Structures and Energetics of Base Flipping of the Thymine Dimer Depend on DNA Sequence

2008 ◽  
Vol 112 (13) ◽  
pp. 4113-4122 ◽  
Author(s):  
Lauren L. O'Nei ◽  
Olaf Wiest
Keyword(s):  
Dna Sequence ◽  
Base Flipping ◽  
Thymine Dimer

Base Flipping of the Thymine Dimer in Duplex DNA§

2007 ◽  
Vol 111 (40) ◽  
pp. 11843-11849 ◽  
Author(s):  
Lauren L. O'Neil ◽  
Alan Grossfield ◽  
Olaf Wiest
Keyword(s):  
Duplex Dna ◽  
Base Flipping ◽  
Thymine Dimer

scholarly journals DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Sabrina Adam ◽  
Hiwot Anteneh ◽  
Maximilian Hornisch ◽  
Vincent Wagner ◽  
Jiuwei Lu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Sequence ◽  
Base Flipping ◽  
Sequence Dependent ◽  
Genome Wide ◽  
Dependent Activity

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

Phylogenetic relationships ofSalvia(Lamiaceae) in China: Evidence from DNA sequence datasets

2012 ◽  
pp. n/a-n/a
Author(s):  
Qian-Quan Li ◽  
Min-Hui Li ◽  
Qing-Jun Yuan ◽  
Zhan-Hu Cui ◽  
Lu-Qi Huang ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships

Corrected DNA Sequence of the Platelet Glycoprotein IX Gene

1997 ◽  
Vol 77 (05) ◽  
pp. 1034-1035 ◽  
Author(s):  
Tomohiro Hayashi ◽  
Keijiroh Suzuki ◽  
Akito Yahagi ◽  
Jiroh Akiba ◽  
Katsushi Tajima ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Platelet Glycoprotein

The Conceptualist Ends of Writing and the End of Conceptualism

CounterText ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 63-77
Author(s):  
Louis Armand
Keyword(s):  
Dna Sequence ◽  
Life Form ◽  
The Sun

This essay examines the convergence of conceptualist poetics with evolutionary code as a form of ‘becoming alien’. The focus is Christian Bök's The Xenotext project: an attempt at translating a ‘short verse about language and genetics’, using a chemical alphabet, into a DNA sequence implanted into the genome of a polyextremophile bacterium capable of enduring conditions in outerspace. Bök describes the project as, ‘in effect, engineering a life-form so that it becomes not only a durable archive for storing a poem, but also as an operant machine for writing a poem – one that can persist on the planet until the sun itself explodes …’. The concrete, constraint-based character of Bök's project evokes a mode of writing between posthumanist aesthetics and a positivist grammatology by turns deconstructive and itself requiring of deconstruction.

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size. </p>

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