Heteroduplex cleavage assay for screening of probable zygosities resulting from CRISPR mutations in diploid single cell lines.

The most common gene editing methods, such as CRISPR, involve random repair of an induced double-stranded DNA break through the non-homologous end joining (NHEJ) repair pathway, resulting in small insertions/deletions. In diploid cells, these mutations can take on one of three zygosities: monoallelic, diallelic heterozygous, or diallelic homozygous. While many advances have been made in CRISPR delivery systems and gene editing efficiency, little work has been done to streamline detection of gene editing events. The only current method to determine the zygosity of an edited gene in a diploid organism is DNA sequencing, which is costly and time-consuming. Here, we describe the development of a T7 endonuclease I (T7EI)-based heteroduplex cleavage assay, along with statistical models relating the percentage of cleaved DNA to the zygosity of a mutation, that provides a rapid screening step prior to DNA sequencing. By isolating candidates likely to contain the desired zygosity for the edited gene, our screening method can decrease the number of clones requiring DNA sequencing.

Validation and long-term assessment of an approach for the high throughput determination of lipophilicity (log POW) values using multiplexed, absorbance-based capillary electrophoresis.

A critical evaluation of the use of 96-capillary multiplexed microemulsion electrokinetic chromatography (MMEEKC) for the indirect determination of octanol-water partition coefficients (log POW values) for a wide range of structurally different compounds is presented. The various components of the microemulsion solution were evaluated and optimized for use in a multiplexed capillary format. A six-component calibration mixture and 23 different solutes (n = 4 each) were analyzed simultaneously, providing a throughput of up to 46 samples/h, which translates to greater than a 20-fold improvement over existing indirect log POW methods. Agreement to within +/-0.5 log P units of literature values was obtained for 51 of the 54 tested neutral and basic (uncharged) solutes. A linear free energy relationship (LFER) analysis performed on the MMEEKC system supports its use as a viable and effective model of the classical shake-flask method for log POW determinations. Moreover, a standard deviation of 0.1 or less log P units was obtained for 35 of 36 solutes analyzed repeatedly over an 8-month time period, documenting the long-term effectiveness of the analysis format. Critical comparisons between the proposed MMEEKC method and existing separation methods for the indirect determination of log POW values are also made. Overall, the results indicate that 96-capillary MMEEKC can serve as a high throughput, cost effective and robust approach and as a valid model for log POW determinations.

Antisense inhibition of isoamylase alters the structure of amylopectin and the physicochemical properties of starch in rice endosperm.

This is the first report on regulation of the isoamylase1 gene to modify the structure of amylopectin and properties of starch by using antisense technology in plants. The reduction of isoamylase1 protein by about 94% in rice endosperm changed amylopectin into a water-insoluble modified amylopectin and a water-soluble polyglucan (WSP). As compared with wild-type amylopectin, the modified amylopectin had more short chains with a degree of polymerization of 5-12, while their molecular sizes were similar. The WSP, which structurally resembled the phytoglycogen in isoamylase-deficient sugary-1 mutants, accounted for about 16% of the total alpha-polyglucans in antisense endosperm, and it was distributed throughout the whole endosperm unlike in sugary-1 mutant. The reduction of isoamylase activity markedly lowered the gelatinization temperature from 54 to 43 degrees C and the viscosity, and modified X-ray diffraction pattern and the granule morphology of the starch. The activity of pullulanase, the other type of starch debranching enzyme, in the antisense endosperm was similar to that in wild-type, whereas it is deficient in sugary-1 mutants. These results indicate that the isoamylase1 is essential for amylopectin biosynthesis in rice endosperm, and that alteration of the isoamylase activity is an effective means to modify the physicochemical properties and granular structure of starch.

Functional interactions between heterologously expressed starch-branching enzymes of maize and the glycogen synthases of Brewer's yeast.

Starch-branching enzymes (SBEs) catalyze the formation of alpha(1-->6) glycoside bonds in glucan polymers, thus, affecting the structure of amylopectin and starch granules. Two distinct classes of SBE are generally conserved in higher plants, although the specific role(s) of each isoform in determination of starch structure is not clearly understood. This study used a heterologous in vivo system to isolate the function of each of the three known SBE isoforms of maize (Zea mays) away from the other plant enzymes involved in starch biosynthesis. The ascomycete Brewer's yeast (Saccharomyces cerevisiae) was employed as the host species. All possible combinations of maize SBEs were expressed in the absence of the endogenous glucan-branching enzyme. Each maize SBE was functional in yeast cells, although SBEI had a significant effect only if SBEIIa and SBEIIb also were present. SBEI by itself did not support glucan accumulation, whereas SBEIIa and SBEIIb both functioned along with the native glycogen synthases (GSs) to produce significant quantities of alpha-glucan polymers. SBEIIa was phenotypically dominant to SBEIIb in terms of glucan structure. The specific branching enzyme present had a significant effect on the molecular weight of the product. From these data we suggest that SBEs and GSs work in a cyclically interdependent fashion, such that SBE action is needed for optimal GS activity; and GS, in turn, influences the further effects of SBE. Also, SBEIIa and SBEIIb appear to act before SBEI during polymer assembly in this heterologous system.