scholarly journals Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches

2020 ◽  
Vol 11 (31) ◽  
pp. 8273-8287 ◽  
Author(s):  
Luciana M. Oliveira ◽  
Adam S. Long ◽  
Tom Brown ◽  
Keith R. Fox ◽  
Gerald Weber
Keyword(s):  
Temperature Measurement ◽  
Melting Temperature ◽  
Molecular Interactions ◽  
Theoretical Evaluation ◽  
Dna Mismatch ◽  
Dna Mismatches ◽  
Insight Into

A comprehensive experimental and theoretical evaluation of all DNA mismatch contexts, providing an insight into the intra-molecular interactions.

scholarly journals Melting Temperature Measurement and Mesoscopic Evaluation of Single, Double and Triple DNA Mismatches

2020 ◽  
Author(s):  
Luciana M. Oliveira ◽  
Adam S. Long ◽  
Tom Brown ◽  
Keith R. Fox ◽  
Gerald Weber
Keyword(s):  
Hydrogen Bonding ◽  
Temperature Measurement ◽  
Melting Temperature ◽  
Theoretical Models ◽  
Nearest Neighbour ◽  
Base Pairs ◽  
Canonical Base ◽  
Nearest Neighbours ◽  
Dna Mismatches ◽  
Sheer Number

Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bondings and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied in varying experiments or theoretical models. Here, we report on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch combinations, including single, double and triple mismatches were covered. These were compared with 64 sequences containing all combination of canonical base pairs in the same location under the same conditions. The mesoscopic calculation, using the Peyrard-Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on-site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking. Our results confirm many of the known properties of mismatches, including the peculiar sheared stacking of tandem GA mismatches. More intriguingly, it also reveals that a number of mismatches present strong hydrogen bonding when flanked on both sites by other mismatches.

scholarly journals Melting Temperature Measurement and Mesoscopic Evaluation of Single, Double and Triple DNA Mismatches

2020 ◽  
Author(s):  
Luciana M. Oliveira ◽  
Adam S. Long ◽  
Tom Brown ◽  
Keith R. Fox ◽  
Gerald Weber
Keyword(s):  
Hydrogen Bonding ◽  
Temperature Measurement ◽  
Melting Temperature ◽  
Theoretical Models ◽  
Nearest Neighbour ◽  
Base Pairs ◽  
Canonical Base ◽  
Nearest Neighbours ◽  
Dna Mismatches ◽  
Sheer Number

Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bondings and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied in varying experiments or theoretical models. Here, we report on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch combinations, including single, double and triple mismatches were covered. These were compared with 64 sequences containing all combination of canonical base pairs in the same location under the same conditions. The mesoscopic calculation, using the Peyrard-Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on-site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking. Our results confirm many of the known properties of mismatches, including the peculiar sheared stacking of tandem GA mismatches. More intriguingly, it also reveals that a number of mismatches present strong hydrogen bonding when flanked on both sites by other mismatches.

Empirical and Theoretical Evaluation of a Tree-Shaped DNA Nanostructure with a Looped Arm (L-DNA)

2021 ◽  
Vol 13 (8) ◽  
pp. 1452-1457
Author(s):  
Jeonghun Kim ◽  
So Yeon Ahn ◽  
Soong Ho Um
Keyword(s):  
Melting Temperature ◽  
Structural Stability ◽  
Building Block ◽  
Dna Structure ◽  
Secondary Structures ◽  
Theoretical Evaluation ◽  
Single Stranded Dna ◽  
Practical Applications ◽  
Dna Nanostructure ◽  
Specific Selectivity

Several nanostructures have been created with the advent of nanotechnology. DNA has been recognized as a new building block material in addition to its genetic coding role because of its unique features (e.g., intrinsic biocompatibility, precise tenability, specific selectivity). DNA can be organized into a variety of self-assembled nanomaterials including a sphere, a ball, and even an emoticon. In particular, a tree-shaped DNA structure possessing characteristic fractural patterns is easily controlled by size and functionality and can be exploited in various fields. Here, we report an empirical and theoretical evaluation of a Y-shaped tree DNA nanostructure with a looped arm (L-DNA). The synthesized L-DNAs were analyzed for thermal and structural stability. The melting temperature (Tm) of a Y-shaped DNA (Y-DNA) as a core unit and a model DNA nanostructure comprising of central Y-DNA and looped arm were measured individually. According to the complexity (e.g., increased length of the single stranded DNA (ssDNA) used), its yield suddenly decreased with the generation of ssDNAs with distinctive secondary structures. A complicated DNA product is predicted by considering the Tm of expected secondary structures, with increased Tm with respect to variation in salt concentrations. Therefore, the new DNA nanostructure may be utilized as a platform for various practical applications.

