Site-specific incorporation of multiple units of functional nucleotides into DNA using a step-wise approach with polymerase and its application to monitoring DNA structural changes

2019 ◽  
Vol 55 (15) ◽  
pp. 2158-2161 ◽  
Author(s):  
Binh Huy Le ◽  
Van Thang Nguyen ◽  
Young Jun Seo
Keyword(s):  
Secondary Structure ◽  
Structural Changes ◽  
New Method ◽  
Site Specific ◽  
Structure Dynamics ◽  
Hairpin Secondary Structure ◽  
Multiple Units

We have developed a new method, a step-wise approach with polymerase, for site-specific incorporation of multiple units of functional nucleotides into DNA for monitoring hairpin secondary structure dynamics.

scholarly journals Speed limit of protein folding evidenced in secondary structure dynamics

2011 ◽  
Vol 108 (40) ◽  
pp. 16622-16627 ◽  
Author(s):  
M. M. Lin ◽  
O. F. Mohammed ◽  
G. S. Jas ◽  
A. H. Zewail
Keyword(s):  
Protein Folding ◽  
Secondary Structure ◽  
Speed Limit ◽  
Structure Dynamics

scholarly journals Photoactivation Mechanism, Timing of Protein Secondary Structure Dynamics and Carotenoid Translocation in the Orange Carotenoid Protein

2018 ◽  
Vol 141 (1) ◽  
pp. 520-530 ◽  
Author(s):  
Patrick E. Konold ◽  
Ivo H. M. van Stokkum ◽  
Fernando Muzzopappa ◽  
Adjélé Wilson ◽  
Marie-Louise Groot ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Protein Secondary Structure ◽  
Structure Dynamics ◽  
Orange Carotenoid Protein

Predicting RNA Secondary Structure Using a Improved BPSO Based on Stem Combination

2013 ◽  
Vol 325-326 ◽  
pp. 1551-1554
Author(s):  
Yi Qi
Keyword(s):  
Secondary Structure ◽  
Sensitivity And Specificity ◽  
Rna Structure ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Experimental Results ◽  
New Method ◽  
Rna Structure Prediction ◽  
New Strategies

In this paper, we present an improved BPSO to predict RNA secondary structure to improve the performance with two new strategies. First one is to reduce the searching space of PSO through super stem set construction. Second is to modify the general BPSO updating process to settle stem permutation and combination problems. The experimental results show that the new method is effective for RNA structure prediction in terms of sensitivity and specificity by different sequence datasets including simple pseudoknot.

Analysis of spatial osteochondral heterogeneity in advanced knee osteoarthritis exposes influence of joint alignment

2020 ◽  
Vol 12 (562) ◽  
pp. eaba9481 ◽  
Author(s):  
Sophie Haberkamp ◽  
Tamás Oláh ◽  
Patrick Orth ◽  
Magali Cucchiarini ◽  
Henning Madry
Keyword(s):  
Weight Loss ◽  
Structural Changes ◽  
Scientific Basis ◽  
Strong Correlations ◽  
Varus Knee ◽  
Varus Malalignment ◽  
Compensatory Mechanisms ◽  
Site Specific ◽  
Knee Oa ◽  
Specific Effects

Osteoarthritis (OA) is considerably affected by joint alignment. Here, we investigate the patterns of spatial osteochondral heterogeneity in patients with advanced varus knee OA together with clinical data. We report strong correlations of osteochondral parameters within individual topographical patterns, highlighting their fundamental and location-dependent interactions in OA. We further identify site-specific effects of varus malalignment on the lesser loaded compartment and, conversely, an unresponsive overloaded compartment. Last, we trace compensatory mechanisms to the overloaded subarticular spongiosa in patients with additional high body weight. We therefore propose to consider and to determine axial alignment in clinical trials when selecting the location to assess structural changes in OA. Together, these findings broaden the scientific basis of therapeutic load redistribution and weight loss in varus knee OA.

