(2) DNA has the thymine base, while RNA has the uridine instead of thymine. The thymine base-pairs with adenine only. The uridine can also pair with guanine in some cases, beside the normal U-A pairing. (3) DNA is commonly present as a double-stranded helix, while RNA is single stra...
torsional angles in order to accommodate the aromatic compound, causing separation of the base pairs with a lengthening of the double helix by approximately 3.4 Å and a decrease of the helical twist, unwinding the DNA in the vicinity of the binding site to less than 36° base pair [9]....
dynamics of the DNA double helixIn this paper, we consider a mathematical model that draws an analogy between a DNA molecule and a mechanical system consisting of two chains of interconnected pendulums. This model is designed to explore the dynamics of the system determined by rotational movements...
DNA ligase is an enzyme that forms a covalent phosphodiester bond between a 3′ OH and 5′ PO4 at the ends of two polynucleotide chains (frequently at a nick in one strand of a double helix). From: DNA Structure and Function, 1994 ...
The two complementary strands with hydrogen bonds between each nucleotide form a secondary structure, the double helix (Figure 2). Figure 1. Nucleotide structure (A) and binding pattern between nucleotides (B). Figure 2. Strands of nucleotides form hydrogen bonds to create a double helix. DNA...
A single base-pair opening at site 2 may increase the flexibility of the DNA at the point where the helix is disrupted, and this increased flexibility may be enough to localize site 2 to an apex. The resulting sharp bending induced at site 1 opposite may require more extensive denaturation ...
Altogether, these results anticipate that a DNA duplex longer than 10 bp will simultaneously bind two sets of B-helix matching residues on two PCNA subunits in a dynamic way. This prediction is supported by our 250 ns MD simulation of a complex of PCNA bound to a 30 bp dsDNA (Supp...
Under appropriate conditions single strands will pair up and twist around each other, forming the famous double helix structure. This pairing occurs because of a mutual attraction, call hydrogen bonding, that exists between As and Ts, and between Gs and Cs. Hence A/T and G/C are called ...
Structural restraints induced by the quadruplex might interfere with base extrusion and therefore glycosylase excision [28]. Monofunctional glycosylases recognize a damaged or modified base, generally in a duplex, and extrude that damaged base from the helix into a binding pocket. Short loops like tho...
The orange object of the helix is a DNA chain, while the green object is the protein sequence (containing helix, fold and loop structure). Blue regions and red regions are the true prediction and false prediction, respectively. In addition, the results of two methods (our method and DP-...