Molecular interactions shaping the tetraspanin web

2017 ◽  
Vol 45 (3) ◽  
pp. 741-750 ◽  
Author(s):  
Sjoerd J. van Deventer ◽  
Vera-Marie E. Dunlock ◽  
Annemiek B. van Spriel
Keyword(s):  
Molecular Interactions ◽  
Intracellular Signaling ◽  
Spatial Organization ◽  
Complex Mixture ◽  
Point Of View ◽  
Intramolecular Interactions ◽  
Fundamental Understanding ◽  
High Degree ◽  
Partner Proteins ◽  
Insight Into

To facilitate the myriad of different (signaling) processes that take place at the plasma membrane, cells depend on a high degree of membrane protein organization. Important mediators of this organization are tetraspanin proteins. Tetraspanins interact laterally among themselves and with partner proteins to control the spatial organization of membrane proteins in large networks called the tetraspanin web. The molecular interactions underlying the formation of the tetraspanin web were hitherto mainly described based on their resistance to different detergents, a classification which does not necessarily correlate with functionality in the living cell. To look at these interactions from a more physiological point of view, this review discusses tetraspanin interactions based on their function in the tetraspanin web: (1) intramolecular interactions supporting tetraspanin structure, (2) tetraspanin–tetraspanin interactions supporting web formation, (3) tetraspanin–partner interactions adding functional partners to the web and (4) cytosolic tetraspanin interactions regulating intracellular signaling. The recent publication of the first full-length tetraspanin crystal structure sheds new light on both the intra- and intermolecular tetraspanin interactions that shape the tetraspanin web. Furthermore, recent molecular dynamic modeling studies indicate that the binding strength between tetraspanins and between tetraspanins and their partners is the complex sum of both promiscuous and specific interactions. A deeper insight into this complex mixture of interactions is essential to our fundamental understanding of the tetraspanin web and its dynamics which constitute a basic building block of the cell surface.

scholarly journals Biological effects of simple changes in functionality on rhodium metalloinsertors

2013 ◽  
Vol 371 (1995) ◽  
pp. 20120117 ◽  
Author(s):  
Alyson G. Weidmann ◽  
Alexis C. Komor ◽  
Jacqueline K. Barton
Keyword(s):  
Cellular Proliferation ◽  
Biological Effects ◽  
High Specificity ◽  
Selective Inhibition ◽  
Binding Affinities ◽  
Structural Modifications ◽  
Dna Mismatch ◽  
Dna Mismatches ◽  
Sensitive Structure ◽  
Function Relationship

DNA mismatch repair (MMR) is crucial to ensuring the fidelity of the genome. The inability to correct single base mismatches leads to elevated mutation rates and carcinogenesis. Using metalloinsertors–bulky metal complexes that bind with high specificity to mismatched sites in the DNA duplex–our laboratory has adopted a new chemotherapeutic strategy through the selective targeting of MMR-deficient cells, that is, those that have a propensity for cancerous transformation. Rhodium metalloinsertors display inhibitory effects selectively in cells that are deficient in the MMR machinery, consistent with this strategy. However, a highly sensitive structure–function relationship is emerging with the development of new complexes that highlights the importance of subcellular localization. We have found that small structural modifications, for example a hydroxyl versus a methyl functional group, can yield profound differences in biological function. Despite similar binding affinities and selectivities for DNA mismatches, only one metalloinsertor shows selective inhibition of cellular proliferation in MMR-deficient versus -proficient cells. Studies of whole-cell, nuclear and mitochondrial uptake reveal that this selectivity depends upon targeting DNA mismatches in the cell nucleus.

Molecular interactions of α-amino acids insight into aqueous β-cyclodextrin systems

Amino Acids ◽  
2013 ◽  
Vol 45 (4) ◽  
pp. 755-777 ◽  
Author(s):  
Deepak Ekka ◽  
Mahendra Nath Roy
Keyword(s):  
Amino Acids ◽  
Molecular Interactions ◽  
Insight Into

Insight into molecular interactions between constituents in polymer clay nanocomposites

Polymer ◽  
2006 ◽  
Vol 47 (14) ◽  
pp. 5196-5205 ◽  
Author(s):  
Debashis Sikdar ◽  
Dinesh R. Katti ◽  
Kalpana S. Katti ◽  
Rahul Bhowmik
Keyword(s):  
Molecular Interactions ◽  
Clay Nanocomposites ◽  
Insight Into
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