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Nucleic Acids Structure Minitutorial

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Molecular Modeling and Simulation: An Interdisciplinary Guide

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Abstract

With the master molecule of heredity, deoxyribonucleic acid (or DNA), so frequently mentioned in the media — in connections ranging from polymerase chain reaction (PCR) applications (e.g., criminology, medical diagnoses) to cloning and art [1112] — it is difficult to imagine today that it was only a few decades ago when Watson and Crick reported their description of the DNAdouble helix [1354–1356]! Based on analysis of DNA fiber diffraction patterns and Chargaff’s rules, they described a spiral image of an orderly helix — two intertwined polynucleotide chains, with a sugar/phosphate backbone on the exterior and pairs of hydrogen-bondednitrogenous bases in the center. See [622] for a historical perspective of this discovery, including the contribution of all key players (a capsule of which is given in Chapter 1), and anniversary issues of DNA, for example issued in 2003 in many journals (e.g., Nature Vol. 421 and Science Vol. 300) at the occasion of DNA’s golden anniversary.

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Notes

  1. 1.

    In transcription, an RNA polymerase glides along onestrand of the DNA double helix and builds an RNA complement by coupling ribonucleotides through dehydration synthesis. The faithful replicate of one DNA strand then functions as the messenger RNA.

  2. 2.

    In translation, the genetic code of the messenger RNA is read by transferRNA molecules on cellular structures called ribosomes. Every transfer RNA molecule carries a specific sequence of three nucleotides on one end of an L-shaped structure and the corresponding amino acid on the other. The transfer RNA’s main task is to deposit its amino acids on the ribosomes in proper sequence. In this process of matching each messenger-RNA codon with the complementary transfer RNA molecule, the polypeptide chain is assembled. As the amino acids link to one another on the ribosomes, polypeptide folding is thought to begin.

  3. 3.

    For example, N6-methyl-dA is a modified adenine base with the N6H2 (attachment to the ring carbon C6) moiety replaced by N6HCH3; 5-methyl-dC is a modified cytosine where the C5H becomes C5CH3.

  4. 4.

    Two classic tautomerization reactions are keto/enol and amino/imino; the keto and amino forms are typically favored and are shown in Figure 5.2. Keto/enol tautomerization involves alteration of the carbonyl group (–C = O) to a hydroxyl group ( = C–O–H), shifting the double bond from the carbonyl group to the nitrogen-carbon bond in the ring (e.g., C6 = O of G becomes C6–OH, accompanied by the change of H–N1–C6 to N1 = C6). Similarly, an amino/imino tautomerization involves a change in an amino nitrogen –NH2 to an imino form, = NH (e.g., C6–NH2 of A becomes C6 = NH, accompanied by the change of N1 = C6 to H–N1–C6).

  5. 5.

    An ester is an –OR group where R represents an organic chemical group.

  6. 6.

    An adiabatic map is a simple way to examine molecular motionby characteristic low-energy paths along a prescribed reaction coordinate (i.e., variations in specific conformational variables). For each combination of these conformational coordinates, the entire potential energy of the system is minimized to approximate behavior for the motion under study. Though simple in principle, specification of the reaction coordinate is difficult in general, and the neglect of other degrees of freedom in the process is clearly an approximation whose validity depends on the motion in question.

  7. 7.

    Namely, each nucleoside is enveloped in a water sphere of radius 11 Å, and the nonbonded interactions are truncated at 12 Å using a 2 Å buffer region, a potential shift function for the electrostatic terms and a potential switch function for the van der Waals terms; see 10Nonbonded Computationschapter.10.566 for details of such procedures.

  8. 8.

    In a right-handed form, a right hand held with the thumb pointingupward in the direction of the helix axis will wrap right (counterclockwise) and around the axis to follow the chain; a left hand with an upward-pointing thumb will wrap to the left (clockwise) to follow the chain direction of a left-handed helix.

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Schlick, T. (2010). Nucleic Acids Structure Minitutorial. In: Molecular Modeling and Simulation: An Interdisciplinary Guide. Interdisciplinary Applied Mathematics, vol 21. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-6351-2_5

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