Websites tab below). Note: You clicked on an external link, which has been disabled in order to keep your shopping session open. Increasing awareness that the still growing use of fossil feedstocks and concomitant emissions of greenhouse gases (GHG) is affecting global climate change1 is one of the main drivers in the search for sustainable, renewable feedstocks for chemicals and materials. Scheme 1 Synthesis of FDCAs via disproportionation reaction (Sacch = saccharification, CDH = cyclodehydration, Ox = oxidation, Disp = disproportionation). Hence, here we report a systematic comparison of polyesters containing 2,5-, 2,4- or 3,4-FDCA, and a series of homologous industrially relevant aliphatic diols. The polycondensation was performed by a conventional two-step melt-polycondensation procedure using titanium(IV) isopropoxide as the catalyst (1.25 mol%).
While the known polyesters based on 2,5-FDCA merely served as benchmark, all 2,4- and 3,4-FDCA polyesters (except for 2,4-PEF and 3,4-PBF) have not been described before. Given the commercial importance of PET, the ethylene glycol (EG) polyesters or PEFs (Table 1, entries 1–3) are the main focus of this study. Furthermore, contrary to observations on the chemical reactivity of monomeric furans, the absence of high oxidation state substituents on C2 and or C5 of the furan ring does not seem to have any detrimental effect on chemical selectivity. In the biobased 1,3-propanediol (PDO) series (Table 1, entries 4–6), the significantly higher molecular weight of the 2,5-PPF is striking, while for the other two FDCA isomers there is little difference with the corresponding EG polyesters.
Detailed analysis of the EG-residue part of the 1H-NMR spectra of the PEF series shows besides end-groups (Mn values obtained by end-group analysis confirm GPC results) also the presence of signals that can be attributed to diethylene glycol (DEG) (see ESI, Fig. We estimated the DEG incorporation in the PEF series to be less than 1% (based on 1H-NMR analysis, see ESI, Fig. Thermogravimetric analysis (TGA) of the FDCA polyesters shows that all new polyesters have comparable or even higher thermal stability compared to the 2,5-FDCA polyesters (Table 2). For all polyesters a single stage decomposition mechanism is observed between 350 and 425 °C. Whereas TGA analysis showed no dramatic differences between the FDCA polyesters, differential scanning calorimetry (DSC) revealed the remarkable effects of the position of the carboxylic groups in the FDCA isomers (Table 2). The effect of the position of the carboxylic acid groups on the Tg of the polyesters is graphically represented in Fig. In order to find an explanation for the observed differences between the FDCA polyesters, we compared the structural characteristics of the FDCA isomers in relation to their phthalic acid analogues, as well as the thermal properties of the ensuing EG polyesters in Table 3. With regard to symmetry, 2,4-FDCA is the least symmetrical diacid in the series under investigation. Both the primers and the target sequence can affect amplification efficiency and specificity and thus the accuracy of qPCR assays.
Commercially available programs such as Beacon Designer software can perform both primer design and target sequence selection. New polyesters based on 2,4-FDCA and 3,4-FDCA isomers with (linear) diols were thoroughly characterised and compared with their as-synthesised 2,5-FDCA analogues. The increasing use of synthetic polymers can contribute to reducing GHG emissions due to the lower weight of those materials compared to e.g. Currently, most synthetic routes to 2,5-FDCA are based on the oxidation of 5-hydroxymethyl-2-furaldehyde (HMF)6 which can be obtained by cyclodehydration of C6 sugars like fructose and glucose.7 In order to avoid possible competition with the food chain we have investigated several other strategies based on the use of non-digestible agro-residues like sugar beet pulp or bagasse.
In order to assess the viability of the Henkel-route it is necessary to gain insight into the value of the separate isomers as polymer building blocks.
