• Journal of the Institute of Electronics Engineers of Korea SC
• /
• v.48 no.2
• /
• pp.86-90
• /
• 2011

The effects of cations are very important in field-effect transistors (FETs) type DNA sensors detecting the intrinsic negative charge between single-stranded DNA and double-stranded DNA without labeling, because the intrinsic negative charge of DNA is neutralized by cations in electrolyte solution. We consider the Debye length, which depends on the concentration of cations in solution, to detect DNA hybridization based on the intrinsic negative charge of DNA. The Debye length is longer in buffer solution with a lower concentration of NaCl and the intrinsic negative charge of DNA is more effective on the channel surface in longer Debye length solution. The shifts in the gate voltage by DNA hybridization with complementary target DNA are 21 mV in 1 mM NaCl buffer solution, 7.2 mV in 10 mM NaCl buffer solution, and 5.1 mV in 100 mM NaCl buffer solution. The sensitivity of FETs to detect DNA hybridization based on charge detection without labeling depends on the Debye length.

• YAKHAK HOEJI
• /
• v.31 no.2
• /
• pp.116-125
• /
• 1987

It is still difficult and time consuming to obtain cDNA sequences that contain the entire nucleotide sequence of the corresponding mRNA. A rapid and high efficient cloning method to obtain full-length cDNA segments is thus developed. The cloning procedure described here consists of the construction of oligo(dT)-tailed vector primer using pWR34 plasmid, polyadenylation of mRNA-cDNA heteroduplex using terminal deoxytransferase, and replacement of MRNA strand with DNA by RNase H and DNA polymerase I. The restriction endonuclease analysis shows that the size of inserted-cDNA is in the range of 1.5~4.0 kb long suggesting that most of cloned cDNA are full-length or nearly full-length cDNA. The plasmid-DNA recombinants obtained were 4$\times$$10^5$~$10^{6}$ per $\mu\textrm{g}$ of rat liver poly (A$^+$)mRNA, which is 4 to 10 fold higher cloning efficiency in comparison to the presently used methods for full-length cDNA cloning. The results indicate that the described cloning system is much simpler, less time consuming, and very efficient cloning method to construct a cDNA library.

• The Plant Pathology Journal
• /
• v.18 no.4
• /
• pp.187-191
• /
• 2002

This paper describes the cloning and sequence analysis of the 5'-terminal region and full-length cDNA production of genomic RNA of Lily symptomless virus (LSV), a Species Of the genus Carlavirus. A sing1e DNA band about 600 bp harboring the 5'-end of genomic RNA of the virus was successfully amplified by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE), and was cloned for nucleotide sequence determination. Sequence analysis of selected RACE cDNA clones revealed that the LSV 5'non-translated region consists of 67 nucleotides long of AT rich stretch followed GC rich from the 5'-end. To produce full-length cDNA products for the viral genomic RNA, a set of LSV-specific primers could be designed based on the obtained sequence in this study and the known sequences of 3'-terminal region for the virus. Full-length cDNA copies of LSV, an 8.4 kb long, were directly amplified by the long-template RT-PCR technique from the purified viral genomic RNA samples. This full-length cDNA copies were analyzed by restriction mapping. The molecules produced in this study can be useful for the production of in vitro infectious cDNA clone, as well as, for the completion of genomic RNA sequence and genome structure for the virus.

• Journal of the Korean Society of Food Science and Nutrition
• /
• v.31 no.4
• /
• pp.594-598
• /
• 2002

The changes in DNA damage were investigated during storage after irradiation. Kiwi, orange and pear were irradiated at 0.1, 0.3, 0.5, 0.7 and 1.0 kGy and stored for 3 months at 4$^{\circ}C$. The comet assay was applied to the sample seeds alt the beginning of irradiation and at the end of storage. Seeds were isolated and crushed, and the suspended cells were embedded in an agarose layer. After lysis of the cells, they were electrophoresed for 2 min and then stained. DNA fragmentation in seeds caused by irradiation was quantified as tail length and tail moment (tail length $\times$ % DNA in tail) by comet image analyzing system. Immediately after irradiation, the differences in tail length between unirradiated and irradiated fruit seeds were significant (p<0.05) in kiwi, orange and pear seeds. With in-creasing the irradiation doses, statistically significant longer extension of the DNA from the nucleus toward anode was observed. The results represented as tail moment showed similar tendency to those of tail length, but tile latter parameter was more sensitive than the former. Similarly even 3 months after irradiation, all the irradiated fruit seeds significantly showed longer tail length than the unirradiated controls. These results indicate that the comet assay could be one of the simple methods of detecting irradiated fruit seeds. Moreover, the method could detect DNA damage even after 3 months after irradiation.

