Rational design of dna hydrogels based on molecular dynamics of polymers

Y Li, R Chen, B Zhou, Y Dong, D Liu - Advanced Materials, 2024 - Wiley Online Library
In recent years, DNA has emerged as a fascinating building material to engineer hydrogel
due to its excellent programmability, which has gained considerable attention in biomedical …

Thermal denaturation of DNA molecules: a comparison of theory with experiment

RM Wartell, AS Benight - Physics reports, 1985 - Elsevier
Experimental and theoretical results on the helix-coil transition of DNA are reviewed. The
theoretical model of the transition is described, and the influence of heterogeneous base …

Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies

TC Lorenz - JoVE (Journal of Visualized Experiments), 2012 - jove.com
In the biological sciences there have been technological advances that catapult the
discipline into golden ages of discovery. For example, the field of microbiology was …

Mfold web server for nucleic acid folding and hybridization prediction

M Zuker - Nucleic acids research, 2003 - academic.oup.com
The abbreviated name,'mfold web server', describes a number of closely related software
applications available on the World Wide Web (WWW) for the prediction of the secondary …

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

J SantaLucia Jr - Proceedings of the National Academy of …, 1998 - National Acad Sciences
A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN)
thermodynamics is presented. DNA NN ΔG° 37 parameters from seven laboratories are …

[HTML][HTML] Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

DH Mathews, J Sabina, M Zuker, DH Turner - Journal of molecular biology, 1999 - Elsevier
An improved dynamic programming algorithm is reported for RNA secondary structure
prediction by free energy minimization. Thermodynamic parameters for the stabilities of …

PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules

M Egholm, O Buchardt, L Christensen, C Behrens… - Nature, 1993 - nature.com
DNA ANALOGUES are currently being intensely investigated owing to their potential as
gene-targeted drugs1–3. Furthermore, their properties and interaction with DNA and RNA …

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

JS McCaskill - Biopolymers: Original Research on …, 1990 - Wiley Online Library
A novel application of dynamic programming to the folding problem for RNA enables one to
calculate the full equilibrium partition function for secondary structure and the probabilities of …

Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson−Crick Base Pairs

T Xia, J SantaLucia Jr, ME Burkard, R Kierzek… - Biochemistry, 1998 - ACS Publications
Improved thermodynamic parameters for prediction of RNA duplex formation are derived
from optical melting studies of 90 oligoribonucleotide duplexes containing only Watson …

Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene

W Fiers, R Contreras, F Duerinck, G Haegeman… - Nature, 1976 - nature.com
Abstract Bacteriophage MS2 RNA is 3,569 nucleotides long. The nucleotide sequence has
been established for the third and last gene, which codes for the replicase protein. A …