• Childhood Kidney Diseases
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• 제12권1호
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• pp.11-22
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• 2008

Telomeres consist of tandem guanine-thymine(G-T) repeats in most eukaryotic chromosomes. Human telomeres are predominantly linear, double stranded DNA as they ended in 30-200 nucleotides(bases,b) 3'-overhangs. In DNA replication, removal of the terminal RNA primer from the lagging strand results in a 3'-overhang of uncopied DNA. This is because of bidirectional DNA replication and specificity of unidirectional DNA polymerase. After the replication, parental and daughter DNA strands have unequal lengths due to a combination of the end-replication problem and end-processing events. The gradual chromosome shortening is observed in most somatic cells and eventually leads to cellular senescence. Telomere shortening could be a molecular clock that signals the replicative senescence. The shortening of telomeric ends of human chromosomes, leading to sudden growth arrest, triggers DNA instability as biological switches. In addition, telomere dysfunction may cause chronic allograft nephropathy or kidney cancers. The renal cell carcinoma(RCC) in women may be less aggressive and have less genomic instability than in man. Younger patients with telomere dysfunction are at a higher risk for RCC than older patients. Thus, telomeres maintain the integrity of the genome and are involved in cellular aging and cancer. By studying the telomeric DNA, we may characterize the genetic determinants in diseases and discover the tools in molecular medicine.

• International Journal of Computer Science & Network Security
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• 제21권8호
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• pp.196-202
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• 2021

DNA sequencing provides fundamental data in genomics, bioinformatics, biology and many other research areas. With the emergent evolution in DNA sequencing technology, a massive amount of genomic data is produced every day, mainly DNA sequences, craving for more storage and bandwidth. Unfortunately, managing, analyzing and specifically storing these large amounts of data become a major scientific challenge for bioinformatics. Those large volumes of data also require a fast transmission, effective storage, superior functionality and provision of quick access to any record. Data storage costs have a considerable proportion of total cost in the formation and analysis of DNA sequences. In particular, there is a need of highly control of disk storage capacity of DNA sequences but the standard compression techniques unsuccessful to compress these sequences. Several specialized techniques were introduced for this purpose. Therefore, to overcome all these above challenges, lossless compression techniques have become necessary. In this paper, it is described a new DNA compression mechanism of pattern matching extended Compression algorithm that read the input sequence as segments and find the matching pattern and store it in a permanent or temporary table based on number of bases. The remaining unmatched sequence is been converted into the binary form and then it is been grouped into binary bits i.e. of seven bits and gain these bits are been converted into an ASCII form. Finally, the proposed algorithm dynamically calculates the compression ratio. Thus the results show that pattern matching extended Compression algorithm outperforms cutting-edge compressors and proves its efficiency in terms of compression ratio regardless of the file size of the data.

• 한국정보과학회논문지:시스템및이론
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• 제32권11_12호
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• pp.578-586
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• 2005

본 논문에서 다루는 문제는 품질 정보를 가지는 서열을 배치(alignment)하는 알고리즘이다. 시퀀싱(sequencing) 작업의 일부인 염기 결정 프로그램(base-calling program)에 의해서 생성되는 DNA 서열은 각 염기가 어느 정도 신뢰할 수 있는 가를 나타내는 품질 정보를 가진다. 그러나 지금까지 개발된 서열 배치 알고리즘들은 이러한 품질 정보를 고려하지 않았다. 본 논문에서는 품질 정보를 가지는 두 서열의 배치를 평가하는 기준을 제시한다. 이 평가 기준에 의한 최적의 서열 배치는 동적 프로그래밍(dynamic programming) 기법에 의해서 찾을 수 있다.

• Bulletin of the Korean Chemical Society
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• 제25권8호
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• pp.1211-1216
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• 2004

The interaction of the antitumour agent doxorubicin with calf thymus DNA is investigated in an aqueous solution at a pH level of 6-7 with molar ratios of 1/10. A UV-resonance Raman spectroscopy and surface enhanced Raman spectroscopy are used to determine the doxorubicin binding sites and the structural variations of doxorubicin-DNA complexes in an aqueous solution. Doxorubicin intercalates with adenine and guanine via a hydrogen bond formation between the N7 positions of purine bases and the hydroxyl group of doxorubicin.

• 약학회지
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• 제54권1호
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• pp.62-66
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• 2010

Benzopyrene is known to be one of the most powerful carcinogens which can build intercalated motif between base pairs in damaged DNA. The dimension of benzopyrene itself is much bigger than any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular mechanics simulation using AMBER program package to go into the conformational characteristics. The condition of the insertion process of the benzopyrene motif from minor groove of the starting structure between the base pairs in the internal area of double helix was investigated using the molecular dynamics simulation at elevated temperature.