• KSII Transactions on Internet and Information Systems (TIIS)
• /
• v.15 no.8
• /
• pp.2923-2943
• /
• 2021

The double helix structure of DNA makes it diverse, stable and can store information with high density, and these characteristics are consistent with the requirements of molecular communication for transport carriers. In this paper, a specific structure of molecular communication system based on DNA length coding is proposed. Transmitter (Tx) adopts the multi-layer golden foil design to control the release of DNA molecules of different lengths accurately, and receiver (Rx) adopts an effective and sensitive design of nanopore, and the biological information can be converted to the electric signal at Rx. The effect of some key factors, e.g., the length of time slot, transmission distance, the number of releasing molecules, the priori probability, on channel capacity is demonstrated exhaustively. Moreover, we also compare the transmission capacity of DNA-based molecular communication (DNA-MC) system and concentration-based molecular communication (MC) system under the same parameter setting, and the peak value of capacity of DNA-MC system can achieve 0.08 bps, while the capacity of MC system remains 0.025 bps. The simulation results show that DNA-MC system has obvious advantages over MC system in saving molecular resources and improving transmission stability.

• Biomedical Science Letters
• /
• v.7 no.1
• /
• pp.1-5
• /
• 2001

A cDNA of coagulation Factor IX gene has been screened from the $\lambda$gt11 human fetal liver cDNA library, and used to construct a 2.8-kb full length cDNA after recombining with the N-terminal fragment from pTZ-FIX. Human genomic DNA was isolated, digested with the restriction endonucleases, TaqI, EcoRI, and HindIII, and Southern hybridization was performed using the full length factor IX cDNA as a probe. The hybridized bands generated by the restriction endonucleases were the followings: TaqI, 0.3, 1.0, 1.6, 1.8, 2.7, 3.7, and 5.3 kb bands; EcoRI, 1.8, 4.8, 4.9, 5.5, 6.8, and 12.6 kb bands; HindIII, 4.1, 4.4, 5.2, 5.8, 7.6, and 12.5 kb bands. When the Southern bands were physically mapped along the genome, about 50-kb continuous region harboring almost all of the genomic region of Factor Ⅸ gene was covered. These results suggest a possibility of using an exonal cDNA probe to diagnose abnormalities including large deletions, insertions, and rearrangements along the genome, if there is any.

• Journal of the Korean Society of Food Culture
• /
• v.19 no.3
• /
• pp.251-258
• /
• 2004

The changes in DNA damage were investigated during storage after irradiation. Potato, garlic were irradiated at 0.05, 0.07, 0.1 and 0.15 kGy and stored for 3 months. Ginger was irradiated at 0.01, 0.02, 0.03, 0.04 and 0.05 kGy and stored for 1 month. The comet assay was applied to the sample immediately after irradiation and at the end of storage. Samples were isolated, grounded and the suspended cells were embedded in an agarose layer. After lysis of the cells, they were electrophoresed for 1 min. and then stained. DNA fragmentation in seeds caused by irradiation was quantified as tail length and tail moment (tail length ${\times}%$ DNA in tail) by comet image analyzing system. Right after irradiation, the differences in tail length between unirradiated and irradiated samples were significant(p<0.05) in potato, garlic and ginger. With increasing the irradiation doses, statistically significant longer extension of the DNA from the nucleus toward anode was observed. The results represented as tail moment showed similar tendency to those of tail length. Similarly in the stored samples, even 1 or 3 months after irradiation, all the irradiated samples significantly showed longer tail length than the unirradiated controls. These results indicate that the comet assay could be one of the simple methods of detecting irradiated samples. Moreover, the method could detect DNA damage even after 1 or 3 months after irradiation.

