Hydrogen bonds deoxyribonucleotide

DNA is a linear polymer of covalently joined deoxyribonucleotides, of four types deoxyadenylate (A), deoxyguanylate (G), deoxycytidy-late (C), and deoxythymidylate (T). Each nucleotide, with its unique three-dimensional structure, can associate very specifically but non-covalently with one other nucleotide in the complementary chain A always associates with T, and G with C. Thus, in the double-stranded DNA molecule, the entire sequence of nucleotides in one strand is complementary to the sequence in the other. The two strands, held together by hydrogen bonds (represented here by vertical blue lines) between each pair of complementary nucleotides, twist about each other to form the DNA double helix. In DNA replication, the two strands separate and two new strands are synthesized, each with a sequence complementary to one of the original strands. The result is two double-helical molecules, each identical to the original DNA. 

O.V. Shishkin et al., Intramolecular Hydrogen Bonds in Canonical 2 -Deoxyribonucleotides An Atoms in Molecules Study. J. Phys. Chem. B 110, 4413-4422 (2006)... 

Shishkin OV, Palamarchuk GV, Gorb L, Leszczynski J (2006) Intramolecular hydrogen bonds in canonical 2 -deoxyribonucleotides An atoms in molecules study. J Phys Chem B 110 4413 -422... 

Fig. 10.12 The left-hand diagram shows two units in one strand of DNA DNA is composed of condensed deoxyribonucleotides and the four possible nucleobases are adenine (A), guanine (G), eytosine (C) and thymine (T). The right-hand diagrams illustrate how complementary base pairs in adjacent strands in DNA internet through hydrogen bonding. (See also Figure 10.15.)...

For the former, the ribosomal pathway, the place to start, is with the genetic code and the carrier of the code, DNA. For the most general case, and as will be seen subsequently (Chapter 14), DNA is composed of four deoxyribonucleotides (i.e., monophosphate ester derivatives of deoxynucleosides) (Figure 12.11) held in chains (Figure 12.12) by the formation of phosphate diesters, linearly from one deoxyribose (5 ) to the next (3 ). The chains are paired, in the classical helical structure, by hydrogen bonding between the purine and pyrimidine bases (A-T and C-G) on opposite chains (Figure 12.12). ... 

Abstract In this chapter we analyze and systematize the data related to intramolecular hydrogen bonds and their impact on molecular geometry of nucleotides. The application of various non-empirical methods of quantum chemistry to determination of conformational characteristics of anions of the canonical 2 -deoxyribonucleotides and their methyl esters, as well as their energetics, is discussed. We revealed an existence of novel intramolecular interactions of the canonical 2 -deoxyribonucleotide anions. They are caused by incorporation of 2 -deoxyribonucleotide anions into DNA as well as by the impact of the nucleobases on the conformational features of the nucleotides and intramolecular interactions of these molecules. The efficient strategy of the evaluation of proton affinity for the different types of nucleotides is described. 

Typically, the experimental studies of DNTs were earned out in the condensed states where their coirformations are significantly affected by intermolecular interactions (hydrogen bonds, interactions with counter ions). This makes uncertain what exactly have been studied and taken into account intramolecular properties of DNTs or the influence of the environment on molecular stracture of DNTs. Therefore, experimental data may not reflect the intrinsic conformational properties of DNTs. Such information may be obtained using gas phase experiments. However, this information is not available for 2 -deoxyribonucleotides. Therefore, in this case a missing data eould be obtained finm investigation of the intrinsic conformational characteristics of DNTs using computational methods. 

Table 5.13 B3LYP/aug-cc-pvdz intramolecular interaction in anti-conformers of methyl ethers of 2 -deoxyribonucleotides in Z-DNA like conformations. True hydrogen bonds are underlined...

Regeneration of reduced enzyme In order for ribonucleotide reductase to continue to produce deoxyribonucleotides, the disulfide bond created during the production of the 2 -deoxy carbon must be reduced. The source of the reducing equivalents is thioredoxin—a peptide coenzyme of ribonucleotide reductase. Thioredoxin contains two cysteine residues separated by two amino acids in the peptide chain. The two sulfhydryl groups of thioredoxin donate their hydrogen atoms to ribonucleotide reductase, in the process forming a disulfide bond (see p. 19). 

Figure 25.11 Ribonucleotide reductase mechanism. (1) An electron is transferred from a cysteine residue on R1 to a tyrosine radical on R2. generating a highly reactive cysteine thiyl radical. (2) This radical abstracts a hydrogen atom from C-3 of the ribose unil. (3) The radica at C-3 releases OH from the C-2 carbon atom. Combined with a proton from a second cysteine residue, the OH is eliminated as water. (4) A hydride ion is transferred from a third cysteine residue with the concomitant formation of a disulfide bond. (5) The C-3 radical recaptures the originally abstracted hydrogen atom. (6) An electron is transferred from R2 to reduce the thiyl radical, which also accepts a proton. The deoxyribonucleotide is free to leave Rl. The disulfide formed in the active site must be reduced to begin another cycle.

---