• Bulletin of the Korean Chemical Society
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• 제31권12호
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• pp.3658-3662
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• 2010

A new bis-Ru(II) complex, in which two [Ru(1,10-phenanthroline)$_2$dipyrido[3,2-a:2',3'-c]phenazine]$^{2+}$ were tethered by a 1,3-bis(4-pyridyl)propane linker, was synthesized and its binding mode and stoichiometry to DNA was investigated by optical spectroscopy including linear dichroism (LD) and fluorescence intensity measurement. The magnitude of the negatively reduced LD signal of the bis-Ru(II) complex in the dipyrido[3,2-a:2',3'-c]phenazine (DPPZ) ligand absorption region appeared to be similar compared to that in the DNA absorption region, which is considered to be a diagnostic for DPPZ ligand intercalation. The binding stoichiometry measured from its LD magnitude and enhanced fluorescence intensity corresponds to one ligand per three DNA bases, effectively violating the nearest neighbouring site exclusion model for classical DNA intercalation. This observation is in contrast with monomer analogue [Ru(1,10-phenanthroline)$_2$dipyrido[3,2-a:2',3'-c]phenazine]$^{2+}$, which is saturated at the DPPZ ligand to DNA base ratio of 0.25, or one DPPZ ligand per four nucleobases.

• 전자공학회논문지
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• 제51권10호
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• pp.118-127
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• 2014

DNA 데이터 저장(Data storage)은 DNA의 염기 서열에 대용량의 디지털 데이터를 저장하는 방법으로, 차세대 정보 저장 매개물로 인식되고 있다. 본 논문에서는 DNA 스테가노그라픽 기반으로 비부호 DNA 서열(Noncoding DNA sequence)에 정보를 저장하는 방법을 제안한다. 제안한 방법은 암호화된 데이터들을 정수 변화표에 의하여 데이터 염기 서열로 변환한 후, 시드 정보, 및 섹터 길이로 구성된 은닉 키에 의하여 비부호 염기 서열에 은닉한다. 따라서 단백질의 유전 기능이 유지되고, 원 DNA 서열없이 정보가 검출되며, 변이에 의하여 발생되는 오류가 검출된다. 기존 방법과의 비교 실험을 통하여 제안한 방법이 높은 bpn를 가지는 저장 효율을 가지며, 패리티 염기에 의하여 은닉된 정보의 오류 위치를 검출할 수 있음을 확인하였다.

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권3호
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• pp.205-211
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• 2005

Water-soluble polyethyleneimine (PE) derivatives containing nucleic acid bases and hydrophilic amino acids such as homoserine (Hse) and serine were prepared by the activated ester method as nucleic acid models. From spectroscopic measurements, the polymers were found to interact with DNA accompanied by an induction of conformational change. Hypochromicity in UV spectra indicated that a stable polymer complex was formed between poly (A) with PEI­Hse-Ura by complementary hydrogen bonding with equimolar nucleic base units (adenine:uracil=1:1). The induced conformation of DNA by the interaction with the polymer containing uracil and homoserine (PEI-Hse-Ura) was concluded to be a super triple helical structure. The formation of the polymer complex, DNA: PEI-Hse-Ura, was found to be affected by the presence of metal ions such as $Ca^{2+}\;and\;Cu^{2+}$.

• Journal of Radiation Protection and Research
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• 제45권1호
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• pp.11-15
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• 2020

Background: There have been various studies to investigate the mechanisms of DNA damage from low-energy electrons. To understand the mechanism of these strand breaks, it is necessary to investigate the dissociation mechanism of the DNA constituents, that is, bases, sugars, and phosphates. Materials and Methods: We studied the dissociation of thymine base upon interaction with low-energy electrons. For this experiment, thymine powder was pressed onto the indium base and irradiated by 5 eV electrons. Results and Discussion: Non-irradiated and irradiated thymine samples were compared and analyzed using the X-ray photoelectron spectroscopic technique to analyze the dissociation patterns of the molecular bonds after low-energy electron irradiation of thymine. Conclusion: With 5 eV electron irradiation, C-C and N-C = O bonds are the primary dissociations that occur in thymine molecules.

• Animal cells and systems
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• 제12권3호
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• pp.117-125
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• 2008

One of the interesting trends in genome research is the study about epigenetic modification above single gene level. Epigenetics refers study about heritable change in the genome, which accompany modification in DNA or Chromatin besides DNA sequence alteration. We used to have the idea that the coding potential of the genome lies within the arrangement of the four bases A, T, G, C; However, additional information that affects phenotype is stored in the distribution of the modified base 5-methylcytosine. This form of information storage is flexible enough to be adapted for different somatic cell types, yet is stable enough to be retained during mitosis and/or meiosis. Epigenetic modification is a modification of the genome, as opposed to being part of the genome, so is known as "epigenetics"(Greek for "upon" genetics). This modification could be methylation on Cytosine base or post translational modification on histone protein(methylation, acetylation, phosphorylation, Sumoylation)($Dimitrijevi\hat{E}$ et al 2005). In this review, we would like to focus on the relationship of DNA methylation and cancer.