scholarly journals Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies

2018 ◽  
Vol 122 (43) ◽  
pp. 9869-9876 ◽  
Author(s):  
David A. Nicholson ◽  
Abhigyan Sengupta ◽  
Hsuan-Lei Sung ◽  
David J. Nesbitt
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Secondary Structure ◽  
Single Molecule ◽  
Single Molecule Studies

Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA

2004 ◽  
Vol 65 (4-5) ◽  
pp. 235-245 ◽  
Author(s):  
Andrea Giro ◽  
Anna Bergia ◽  
Giampaolo Zuccheri ◽  
Hugo H.J. Bink ◽  
Cornelis W.A. Pleij ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Single Molecule ◽  
Rna Secondary Structure ◽  
Viral Rna ◽  
Single Molecule Studies

Single molecule studies of surface-induced secondary structure in a model peptide

2004 ◽  
Author(s):  
Douglas S. English ◽  
Joy A. Cunningham ◽  
Sarah C. Wehri ◽  
Amy F. Petrik ◽  
Kenji Okamoto
Keyword(s):  
Secondary Structure ◽  
Single Molecule ◽  
Model Peptide ◽  
Single Molecule Studies

scholarly journals DNA hybridisation kinetics using single-molecule fluorescence imaging

2021 ◽  
Author(s):  
Rebecca Andrews
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
Biological Processes ◽  
Single Molecule Fluorescence ◽  
Extrinsic Factors ◽  
Factors Affecting ◽  
Dna Hybridisation ◽  
Single Molecule Studies ◽  
Kinetics Of ◽  
Insight Into

Abstract Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about the process which are still unknown. Prior to the invention of single-molecule microscopy, DNA hybridisation experiments were conducted at the ensemble level, and thus it was impossible to directly observe individual hybridisation events and understand fully the kinetics of DNA hybridisation. In this mini-review, recent single-molecule fluorescence-based studies of DNA hybridisation are discussed, particularly for short nucleic acids, to gain more insight into the kinetics of DNA hybridisation. As well as looking at single-molecule studies of intrinsic and extrinsic factors affecting DNA hybridisation kinetics, the influence of the methods used to detect hybridisation of single DNAs is considered. Understanding the kinetics of DNA hybridisation not only gives insight into an important biological process but also allows for further advancements in the growing field of nucleic acid biotechnology.

Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 445-458 ◽  
Author(s):  
Nick Goldman ◽  
Jeffrey L Thorne ◽  
David T Jones
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Protein Evolution ◽  
Solvent Accessibility ◽  
Strong Association ◽  
Length Distribution ◽  
Parametric Bootstrap ◽  
Amino Acid Replacement ◽  
Physical Constraints ◽  
The Impact

Abstract Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution—both above and below the species level—will not be well understood until the physical constraints that affect protein evolution are identified and characterized.

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