scholarly journals New insights into solvent-induced structural changes of 13C labelled metal–organic frameworks by solid state NMR

2019 ◽  
Vol 55 (62) ◽  
pp. 9140-9143 ◽  
Author(s):  
Marcus Rauche ◽  
Sebastian Ehrling ◽  
Simon Krause ◽  
Irena Senkovska ◽  
Stefan Kaskel ◽  
...  
Keyword(s):  
Solid State Nmr ◽  
Structural Changes ◽  
Metal Organic Frameworks ◽  
Site Specific ◽  
Isotope Labelling ◽  
Specific Host ◽  
Depth Analysis ◽  
Adsorption Complexes ◽  
Metal Organic ◽  
Labelling Scheme

The proposed 13C isotope-labelling scheme enables the in-depth analysis of site-specific host–guest interactions and adsorption complexes formed in MOFs.

scholarly journals AMINOACRIDINE DYES AND THE SECONDARY STRUCTURE OF DNA IN SITU

1971 ◽  
Vol 19 (12) ◽  
pp. 761-765 ◽  
Author(s):  
MANUEL DIAZ ◽  
JOSE HIERRO ◽  
GRACIELA DEMICHELI DE DIAZ
Keyword(s):  
Secondary Structure ◽  
Acid Solution ◽  
Nitrous Acid ◽  
Deoxyribonucleic Acid ◽  
New Method ◽  
Green Fluorescence ◽  
Double Stranded Dna

A new method is proposed to study the secondary structure of deoxyribonucleic acid (DNA) in situ in fixed chromatin. It is based on acriflavine staining and on differentiation with a nitrous acid solution of the fixed cytologic preparation. The presence of green fluorescence after this treatment is regarded as indicative of double stranded DNA. Experiments are described with DNA-acriflavine mixtures in solution, DNA-agar models and cytologic preparations submitted to different pretreatments. The feasibility and limitations of the method are discussed in the light of the results reported upon.

scholarly journals A multicrystal diffraction data-collection approach for studying structural dynamics with millisecond temporal resolution

IUCrJ ◽  
2016 ◽  
Vol 3 (6) ◽  
pp. 393-401 ◽  
Author(s):  
Robin Schubert ◽  
Svetlana Kapis ◽  
Yannig Gicquel ◽  
Gleb Bourenkov ◽  
Thomas R. Schneider ◽  
...  
Keyword(s):  
Data Collection ◽  
Radiation Damage ◽  
Temporal Resolution ◽  
Diffraction Data ◽  
Structural Changes ◽  
Structural Information ◽  
Data Sets ◽  
Enzymatic Reactions ◽  
Time Resolved ◽  
Site Specific

Many biochemical processes take place on timescales ranging from femtoseconds to seconds. Accordingly, any time-resolved experiment must be matched to the speed of the structural changes of interest. Therefore, the timescale of interest defines the requirements of the X-ray source, instrumentation and data-collection strategy. In this study, a minimalistic approach forin situcrystallization is presented that requires only a few microlitres of sample solution containing a few hundred crystals. It is demonstrated that complete diffraction data sets, merged from multiple crystals, can be recorded within only a few minutes of beamtime and allow high-resolution structural information of high quality to be obtained with a temporal resolution of 40 ms. Global and site-specific radiation damage can be avoided by limiting the maximal dose per crystal to 400 kGy. Moreover, analysis of the data collected at higher doses allows the time-resolved observation of site-specific radiation damage. Therefore, our approach is well suited to observe structural changes and possibly enzymatic reactions in the low-millisecond regime.

New method of controlling structural changes in glass-crystalline materials

1964 ◽  
Vol 21 (3) ◽  
pp. 131-133 ◽  
Author(s):  
A. F. Borisov ◽  
V. I. Zadumin
Keyword(s):  
Structural Changes ◽  
New Method ◽  
Crystalline Materials
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