Base-pairing, nucleic acids Watson-Crick

One of the most prominent hydrogen-bonded systems is DNA. Despite numerous experimental and theoretical investigations on vibrational spectra of nucleic acid bases [7-13], information on inter- and intramolecular interactions in base pairs and DNA oligomers is still limited [14-25]. A recent example is the work on single adenine-uracil (AU) base pairs in the Watson-Crick geometry in solution, which showed an enhancement of vibrational energy... 

Figure 5-6 Outlines of the purine and pyrimidine bases of nucleic acids showing van der Waals contact surfaces and some of the possible directions in which hydrogen bonds may be formed. Large arrows indicate the hydrogen bonds present in the Watson-Crick base pairs. Smaller arrows indicate other hydrogen bonding possibilities. The directions of the green arrows are from a suitable hydrogen atom in the base toward an electron pair that serves as a hydrogen acceptor. This direction is opposite to that in the first edition of this book to reflect current usage.

Although the base triplets are of only minor importance in double-stranded nucleic acids, they have a structural role in determining and stabilizing the tertiary structure of transfer RNA, as discussed in Chapter 20. Base quadruplets where two Watson-Crick base pairs are associated as shown in Fig. 16.17 have been invoked to play a role in DNA-DNA aggregation and DNA recombination, but there is no direct evidence for their occurrence. 

The bases in nucleic acids can interact via hydrogen bonds. The standard Watson-Crick base pairs are G-C, A T (in DNA), and A U (in RNA). Base pairing stabilizes the native three-dimensional structures of DNA and RNA. 

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. 

The formation of three-stranded nucleic acid complexes was first demonstrated over five decades ago [56] but the possible biological role of an extended triplex was expanded by the discovery of the H-DNA structure in natural DNA samples [57-59]. H-DNA is an intermolecular triplex that is generally of the pyrimidine-purine x pyrimidine type ( dot -Watson-Crick pairing and cross Hoogsteen base paring) and can be formed at mirror repeat sequences in supercoiled plasmids [59]. 

Santamaria, R., Charro, E., Zacarias, A., Castro, M., 1999, Vibrational Spectra of Nucleic Acid Bases and Their Watson-Crick Pair Complexes , J. Comput. Chem., 20, 511. 

In molecular biology, a set of two hydrogen-bonded nucleotides on opposite complementary nucleic acid strands is called a base pair. In the classical Watson-Crick base pairing in DNA, adenine (A) always forms a base pair with thymine (T) and guanine (G) always forms a base pair with cytosine (C). In RNA, thymine is replaced by uracil (U). 

The antisense approach is use of nucleic acids to reduce the expression of a specific target gene. As shown in Figure 58.2, a small piece of DNA, an oligodeoxynu-cleotide that is in the reverse orientation (antisense) to a portion of a target messenger RNA (mRNA) species, is introduced into a cell and a DNA-RNA duplex is formed by complementary Watson-Crick base pairing. Cessation of protein synthesis then may result from the rapid... 

Scheurer and Briischweiler71 calculated 2hJ(N,N) couplings in three nucleic acid base pairs, namely, Watson-Crick uracil-adenine (U A) [4a] and cytosine-guanine (C-G) base pairs [4b] and in the Hoogsteen adenine thymine (A-T) base pair [7]. 

---