Melt polycondensation of the dimethyl esters of 2,5-, 2,4- or 3,4-FDCA with linear (potentially) biobased aliphatic diols (ethylene glycol (EG), 1,3-propanediol (PDO), 1,4-butanediol (1,4-BDO), and 2,3-butanediol (2,3-BDO)) yielded a set of 12 polyesters, of which 6 are novel (Scheme 2). The pre-polymerization was performed at 160 °C for 12 h, followed by further polycondensation at 210–215 °C for 2 h under reduced pressure (0.02 mbar) in the second-step. The structures of all the polyesters were confirmed by NMR (1H and 13C) (see ESI†) and FTIR spectroscopy. The reference polymer 2,5-PEF was obtained with an excellent Mn of 19100 (PDI 1.8), which is comparable to literature values,5,14 thereby validating our polycondensation procedure. One major difference in this series is that while 2,5-PEF is opaque after cooling down from the melt, the 2,4- and 3,4 analogues are translucent, indicative of a lower degree of crystallinity, or lower rate of crystallisation. This secondary diol is less reactive than its primary isomer 1,4-BDO, which is obvious from the significantly lower Mws. 1 shows the 1H-NMR spectra of the three isomeric PEF polymers (13C-NMR spectra are shown in the ESI†). The consistently higher thermal stability of the 2,4-FDCA based polyesters is remarkable given the fact that these materials have on average the lowest Mws according to GPC (see Table 1). 2 TGA traces of (crude) polyethylene furandicarboxylates and polyethylene terephthalates recorded from 30 to 600 °C at 10 °C min?1 under a N2 atmosphere.
In the PEF series the Tg of 2,4-PEF (Table 2, entry 2) is only 6 °C lower than that of 2,5-PEF, while the Tg of 3,4-PEF is significantly lower (Table 2, entry 3). 2,3-BDO is known to increase the Tg due to hindered rotation about the C2–C3 axis (compared to EG). 3, which makes it even more clear that the 2,4-analogue is highly comparable to the 2,5-isomer. The data are arranged in descending order with respect to the interatomic distance (D) between the carboxylic acid groups in the respective diacids. Comparison of the D and the projected angle between the C1–C2 bond and the C5–C6 bond (?) leads to the conclusion that contrary to common opinion in the literature the 2,5-FDCA isomer is not similar to TA, but rather to IPA. 7 shows the wide angle X-ray diffraction (WAXD) patterns of the isomeric PEFs which were used to calculate the degree of crystallinity of these polymers after precipitation from methanol (see also Table 4). 7 WAXD diffractograms of 2,5-PEF ((a) annealed at 175 °C for 15 h, (b) precipitated from MeOH) and precipitated 2,4-PEF and 3,4-PEF. All polymers were obtained by melt polycondensation of linear diols with FDCA dimethyl esters and exhibit molecular weights in the range Mw = 34000–65000 and polydispersities close to 2.0. Pectinic sugars like galacturonic acid can be converted into galactaric acid8 and subsequently into 2,5-FDCA. Whereas there is a limited, yet steadily increasing amount of literature on the synthesis and properties of 2,5-FDCA based polyesters, surprisingly only a very few reports on either 2,4- or 3,4-FDCA polyesters can be found. The polyesters were obtained in excellent isolated yields (80–98%), while after precipitation from methanol all polyesters were obtained as white powders. Gel permeation chromatography (GPC) of the furandicarboxylate polyesters showed that all polymers were obtained in medium to high molecular weights, with polydispersity index (PDI) values close to 2 (Table 1). Polycondensation of either 2,4- or 3,4-FDCA with EG yielded materials with comparable molecular weights, polydispersities and crude isolated yields. For comparison, two PET examples are included in Table 1; an as-synthesised sample (polycondensation conditions are described in the Experimental section) and a commercial, bottle-grade PET sample. While the reference 2,5-P23BF is obtained with a similar Mn as reported in the literature,16 the 2,4-analogue was obtained as low Mw material only. Due to the symmetry of 2,5-FDCA, the 1H-NMR spectrum of 2,5-PEF shows only 1 furanic proton, and 1 broad singlet for the ethylene glycol residue (Fig.
This is not surprising since the dehydration of ethylene glycol in the presence of acid catalyst leads to the formation of diethylene glycol which was identified as one of the most important side products in PET synthesis.17–20 The incorporation of DEG as a co-monomer in PET synthesis results in a decrease in melting temperature of about 5 °C (for each percent increase in DEG concentration).

With regard to melting transitions the position of the carboxylic acid groups in FDCA has a dramatic impact.
The absence of cold crystallization in the case of 2,4- and 3,4-PEF (as compared to the 2,5-analogue) further indicates that these polymers have very low rates of crystallization.
