scholarly journals The variations of human miRNAs and Ising like base pairing models

2018 ◽  
Author(s):  
Jyoti Prasad Banerjee ◽  
Jayanta Kumar Das ◽  
Pabitra Pal Choudhury ◽  
Sayak Mukherjee ◽  
Sk. Sarif Hassan ◽  
...  
Keyword(s):  
Ising Model ◽  
Base Pair ◽  
Nearest Neighbor ◽  
Chemical Properties ◽  
Mirna Sequence ◽  
Base Pairing ◽  
Rna Molecules ◽  
Human Mirnas ◽  
Statistical Variations ◽  
Meaningful Word

AbstractmiRNAs are small about 22-base pair long, RNA molecules are of extreme biological importance. Like other longer RNA molecules, messages in miRNAs are encoded by the permutations of only four nucleotide bases represented by A, U, C and G. However, just like words in any language, not all combination of these alphabets make a meaningful word. In fact, we find that the distributions of nucleotides bases in human miRNAs show significant deviation from randomness. First, a miRNA sequence containing four bases are mapped into a binary string with three kinds of classifications according to their chemical properties. Then, we propose a simple nearest neighbor model (Ising model) to understand the statistical variations in human miRNAs.

scholarly journals Base pairing and stacking contributions to double stranded DNA formation

2020 ◽  
Author(s):  
Martin Zacharias
Keyword(s):  
Base Pair ◽  
Nearest Neighbor ◽  
Base Pairing ◽  
Base Stacking ◽  
Dsdna Molecule ◽  
Double Stranded Dna ◽  
The Stability ◽  
Free Energy Contribution ◽  
Formed Hydrogen ◽  
Adenine Thymine

AbstractDouble-strand (ds)DNA formation and dissociation are of fundamental biological importance. The negatively DNA charge influences the dsDNA stability. However, the base pairing and the stacking between neighboring bases are responsible for the sequence dependent stability of dsDNA. The stability of a dsDNA molecule can be estimated from empirical nearest-neighbor models based on contributions assigned to base pair steps along the DNA and additional parameters due to DNA termini. In efforts to separate contributions it has been concluded that base-stacking dominates dsDNA stability whereas base-pairing contributes negligibly. Using a different model for dsDNA formation we re-analyze dsDNA stability contributions and conclude that base stacking contributes already at the level of separate ssDNAs but that pairing contributions drive the dsDNA formation. The theoretical model also predicts that stability contributions of base pair steps that contain only guanine/cytosine, mixed steps and steps with only adenine/thymine follows the order 6:5:4, respectively, as expected based on the formed hydrogen bonds. The model is fully consistent with available stacking data and nearest-neighbor dsDNA parameters. It allows to assign a narrowly distributed value for the effective free energy contribution per formed hydrogen bond during dsDNA formation of −0.72 kcal·mol-1 based entirely on experimental data.

scholarly journals The base-pairing ability of the base pair-mimic nucleosides

2007 ◽  
Vol 51 (1) ◽  
pp. 71-72
Author(s):  
S.-i. Nakano ◽  
K. Uenishi ◽  
M. Fujii ◽  
N. Sugimoto
Keyword(s):  
Base Pair ◽  
Base Pairing

scholarly journals Analysis of base-pairing probabilities of RNA molecules involved in protein–RNA interactions

2013 ◽  
Vol 29 (20) ◽  
pp. 2524-2528 ◽  
Author(s):  
Junichi Iwakiri ◽  
Tomoshi Kameda ◽  
Kiyoshi Asai ◽  
Michiaki Hamada
Keyword(s):  
Base Pairing ◽  
Rna Molecules

scholarly journals Supercoiling and looping promote DNA base accessibility and coordination among distant sites

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan M. Fogg ◽  
Allison K. Judge ◽  
Erik Stricker ◽  
Hilda L. Chan ◽  
Lynn Zechiedrich
Keyword(s):  
Mechanical Stress ◽  
Genomic Instability ◽  
Base Pair ◽  
Base Pairing ◽  
Complex Interplay ◽  
Site Specific ◽  
Torsional Strain ◽  
Dna Base ◽  
Dna Backbone ◽  
Negative Supercoiling

AbstractDNA in cells is supercoiled and constrained into loops and this supercoiling and looping influence every aspect of DNA activity. We show here that negative supercoiling transmits mechanical stress along the DNA backbone to disrupt base pairing at specific distant sites. Cooperativity among distant sites localizes certain sequences to superhelical apices. Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to relieve torsional strain. The coupling of these processes may help prevent extensive denaturation associated with genomic instability. Our results provide a model for how DNA can form short loops, which are required for many essential processes, and how cells may use DNA loops to position nicks to facilitate repair. Furthermore, our results reveal a complex interplay between site-specific disruptions to base pairing and the 3-D conformation of DNA, which influences how genomes are stored, replicated, transcribed, repaired, and many other aspects of DNA activity.

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