A Striking Resemblance: DNA Dissociation as a Rhythmic Event
by David Lindsay
Copyright 2002. All right reserved.


In seeking new interpretations of genetics, a number of scientists and musicians have generated musical sequences based on patterns that can be found in DNA. As the field of genomics expands, so have the methods of arriving at musical representations of DNA multiplied. The present paper offers a new approach that concentrates on the element of rhythm.

Most musical interpretations of DNA to date have been concerned with the possible tonal qualities of the four nucleic acids that make up the genetic code, with an emphasis on the proteins that are created from them. As an alternative, one may look to the natural processes during which the DNA strands are dissociated, or broken apart. During replication and transcription, the strands dissociate sequentially and so raise the possibility of a characteristic temporal event.

Gena and Strom have pursued the subject of dissociation as it relates to the creation of amino acids, with significant results.1 The present approach begins one step earlier, investigating the DNA dissociation process apart from subsequent coding events. By looking solely at DNA dissociation, to the exclusion of the amino acids and proteins generated, we are able to include the process of replication within our scope.

The basic processes and elements of DNA dissociation are well known. The pairing of nucleic acids in the DNA molecule follows a uniform rule: adenine (A) is paired with thymine (T) on the opposite strand, and cytosine (C) with guanine (G.)

A C G T
T G C A

These pairs are held together with hydrogen bonds (H-bonds), which also obey a fixed principle: A and T are bound by two H-bonds, C and G by three H-bonds. Thus a DNA molecule can be thought of as a ladder with rungs that are clustered in groups of either two or three:

A C G T
|| ||| ||| ||
T G C A

In order to separate the opposing DNA strands, the H-bonds must be broken. Indeed, it is the breaking of the H-bonds that constitutes the dissociation of DNA. This breakage is achieved through a chain of events in which ATP molecules--the basic source of energy in biological organisms--play a determining role.

Because more energy is needed to break three H-bonds than is needed to break two, dissociation suggests a non-uniform expenditure of energy. Alternatively, one may say that a uniform expenditure of energy lower than a certain threshold value will yield a non-uniform event, as governed by the number of H-bonds in any given base pair. We will call this relationship between energy expended and the result that follows the governing algorithm, which will be expressed, where the energy is constant, by the following coefficients:

A=2
C=3
G=3
T=2

Given an arbitrary DNA sequence:

A C G T A A T A T T C T

the governing algorithm will generate a set of twos and threes:

2 3 3 2 2 2 2 2 2 2 3 2

Certain formal aspects of DNA dissociation in its biological state constrain the expression of the governing algorithm. When dissociation is initiated artificially (by heating), for example, the entire DNA molecule is effected more at less at once. In such a case, A-T rich regions will tend to separate sooner than regions rich in C-G pairs. In vivo, however, the H-bonds are broken linearly, as the dissociation progresses away from the initiation site:

A C G T A A T A T T C T
-------> ||| || || || || || || || ||| ||
T G C A T T A T A A G A

Thus, when derived from a sequence of DNA, the governing algorithm can be used to generate a predictable and unique temporal event.

H-bonds have been observed (again in vivo) to break in a four-based stagger, meaning that there is a pause in the dissociation after four sets of H-bonds. (In this regard, the investigation of DNA dissociation differs markedly from those concerned with the creation of proteins, which emphasize the three-base pattern created by the codons that constitute the genetic code.) The governing algorithm set generated above would, under such conditions, be expressed in groups of four:

2332 2222 2232

Another formal aspect of DNA dissociation that will limit its expression is bidirectionality. Dissociation takes place in two opposite directions along the DNA molecule, to form what is known as a replication bubble or replicon. As a result, two sequences of H-bond breakage are activated simultaneously:

A C G T A A T A T T C T
|| ||| ||| || <-------------> || || ||| ||
T G C A T T A T A A G A

The presence of all these conditions -- i.e., a governing algorithm expressed linearly in opposite directions in a four-base stagger -- will constitute a rhythm engine. These conditions may be applied equally to molecular processes or musical ones.

Furthermore, the energy applied to make a rhythm engine run (ATP in the case of DNA, mechanical energy in the case of music) may vary, and indeed may be intentionally varied. We will call the way in which it is varied its energy profile.

The variety of energy profiles is theoretically unlimited. One could, for example, propose an energy profile in which the force is sufficient to travel along the successive H-bonds at a statistically uniform rate, while releasing more energy from a cluster of three than from a cluster of two. If the energy used for this profile were mechanical, the governing algorithm would be converted to a series of stress and unstressed “beats,” such that:

A=2=unstressed beat (-)
C=3=stressed beat (´)
G=3=stressed beat (´)
T=2=unstressed beat (-)

Such an outcome, of course, describes a metrical system of scansion. It should be noted that the observation on the four-base stagger is not founded on comprehensive study, and that staggers occurring after any other number of H-bonds may be common. Nevertheless, the similarity to scansion applies equally to any instance of pauses in the dissociation process.

Perhaps the chief virtue of the rhythm engine, and its attending energy profile, is its adaptability. A set of rhythm engines based on close observation of DNA dissociation holds out the promise of generating music as yet unexpressed by other means. (This is especially so given the unique bidirectional nature of DNA dissociation, which has few if any analogues in nature.) By the same token, this field of inquiry may cast new light on genetic processes. For the moment, one implication will suffice.

Its seems eminently logical that repetitve DNA sequences would facilitate synchronized breakage of H-bonds, simply because, in such cases, the breakage in both directions will follow a built-in symmetry. In other words, H-bonds, or groups of H-bonds on either side of the origin site will tend to break at the same time and so move toward resonance.

Non-repetitive sequneces, on the other hand, will be less likely to fall into sychronization or resonance. By this reasoning, where the DNA strand is attached at its ends, non-repetitive sequences will tend to transmit energy to the attached substance (the nucleus wall, for example) or else be contained as heat, while repetitive sequences will tend to disperse energy into the nucleus itself. This assumption, which is testable, follows the same physics as those involved in engineering a suspension bridge.

The distinction bears investigating in relation to coding and non-coding DNA. It is well known that non-coding DNA (so-called because it does not code for protein) tends to be highly repetitive in comparison to coding-DNA. By extension, it is proposed here that the properties of non-coding DNA during dissociation may serve to regulate the energy involved in the processes of replication and transcription.

1. Gena, Peter and Charles Strom. “Musical Synthesis of DNA Sequences,” Proceedings of the Sixth International Symposium on Electronic Arts (Sept. 1995).


For a description of the author's inquiries into genetic copyrighting and how those inquiries led to this paper, click here.

A Thousand Apologies - a sample of music based on these principles. For an explanation of how this track was composed, click here.

Also see - http://www.whozoo.org/mac/Music/Sources.htm - an excellent website devoted to genetic music, run by M.A. Clark of Texas Wesleyan University.