Nucleic base pair

Table 8. The relative energies of the lowest excited states (singlet) in the nucleic base pairs (A-T and G-C) and in the isolated bases. The results of embedding calculations with not-polarized environment are given in parentheses. Data taken from [Wesolowski, J. Am. Chem. Soc., 126, (2004) 11444].

DNA. Since polylysine binds preferentially to AT-rich DNA, hydrogen bonding in addition to salt bridge formation is likely to occur. Complex formation between polylysine or polycytosine is also reversible and may lead to rod-like structures (Haynes et al., 1970). Small cationic peptides with an aromatic amino acid, e.g., the tripeptide Lys-Tep.Lys, first add to double-stranded DNA and then force the aromatic side chain to intercalate between two nucleic base pairs. Bending of the DNA is then observed (Gabbay et al., 1973). 

The SERS spectrum of methylated DNA shows new Raman bands at 656 cm , 700 cm and 1360 cm" which correspond to characteristic vibrations of 7-MeGua residues in adsorbed methylated DNA (cf. Table 4). Furthermore, the decrease of the band at 1200 cm and the 13(K)cm" shoulder of the band centered at 1332 cm" in the SERS spectrum of native DNA upon methylation can be related to a conformational change of DNA at the location of modified nucleic base pairs 7-MeGua-cytosine. Thus, at a rather positively charged surface, the SERS spectra reveal substantial changes in the adsorption behaviour of methylated DNA. 

Munoz et al investigated the influence of divalent metal cation binding on the nucleic base pairing. A topological analysis included AIM and ELF. 

The probability of finding a nucleic acid unit in the certain conformation according to our results is never equal to the unit. It agrees with the idea that NAs are not static but fluctuating, breathing , objects [23]. For example, in RNA molecule with 10 base pairs at the room temperature about 510 base pairs do not take part in the stacking and are not connected with H -bonds [2]. 

DNA polymerase enzymes all synthesize DNA by adding deoxynucleotides to the free 3 -OH group of an RNA or DNA primer sequence. The identity of the inserted nucleotide is deterrnined by its abiHty to base-pair with the template nucleic acid. The dependence of synthesis on a primer oligonucleotide means that synthesis of DNA proceeds only in a 5%o V direction if only one primer is available, all newly synthesized DNA sequences begin at the same point. 

Interactive to learn to recognize classes of nucleic acids and their base-pair partners. 

It can be seen from the figure that the electrostatic repulsive forces between the macrocations are overwhelmed, probably by hydrophobic attractive forces between their hydrophobic side groups. It should be noted that the complimentary base-base pairing is unimportant in the present case. If this is not the case, the mixtures of APVP and TPVP should show the largest hypochromicity. This, however, is not the case. The importance of the hydrophobic interactions between nucleic acid bases has been proposed by Ts o et al.I9 from thermodynamic parameters of various nucleic acid bases or nucleosides in aqueous media. 

RUM H., Nielsen P.E., Egholm M., Berg R.H., Buchardt O., Stanley C. Single base pair mutation analysis by PNA directed PCR clamping. Nucleic Acids Res. 1993 21 5332-5336. 

The fundamental a-hehcal peptide nucleic acid (aPNA) concept is illustrated in Fig. 5.2. Our prototype aPNA module incorporated five nucleobases for Watson-Crick base pairing with a single-stranded nucleic acid target. These nucleobases... 

The amino acid sequence of our first aPNA (which we termed backbone 1 or bl) was designed based on this amphipathic hehx sequence (Fig. 5.3 B). Specifically, this aPNA backbone included hydrophobic amino acids (Ala and Aib), internal salt bridges (Glu-(aa)3-Lys-(aa)3-Glu), a macrodipole (Asp-(aa)i5-Lys), and an N-ace-tyl cap to favor a-helix formation. The C-termini of these aPNA modules end in a carboxamide function to preclude any potential intramolecular end effects. Each aPNA module incorporates five nucleobases for Watson-Crick base pairing to a target nucleic acid sequence. 

All of the hybridization procedures discussed in this section depend on the specific base-pairing properties of complementary nucleic acid strands described above. Perfect matches hybridize readily and withstand high temperatures in the hybridization and washing reac-... 

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