Enhancements and modifications of primer design program Primer3

T Koressaar, M Remm - Bioinformatics, 2007 - academic.oup.com
The determination of annealing temperature is a critical step in PCR design. This parameter
is typically derived from the melting temperature of the PCR primers, so for successful PCR …

A coarse grain model for DNA

TA Knotts, N Rathore, DC Schwartz… - The Journal of chemical …, 2007 - pubs.aip.org
Over the past two decades, significant experimental advances have increased our ability to
control and manipulate individual DNA molecules. This capability has permitted …

Nucleic acid hydration: a volumetric perspective

TV Chalikian, RB Macgregor Jr - Physics of life reviews, 2007 - Elsevier
Hydration represents a major force governing the conformational preferences and drug
binding properties of nucleic acids. Volumetric measurements have proven useful in …

Specific binding of different vesicle populations by the hybridization of membrane-anchored DNA

PA Beales, TK Vanderlick - The Journal of Physical Chemistry A, 2007 - ACS Publications
We demonstrate a method of heterogeneous vesicle binding using membrane-anchored,
single-stranded DNA that can be used over several orders of magnitude in vesicle size, as …

[HTML][HTML] RNA helix stability in mixed Na+/Mg2+ solution

ZJ Tan, SJ Chen - Biophysical journal, 2007 - cell.com
A recently developed tightly bound ion model can account for the correlation and fluctuation
(ie, different binding modes) of bound ions. However, the model cannot treat mixed ion …

Measurement of the effect of monovalent cations on RNA hairpin stability

J Vieregg, W Cheng, C Bustamante… - Journal of the American …, 2007 - ACS Publications
Using optical tweezers, we have measured the effect of monovalent cation concentration
and species on the folding free energy of five large (49− 124 nt) RNA hairpins, including HIV …

Unlabeled oligonucleotides as internal temperature controls for genotyping by amplicon melting

MT Seipp, JD Durtschi, MA Liew, J Williams… - The Journal of Molecular …, 2007 - Elsevier
Amplicon melting is a closed-tube method for genotyping that does not require probes, real-
time analysis, or allele-specific polymerase chain reaction. However, correct differentiation …

Optimal primer design using the novel primer design program: MSPprimer provides accurate methylation analysis of the ATM promoter

JC Brandes, H Carraway, JG Herman - Oncogene, 2007 - nature.com
Methylation-specific polymerase chain reaction (PCR)(MSP) is frequently used to study
gene silencing by promoter hypermethylation. However, non-specific primer design can lead …

PEMC-based method of measuring DNA hybridization at femtomolar concentration directly in human serum and in the presence of copious noncomplementary …

K Rijal, R Mutharasan - Analytical chemistry, 2007 - ACS Publications
Piezoelectric-excited, millimeter-sized cantilever (PEMC) sensors having high-mode
resonance near 1 MHz are shown to exhibit mass change sensitivity of 1− 300 ag/Hz. Gold …

Relationship between the structure and the DNA binding properties of diazoniapolycyclic duplex-and triplex-DNA binders: efficiency, selectivity, and binding mode

S Basili, A Bergen, F Dall'Acqua, A Faccio… - Biochemistry, 2007 - ACS Publications
The association of dicationic polycyclic ligands, namely, four diazoniapentaphene
derivatives, three diazoniaanthra [1, 2-a] anthracenes, diazoniahexaphene, and a partly …