With the increase in the number of large, 3D, high-resolution nucleic acid structures, particularly of the 30S and 50S ribosomal subunits and the intact bacterial ribosome, advancements in the visualization of nucleic acid structural features are essential. Large molecular structures are complicated and detailed, and one goal of visualization software is to allow the user to simplify the displa...

This paper describes and discusses nucleic acid conformations, the energy contributions that stabilize them, and the ways the stable conformations are formed. Preferred conformations of nucleotides and of double, triple and super helices in nucleic acids are described briefly. Next the enthalpy and entropy of nucleic acid order/disorder transitions are reviewed. It is concluded that (a) the dou...

The nuclei of mammalian liver cells have been shown to contain, in addition to desoxypentose nucleic acid (DNA), a pentose nucleic acid (PNA) which is functionally different from the PNA of the cytoplasm (1). In the investigations to be described here the proport,ions of purine and pyrimidine in these two types of PNA in calf liver, kidney, thymus, and heart have been found to be strikingly dif...

Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 Å). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150–200 atoms with enough large basis sets (for example,...

introduction: p. aeruginosa is an important multi-drug resistant (mdr) opportunistic pathogen in hospital-acquired infections. several methods based on dna analysis have been used for investigating genetic diversity of p. aeruginosa isolates. among them, rep‑pcr typing has been introduced as a rapid, low cost method with high discriminatory power. the aims of this study were to investigate geno...

conclusions nucleic acid amplification tests (naats) are very appropriate in detection of infected individuals. detection techniques such as naats are independent of bacterial viability, and have a potential to limit false negative samples, therefore, in our country, the application of different laboratory diagnosis methods including naats with culture as gold standard for determination antimic...

Here, we propose an efficient strategy for enzyme- and hairpin-free nucleic acid detection called an entropy beacon (abbreviated as Ebeacon). Different from previously reported DNA hybridization/displacement-based strategies, Ebeacon is driven forward by increases in the entropy of the system, instead of free energy released from new base-pair formation. Ebeacon shows high sensitivity, with a d...

Nucleic acid higher order structure is of intense interest in antisense and antigene strategies toward novel chemotherapeutic agents. Understanding how structural characteristics affect solution-phase properties is essential for a rational approach to nucleic acid-targeted drug design. The most dominant nucleic acid secondary structure is the hairpin, formed by intrastrand hydrogen bonding betw...

Retrovirus particles contain a small, basic protein, the nucleocapsid (NC) protein, that possesses 'nucleic acid chaperone' activity--that is, the NC protein can catalyze the rearrangement of a nucleic acid molecule into the conformation that has the maximal number of base pairs. The molecular mechanism that underlies this effect is not understood. Because the chaperone activity is apparently c...

We measured the helical repeats of a non-natural nucleic acid, locked nucleic acid (LNA), by incorporating LNA strands into the outer arms of a DNA double crossover (DX) molecule; atomic force microscopy (AFM) imaging of the two-dimensional (2D) arrays self-assembled from these DX molecules allows us to derive the helical repeat of the LNA/DNA hetero-duplex to be 13.2 +/- 0.9 base pairs per turn.