• Journal of Life Science
• /
• v.23 no.10
• /
• pp.1260-1266
• /
• 2013

The ribosomal DNA (rDNA) clusters of Hypsizygus marmoreus 3-10 and H. marmoreus 1-1 were analyzed in this study. The small subunit (SSU) and intergenic spacer 2 (IGS 2) was partially sequenced. The internal transcribed spacer 1 (ITS 1), 5.8S, internal transcribed spacer 2 (ITS 2), large subunit (LSU), intergenic spacer 1 (IGS 1), and 5S were completely sequenced. The rDNA clusters of H. marmoreus 3-10 and H. marmoreus 1-1 were 7,049 bp in length. The sequence of SSU rDNA, which corresponded to 18S rDNA, was 1,796 bp in length, and the sequence of LSU rDNA, which corresponded to 28S rDNA, was 3,348 bp in length. The ITS region that variable region and IGS region that non-transcribed spacer was 462 bp and 1,290 bp in length. The sequence of 5.8S rDNA and 5S rDNA was 153 bp and 43 bp in length, respectively. The 17 bp of the rDNA cluster in the H. marmoreus 3-10 strain was different to that in the H. marmoreus 1-1 strain, with 2 bp in the SSU, 3 bp in the ITS, 9 bp in the LSU, and 3 bp in the IGS. The analysis of the secondary structure revealed that the ITS regions of H. marmoreus 3-10 and H. marmoreus 1-1 have five stem-loop structures. Interestingly, among these structures, one different nucleotide sequence resulted in a different secondary structure in stem-loop V.

• Bulletin of the Korean Chemical Society
• /
• v.24 no.7
• /
• pp.943-947
• /
• 2003

We have studied the migration behavior of single-stranded DNA using capillary gel electrophoresis under various conditions. It was found that optimum electric fields should be less than 150 V/cm for the good tradeoff between the separation time and the resolution. It seems that the gel matrix with the combination of different polymer average molecular weights is important to extend the maximum readable DNA bases. The total gel concentration less than 3.1% in the mixed gel system showed good separation efficiency up to 600 bases. The best result was obtained with the poy(ethylene)oxide (PEO) gel concentration of 1.2% of Mr 8,000,000 and 1.8% of Mr 600,000. We observed that the capillary length between 50 cm to 100 cm (effective length) should be employed for the optimization between the total DNA migration time and the maximum readable length. A trizma base-boric acid-ethlyenediaminetetraacetic acid (EDTA) (TBE) buffer was commonly used for DNA sequencing, but we found that 3-[tris(hydroxymethyl)methyl amino]-1-propane sulfonic acid (TAPS) buffer worked as well for the single-stranded DNA separation. Especially, TAPS buffer showed a good resolution for very short DNA bases (1 to 30 bases).

• Korean Journal of Food Science and Technology
• /
• v.31 no.4
• /
• pp.906-911
• /
• 1999

This study was to determine whether DNA 'Comet Assay' can be applied to the detection of grains irradiated with low doses of Co-60 gamma radiation. Sesame, perilla, wheat, barley and rice were exposed to different doses of 0.1, 0.3, 0.5, 0.7 and 1.0 kGy. The cells isolated from the samples were embedded in a agarose gel on a microscope slide, lysed in lysis solution, and subjected to electrophoresis. DNA and its fragments migrated in the gel produced the characteristic pattern of DNA comet, of which the tail length was measured in a microscope. All the samples irradiated at 0.3 kGy and higher were applicable to detect post-irradiation by the tail length of their comets. Irradiated samples showed comets with long tails and their tail length increased with the dose, while unirradiated samples showed no or very short tails. Especially, sesame, perilla and wheat irradiated at 0.1 kGy could be distinguished from unirradiated samples by visual inspection of the slide in a microscope. Thus, DNA 'Comet Assay' might be applied to the detection of irradiated grains as a simple, inexpensive and rapid screening test.