Development of coarse-graining DNA models for single-nucleotide resolution analysis

2010 ◽  
Vol 368 (1920) ◽  
pp. 2615-2628 ◽  
Author(s):  
Kentaro Doi ◽  
Tomoaki Haga ◽  
Hirofumi Shintaku ◽  
Satoyuki Kawano
Keyword(s):  
Dna Sequences ◽  
Persistence Length ◽  
Analytical Techniques ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Wide Range ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Recently, analytical techniques have been developed for detecting single-nucleotide polymorphisms in DNA sequences. Improvements of the sequence identification techniques has attracted much attention in several fields. However, there are many things that have not been clarified about DNA. In the present study, we have developed a coarse-graining DNA model with single-nucleotide resolution, in which potential functions for hydrogen bonds and the π -stack effect are taken into account. Using Langevin-dynamics simulations, several characteristics of the coarse-grained DNA have been clarified. The validity of the present model has been confirmed, compared with other experimental and computational results. In particular, the melting temperature and persistence length are in good agreement with the experimental results for a wide range of salt concentrations.

scholarly journals iMethyl-Deep: N6 Methyladenosine Identification of Yeast Genome with Automatic Feature Extraction Technique by Using Deep Learning Algorithm

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 529 ◽  
Author(s):  
Omid Mahmoudi ◽  
Abdul Wahab ◽  
Kil To Chong
Keyword(s):  
Learning Algorithm ◽  
Feature Representation ◽  
Yeast Genome ◽  
Single Nucleotide ◽  
Automatic Feature Extraction ◽  
Deep Learning Algorithm ◽  
Wide Range ◽  
Benchmark Datasets ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

One of the most common and well studied post-transcription modifications in RNAs is N6-methyladenosine (m6A) which has been involved with a wide range of biological processes. Over the past decades, N6-methyladenosine produced some positive consequences through the high-throughput laboratory techniques but still, these lab processes are time consuming and costly. Diverse computational methods have been proposed to identify m6A sites accurately. In this paper, we proposed a computational model named iMethyl-deep to identify m6A Saccharomyces Cerevisiae on two benchmark datasets M6A2614 and M6A6540 by using single nucleotide resolution to convert RNA sequence into a high quality feature representation. The iMethyl-deep obtained 89.19% and 87.44% of accuracy on M6A2614 and M6A6540 respectively which show that our proposed method outperforms the state-of-the-art predictors, at least 8.44%, 8.96%, 8.69% and 0.173 on M6A2614 and 15.47%, 28.52%, 25.54 and 0.5 on M6A6540 higher in terms of four metrics Sp, Sn, ACC and MCC respectively. Meanwhile, M6A6540 dataset never used to train a model.

scholarly journals Single-Nucleotide-Resolution Computing and Memory in Living Cells

2018 ◽  
Author(s):  
Fahim Farzadfard ◽  
Nava Gharaei ◽  
Yasutomi Higashikuni ◽  
Giyoung Jung ◽  
Jicong Cao ◽  
...  
Keyword(s):  
Living Cells ◽  
Single Nucleotide ◽  
Gene Circuits ◽  
Synthetic Gene Circuits ◽  
Wide Range ◽  
Artificial Learning ◽  
Nucleotide Resolution ◽  
Cellular Phenotypes ◽  
Cellular Circuits ◽  
Single Nucleotide Resolution

AbstractComputing and memory in living cells are central to encoding next-generation therapies and studying in situ biology, but existing strategies have limited encoding capacity and are challenging to scale. To overcome this bottleneck, we developed a highly scalable, robust and compact platform for encoding logic and memory operations in living bacterial and human cells. This platform, named DOMINO for DNA-based Ordered Memory and Iteration Network Operator, converts DNA in living cells into an addressable, readable, and writable computation and storage medium via a single-nucleotide resolution read-write head that enables dynamic and highly efficient DNA manipulation. We demonstrate that the order and combination of DNA writing events can be programmed by biological cues and multiple molecular recorders can be coordinated to encode a wide range of order-independent, sequential, and temporal logic and memory operations. Furthermore, we show that these operators can be used to perform both digital and analog computation, and record signaling dynamics and cellular states in a long-term, autonomous, and minimally disruptive fashion. Finally, we show that the platform can be functionalized with gene regulatory modules and interfaced with cellular circuits to continuously monitor cellular phenotypes and engineer gene circuits with artificial learning capacities. We envision that highly scalable, compact, and modular DOMINO operators will lay the foundation for building robust and sophisticated synthetic gene circuits for numerous biotechnological and biomedical applications.One Sentence SummaryA programmable read-write head with single-nucleotide-resolution for genomic DNA enables robust and scalable computing and memory operations in living cells.

scholarly journals Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus

2021 ◽  
Vol 22 (4) ◽  
pp. 1832
Author(s):  
Eugene Metakovsky ◽  
Laura Pascual ◽  
Patrizia Vaccino ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Snp Markers ◽  
Group Iv ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
B Genome

The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.

scholarly journals Chemical probing of the homopurine·homopyrimidine tract in supercoiled DNA at single-nucleotide resolution

FEBS Letters ◽  
1988 ◽  
Vol 234 (2) ◽  
pp. 295-299 ◽  
Author(s):  
M. Vojtíšková ◽  
S. Mirkin ◽  
V. Lyamichev ◽  
O. Voloshin ◽  
M. Frank-Kamenetskii ◽  
...  
Keyword(s):  
Single Nucleotide ◽  
Supercoiled Dna ◽  
Chemical Probing ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution
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