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Khao-Mao producer group in Thailand’s Nakhon Phanom province’s Phon Sawan district, Na Hua Bo sub-district is a community that has produced Khao-Mao according to conventional wisdom, for a very long time. Khao-Mao has an emerald, green color, fragrant, delicate texture, and delicious taste, however the essential nutritional facts are not provided. Consequently, this study’s goal was to evaluate nutritional values by proximate analysis. All 6 types of young flattened rice-: Laos Wan, Kor Khor 6(RD6), Ai Lueng, San Pa Tong, Yee Pun, and Hom Nang Nuan have phenolic compounds by Folin-Ciocalteu method and antioxidant properties by 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay. According to the findings, rice's primary constituents are carbohydrates, which range from 69.76 to 73.07 %, protein, which ranges from 4.79 to 6.11 %, crude fat, which ranges from 1.68 to 2.22 %, fiber, which ranges from 0.00 to 0.03 % moisture, which ranges from 17.96 to 21.31 %, and ash, which ranges from 1.13 to 1.70 %. The San Pa Tong Khao-Mao has the highest 6.11% of protein content. Ai Lueng Khao-Mao has the greatest levels of total phenolic compounds, 0.79 mg/g dry weight. The DPPH radical scavenging assay test was used to measure the antioxidant activity. Their half-maximal inhibitory concentration (IC50) value falls between 1.18 and 2.00 mg/mL. The Hom Nang Nuan Khao-Mao has the lowest 1.18 mg/mL of IC50. According to the study’s findings, this community’s Khao-Mao has good nutritional and antioxidant properties. HIGHLIGHTS Khao-Mao has high proximate composition and high energy value Khao-Mao has relatively high quantities of protein and phenolic compounds Khao-Mao is a dish with a high-level antioxidant activity GRAPHICAL ABSTRACT

Peptide nucleic acid (PNA) is a powerful biomolecule with a wide variety of important applications. In this work, the molecular structures and binding affinity of PNA with a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) that binds to both DNA and RNA were studied using molecular dynamics simulations. The simulated structures of acpcPNA-DNA and acpcPNA-RNA duplexes more closely resembled the typical structures of B-DNA and A-RNA than the corresponding duplexes of aegPNA. The calculated binding free energies are in good agreement with the experimental results that the acpcPNA-DNA duplex is more stable than the acpcPNA-RNA duplex regardless of the base sequences. The results provide further insights in the relationship between structure and stability of this unique PNA system.

Suitable conformations for peptide nucleic acid (PNA) self-hybrids with (2′R,4′R)- and (2′R,4′S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbones (namely, acpcPNA and epi-acpcPNA, respectively) were investigated based on molecular dynamics simulations. The results revealed that hybridization of the acpcPNA was observed only in the parallel direction, with a conformation close to the P-type structure. In contrast, self-hybrids of the epi-acpcPNA were formed in the antiparallel and parallel directions; the antiparallel duplex adopted the B-form conformation, and the parallel duplex was between B- and P-forms. The calculated binding energies and the experimental data indicate that the antiparallel epi-acpcPNA self-hybrid was more stable than the parallel duplex.

The binding capability of pyrrolidinyl peptide nucleic acids (PNAs) to DNA have been studied experimentally, also the high affinity and sequence specificity were reported. However, to date a detailed understanding of these properties is unclear due to a lack of crystallographic data. In this work, molecular dynamics (MD) simulations of pyrrolidinyl PNA with different stereochemistry, (2′R,4′R)- and (2′R,4′S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid (namely acpcPNA and epi-acpcPNA, respectively), binding to DNA were performed. MD simulations of three different forms (A-, B- and P-forms) were conducted to investigate the probable duplex conformation, which revealed that the MD structures were close to B-type duplex. It was found that acpcPNA and epi-acpcPNA backbones play a minor role in the hydrogen bond geometry of base pair, however, these greatly influence the interactions between PNA and DNA strands, leading to the differences in duplex stability. The calculated binding free energy revealed the higher thermodynamic stability of acpcPNA-DNA compared to epi-acpcPNA-DNA system, which is in good agreement with published experimental data. This work offers new insights into the conformational and energetic properties of pyrrolidinyl PNA-DNA duplexes at a molecular level.

This work aims to explore a new clickable carbazole-based fluorescent label, its incorporation into pyrrolidinyl peptide nucleic acid (acpcPNA), and the interactions between the labeled PNA probe and DNA by fluorescence spectrophotometry and molecular dynamics simulation. A carbazole derivative, namely 3,6-diaminocarbazole (DAC), was synthesized and incorporated into the internal and terminal positions of azide-modified acpcPNA via a sequential reductive alkylation and click reaction previously developed by our group. The DAC-modified acpcPNA can form a stable hybrid with complementary DNA with somewhat lower stability compared to unmodified acpcPNA. Most importantly, the DAC-modified acpcPNA exhibits a remarkable fluorescence increase in the presence of DNA (up to 35.5 fold with complementary DNA). Non-complementary as well as single mismatched DNA targets gave a smaller fluorescence increase (1.1 to 18.6 fold), and the discrimination could be further improved by increasing the temperature to dissociate the mismatched hybrids. Molecular dynamic simulations revealed that the DAC interacts with adjacent nucleobases in single stranded PNA, resulting in quenching of the fluorescence signal. When the PNA formed a hybrid with DNA, the DAC was pushed away from the duplex, resulting in a fluorescence increase. Thus, the DAC-labeled acpcPNA is a potential candidate as a self-reporting probe for determination of DNA sequences.

Nucleic acids or nucleic acid analogues carrying an environment sensitive fluorophore that can change optical properties in response to hybridization with complementary DNA or RNA targets are potentially useful as self-reporting hybridization probes that do not require a quencher. In this study, pyrrolidinyl peptide nucleic acids (acpcPNA) carrying a pyrene label at terminal, or internal positions were synthesized and their fluorescence properties investigated. Significant fluorescence increases, between 2.9 and 73 fold, were observed only with internally pyrene-labeled acpcPNA upon hybridization with complementary DNA under a variety of sequence contexts. Hybridization with mismatched DNA targets yielded mostly unchanged or decreased fluorescence, depending on the type and position of the mismatch base. Non-specific fluorescence increase due to the presence of a mismatch located away from the pyrene label could be eliminated by digestion with S1 nuclease, which allows unambiguous discrimination between complementary and all single mismatched DNA targets. The terminally pyrene-labeled acpcPNA showed a much smaller fluorescence change upon hybridization with both complementary and mismatched DNA targets, and the change was in the opposite direction to the internally pyrene-labeled acpcPNA. These results were rationalized by the use of molecular dynamics simulations, which suggested that the pyrene label adopts a different conformation when located at different positions of the acpcPNA probes.

The structural properties and stability of two different stereoisomers of (1S,2S)-2-aminocyclopentanecarboxylic acid (acpcPNA) binding to DNA and self hybrid DNA duplex were investigated using a molecular dynamics simulation. The thermodynamics stability was estimated and revealed that the stability of the simulated duplexes is of the order of (2′R,4′R)-acpcPNA·DNA > (2′R,4′S)-acpcPNA·DNA > DNA·DNA, which is in good agreement with experimental thermal stability. The lowest stability of DNA duplex is caused by a repulsion of two negatively charged backbones. The repulsion is decreased significantly by replacing a non-charged acpcPNA backbone, leading to a strong binding ability of acpcPNA with its complementary DNA.