While the 2,4-isomer is closer to TA, the 3,4-isomer has characteristics comparable to PA (Fig. The 2,5-isomer showed only a surprisingly low degree of crystallinity of 14% (after subtraction of the amorphous halo, see ESI†). Winship, “An improved method for directly sequencing PCR amplified material using dimethyl sulphoxide,” Nucleic Acids Research, vol.
The use of PCR primers specifically designed and validated for qPCR assays with your target of interest is highly recommended. Thermogravimetric analysis (TGA) of the new polyesters shows that they have comparable or even higher thermal stability compared to the 2,5-FDCA polyesters. However, this trend can only become truly positive when these polymeric materials are based on renewable resources.
This indicates that under comparable polycondensation conditions, the position of the carboxylic acid groups on the furan ring has no significant influence on reactivity. While the Mn values of 2,5- and 2,4-P14BF are very similar, the former deviates with regard to PDI.
As the Mws of the 2,3-BDO series are significantly lower compared to EG series, the Tg increasing effect of 2,3-BDO is quite dramatic. The observed melting points for the 2,5-FDCA based polyesters are all in good agreement with those reported in the literature.5,14,39 Whereas 2,5-PEF already has a substantially lower Tm than PET (209 °C vs.
Dividing the melting enthalpy of the first DSC heating run (corrected for cold crystallization) by the degree of crystallinity of the sample allows for estimating the heat of fusion of the 100% crystalline material. This section provides information and tips on designing qPCR assay primers and probes, choosing a target sequence, multiplexing, selecting reporters and quenchers, and validating and optimizing qPCR assays. Interestingly, the glass-transition temperatures (Tg) of 2,4-FDCA derived polyesters are similar to those of the 2,5-FDCA isomers. Due to the high oxygen content of the most abundantly available biomass components like polysaccharides and lignin, one can debate whether it is viable to use such feedstock for the production of highly defunctionalised “drop-in” chemical building blocks like olefins.
In this series the 3,4-FDCA isomer yields the highest molecular weight polyester, while all polyesters were obtained as opaque materials from the melt.
From the data in Table 1 no obvious correlation can be found between the FDCA substitution pattern and reactivity as would follow from systematic differences in molecular weight build-up.
245 °C), no melting point was observed in the case of 2,4-PEF even after annealing at 90 °C for 5 h. When this is done for the precipitated 2,5-PEF an unrealistically high value of 314 J g?1 is obtained (compared to reference values for e.g.
Both differential scanning calorimetry (DSC) and wide-angle X-ray diffraction (WAXD) analyses showed that 2,4-PEF is amorphous, while 2,5-PEF and 3,4-PEF are semi-crystalline materials.
A different approach would be to transform biomass components into “new” chemical building blocks with unique structures and functionalities, following thermodynamically more favorable pathways. The higher thermal stability of the commercial sample is probably due to the higher Mw and the presence of stabilisers. In contrast, for 3,4-PEF a melting point of 155 °C was recorded after annealing at 100 °C for 5 h. While the chemical shift of the EG residue is similar to that of the 2,5-analogue, H3 has shifted downfield in 2,4-PEF, while H5 resonates even further downfield due to the neighboring oxygen group (Fig. 40 °C) is only slightly larger compared to the ones observed for the 2,5- and 2,4-isomers (approx. The surprising absence of melting point of 2,4-PEF is in sharp contrast to its high Tg of 73 °C. This prompted us to anneal the sample (for 15 h at 175 °C), resulting in a significantly higher degree of crystallinity of 56%, and a heat of fusion of 109 J g?1 (DSC traces for annealed 2,5-PEF are shown in the ESI†). Out of these three genes, Rv0774c gene was amplified with normal primers under standard PCR conditions, while no amplification was observed in case of Rv0519c and ML0314c genes.
2 it is clear that the PEF series is intrinsically less thermally stable at temperatures in excess of 350 °C. In contrast, no unambiguous correlation can be found between ? and Tg or Tm of the EG polyesters (Fig. In the case of 2,4-PEF, no melting was observed in the DSC of the precipitated material, which was supported by the absence of crystalline reflections in the WAXD diffractogram (Fig.
