How is the principle of natural rights reflected in the Declaration of Independence or the Articles of Confederation?

Since the other answer spoke of the Articles of Confederation, I'll give details about the Declaration of Independence.
The principle of natural rights is reflected in the Declaration of Independence's claims that the American colonists had inalienable rights which were being trampled on by the British government, and thus the colonists were right to assert their independence from Britain.
Explanation/details:
Enlightenment thinkers believed that using reason will guide us to the best ways to operate in order to create the most beneficial conditions for society. For John Locke, one of the earliest of the Enlightenment philosophers, this included a conviction that all human beings have certain natural rights which are to be protected and preserved. Locke's ideal was one that promoted individual freedom and equal rights and opportunity for all. Each individual's well-being (life, health, liberty, possessions) should be served by the way government and society are arranged. The American founding fathers accepted the views of Locke and other Enlightenment thinkers and acted on them.
The Declaration of Independence states Locke's natural rights idea in this way: "We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness."
John Locke, in his Second Treatise on Civil Government (1690), had expressed those same ideas in these words:
The state of nature has a law of nature to govern it, which obliges every one: and reason, which is that law, teaches all mankind, who will but consult it, that being all equal and independent, no one ought to harm another in his life, health, liberty, or possessions… (and) when his own preservation comes not in competition, ought he, as much as he can, to preserve the rest of mankind, and may not, unless it be to do justice on an offender, take away, or impair the life, or what tends to the preservation of the life, the liberty, health, limb, or goods of another

Independent executive agencies are more specialised.