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The proline located close to the tip of the recognition loop intercalates between the base pair plane.
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EtBr is a DNA intercalator, inserting itself between the base pairs in the double helix.
Molecular docking studies confirmed that harmine intercalates between the base pairs of DNA structure but energetically prefers intercalation between GC base pairs.
The intense fluorescence of EtBr after binding with DNA is probably due to the hydrophobic environment found between the base pairs.
Fluorescence polarization and denatured DNA studies also applied strong evidences that DNR-A molecule was intercalated between the base pairs of ctDNA.
Single-stranded DNA (ss-DNA) was employed to functionalize GR-forming ss-DNA/GR nanocomposite via noncovalent π-π conjugation between the base pairs of DNA and GR.
The interactions between the nucleic acid strands in duplexes were also evaluated; these interactions between the base pairs were different because of the different "G…C A…T" ratios in the DNA molecules studied.
The basis for the high specificity of the biorecognition process is the uniqueness of complementary nature of this binding reaction between the base pairs, i.e. adenine-thymine and cytosine-guanine.
Assembling of DNA@ Mn3(PO4)2 nanoparticles onto GO nanosheets was achieved by π-π non-covalent conjugation and electrostatic interaction between the base pairs of DNA and the functionalized surface of GO nanosheets.
The combined results show that these acridone derivatives interact with DNA duplex by intercalation between the base pairs, possess higher affinity to GC than AT base pairs of the DNA and they could not interact noncovalently with the minor grooves of the DNA in solution-free gas phase.
TPT is found to be intercalated between the base pairs −1/+1, at the level of the cleavage site (Figure 1A), and in direct interaction with several protein residues [20].
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