In the present investigation a modified primer based approach was successfully used for amplification of GC rich sequence of Rv0519c through codon optimization without changing the native amino acid sequence. The 3,4-isomer is symmetrical, resulting in singlets for the furanic proton and the EG residue respectively. Nevertheless, all polyfurandicarboxylates are stable up to 300 °C, which still allows for a very broad processing window for these materials. The 1,4-BDO series again displays a comparable trend; while the Tg decreases further, the difference between the 2,5- and 2,4-PBFs remains small, while no further decrease for the 3,4-isomer is observed. The strategy was successfully confirmed by redesigning the standard primers with similar modifications followed by amplification of ML0314c gene.1. Attempts to induce crystallinity in 2,4-PEF by annealing for up to 5.0 h at 90 °C were unsuccessful. IntroductionPolymerase chain reaction (PCR) based cloning of gene of interest with high GC content is a long recognized problem. Hunsmann, “Improvement of PCR amplified DNA sequencing with the aid of detergents,” Nucleic Acids Research, vol.
The main difference between 2,4-FDCA and the other diacids is the lower symmetry of the former. In contrast, precipitated 3,4-PEF proved to be highly crystalline from the WAXD analysis (55%), giving an estimated 116 J g?1 for the heat of fusion at 100% crystallinity. PCR is a most sensitive tool and various factors have to be optimized for amplification of gene of interest.
The 2,4-FDCA based polyester showed multimodal melting behavior after annealing at 60 °C for 5 h, with the lowest melting point again approx. High GC content of the gene generates complication during primer designing like mismatch and high annealing temperature, self-dimer formation, and secondary structure.
Comparable multimodal melting behavior was observed for 3,4-P14BF after annealing at 40 °C for 5 h. The most prominent problem associated is hairpin loop, which directly interferes during annealing of primers on difficult DNA template that leads to no amplification. Medrano, “Organic solvents as facilitators of polymerase chain reaction,” BioTechniques, vol.
Use of DMSO and glycerol was reported to reduce the annealing temperature and denaturation temperature, increase the chances of breakage of secondary structure, and increase the efficiency of amplification [1–5].
The Mycobacterium genome has very high GC content (66%) which raised the possibility of hairpin structure in the genomic structure. Skinner, “Denaturants or cosolvents improve the specificity of PCR amplification of a G + C-rich DNA using genetically engineered DNA polymerases,” Gene, vol.

From genome sequence analysis it was observed that PPE, PE, and PGRS multigene family code for proteins of approximately 110–80 amino acids rich in proline and glutamic acid at N-terminal position. Proline and glutamic acid residues are mainly coded by triplet of GC bases in Mycobacterium genome.
Presence of high GC content increased the annealing temperature beyond the extension temperature (72°C) and also repeated stretches generate the hairpin structure.
In such cases, effectiveness and reproducibility of PCR amplification depend on detailed analysis of the possible secondary structures of the oligonucleotide primers as well as formation of self-dimers and cross-dimers with other interrelating oligonucleotides [7]. Though these problems have been considered by several investigators, no systematic details are available to approach this problem.In an attempt to clone GC rich genes (Rv0519c and Rv0774c from M. Lanchbury, “Strategy for controlling preferential amplification and avoiding false negatives in PCR typing,” BioTechniques, vol. We could amplify Rv0774c gene, but Rv0519c and ML0314c genes having high GC content at terminal region were not amplified by standard PCR procedures. Parkhill et al., “Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence,” Nature, vol. Therefore, an attempt has been made in the present investigation to standardize the conditions and ingredients that favor the amplification of GC rich sequences.2. The strain Mycobacterium tuberculosis H37Ra was a kind gift from Director of National Institute of Leprosy and Other Mycobacterial Diseases, Agra, India. Bharadwaj, “Oligonucleotide properties determination and primer designing: a critical examination of predictions,” Bioinformatics, vol. Zhou, “Cloning and sequencing of the complicated rDNA gene family of Bos taurus,” Czech Journal of Animal Science, vol. Modification of Primers by Codon OptimizationDegeneracy of codon is normally used to overcome the existing problem including change of base at wobble position specific for coding sequence of Mycobacterium genome. Designed forward primer of Rv0519c contributes about 64% GC content and stretches of GC led to generation of complicated hairpin structure with high value of free energy change G. The incorporation we opted in the primer sequence was as follows: guanine (G) base turned into adenosine (A) at wobble position of third codon CGG and thymine (T) to adenine (A) in codon CGT (Table 1). Similarly in reverse primer of Rv0519c primer sequence, the adenosine (A) base was turned into thymine (T) at wobble position of last sixth codon CGA.
