In one sense, it is impossible to find the literary theory of deconstruction "in" Joseph Conrad's 1899 novel Heart of Darkness at all, as deconstruction was not invented until the work of Jacques Derrida in the 1960s, almost half a century after the publication of Conrad's novel. Thus while we can apply the characteristic vocabulary, methods, and thematic concerns of deconstruction to Heart of Darkness, that is a post hoc interpretive choice. Even more pertinent is the notion that for the strict deconstructive theorist, nothing actually exists in the text, but rather texts are constructed by their readers.
In approaching Heart of Darkness via a deconstructive theoretical framework on a graduate level, you will need to read and cite Miller's seminal essay:
Miller, J. Hillis. “Heart of Darkness Revisited.” In Conrad Revisited: Essays for the Eighties, edited by Ross C. Murfin, pp. 31-50. University: The University of Alabama Press, 1985.
The main issue Miller engages in the essay is deconstructing the binary of experience versus interpretation. As interpreters, it can be argued, we have knowledge of Africa only indirectly or secondhand, via Conrad's recounting of Marlowe's account of Kurtz. Miller points out, though, that Marlowe does not himself access the "heart of darkness" in an unmediated fashion, but only through Kurtz. Moreover, interpretation simultaneously reveals and conceals, illuminating as it mediates. Thus the narrative structure of all parts of the text can be deconstructed both in terms of the text itself and in terms of the hierarchical nature of the critic/creator binary, in which the interpreter is shown to be no less "creative" than the creator.
This quest for meaning in the Heart of Darkness can be analyzed in terms of another typical theme of deconstruction. With Kurtz's death and enigmatic final words, we have an example of the infinite deferral of meaning. We search for meaning in Conrad's novel, which the auditors seek in Marlowe's tale, in which Marlowe seeks meaning in Africa via Kurtz's privileged knowledge, and Kurtz himself finds only horror and then dies.
Other possible binaries you could deconstruct within the novel include those of race, class, and gender, but that would move away from the more purely deconstructive approach toward more recent theoretical formations of cultural critique.