These sets of primers were used to clone Rv0774c and Rv0519c genes from isolated genomic DNA of M. The gene sequences of Rv0519c and ML0314c were analysed and the modified primers were reconstructed for the amplification of gene. To confirm the sequence of amplified product, the purified PCR products for all three genes were sent for sequencing with specific primers.3. Problem with Amplification of Mycobacterium GeneStrategies for the cloning of complicated DNA sequences are of the most significance and it has to be optimised through simple procedures. For PCR based cloning of genes, primer is one of the crucial factors for successful amplification of the genes to be cloned. Length of primer and annealed matches increase the specificity of the reaction but it may not always be an authentic reason to get desired amplicons. With the development of sequencing technology, many tools have been developed to design primers. But the noticeable points with these databases were the variability of primers properties like annealing temperature, prediction of secondary structure, and so forth. High GC content in the genes of Mycobacterium species generate stable secondary structures which often form in the oligos DNA that halt the progression of DNA polymerase during amplification (Figures 1(a) and 1(b)). The primer properties were evaluated through different most widely used oligo designing tools such as IDT, Sigma, OC, and manual.
Current study illustrated the need to balance length and melting temperature with respect to GC content of gene at terminal sites, while designing primers for the PCR. It also emphasised the importance of careful investigation of sequences for GC-rich repeats, giving rise to complicated secondary structures, which could reduce the efficiency of amplification [8]. We successfully amplified the Rv0774c gene with normal PCR primers and procedure (Figure 2(a), lane 3).
On the other hand, no amplification was observed in case of Rv0519c gene (GC content 69%) under same reaction conditions (Figure 2(a), lane 4). Attempt had been made to amplify the gene with a long range of annealing temperatures but without success. The presence of stable hairpin structures was not observed in case of Rv0774c, despite the high GC content while the high GC content at terminal region of Rv0519c gene led to formation of strong hairpin loop structure formation during normal primer designing procedure (Table 1). Such high −G value and complicated hairpin structure might create problem during amplification procedures. Thus, it was essential to decrease the GC content and change of corresponding nucleotides of oligos according to the wobble hypothesis approach. Therefore, we designed the primers by using the degeneracy of codon and checked the hairpin loop formation by integrative DNA-oligoanalyser. All the introduced modifications at wobble position were analysed on IDT tools for their effectiveness to distort hairpin.
We introduced small change at nucleotide level, starting with codon CGG to CGA and CGT to CGA during designing of forward primer sequence while single nucleotide change CGT to CGA in case of reverse primer distorted the possible hairpin structure. Similar problem was observed in amplification of ML0314c gene (GC content, 60%) from M. Primers designed for ML0314c gene from normal procedures demonstrated mismatch annealing temperature as well as strong hairpin loop structure (Table 1). This problem was also tackled successfully by changing nucleotide as well as addition of nucleotide at terminal position, upstream to the restriction sites to sort out the annealing mismatch between the primers.
The single nucleotide modification at wobble position TCG to TCC distorted the whole hairpin structure. The strategy was successfully confirmed by amplification of ML0314c gene (Figure 2(d), lane 1) from M.
Sequencing of PCR products confirmed the amplification of specific genes.A major benefit of this protocol was to resolve the problem of Tm mismatch as well as existence of secondary structure in the primer pairs of high GC rich sequences. By using this approach we could adjust the Tm mismatch without increasing the length of primers which may be responsible for dimerization. The high Tm of primers, which become a setback in carrying out PCR, was easily solved by this method (Figure 3).
ConclusionBy using the wobble hypothesis approach in primer designing, we were able to tackle the ongoing amplification problem associated with complicated gene of Mycobacterium with high GC content. In this approach a single modification at base level distorted the secondary structure and resolved the primer Tm mismatch.

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