Generate and Sign Certificate Request using pure .net Framework

Short answer: You can starting in .NET Framework 4.7.2.

This functionality was originally added to .NET Core 2.0 in the form of the CertificateRequest class, which can build a PKCS#10 certification signing request or an X.509 (self-signed or chained) public key certificate.

The classes for that feature were made available in .NET Framework 4.7.2.

using (RSA parent = RSA.Create(4096))
using (RSA rsa = RSA.Create(2048))
{
    CertificateRequest parentReq = new CertificateRequest(
        "CN=Experimental Issuing Authority",
        parent,
        HashAlgorithmName.SHA256,
        RSASignaturePadding.Pkcs1);

    parentReq.CertificateExtensions.Add(
        new X509BasicConstraintsExtension(true, false, 0, true));

    parentReq.CertificateExtensions.Add(
        new X509SubjectKeyIdentifierExtension(parentReq.PublicKey, false));

    using (X509Certificate2 parentCert = parentReq.CreateSelfSigned(
        DateTimeOffset.UtcNow.AddDays(-45),
        DateTimeOffset.UtcNow.AddDays(365)))
    {
        CertificateRequest req = new CertificateRequest(
            "CN=Valid-Looking Timestamp Authority",
            rsa,
            HashAlgorithmName.SHA256,
            RSASignaturePadding.Pkcs1);

        req.CertificateExtensions.Add(
            new X509BasicConstraintsExtension(false, false, 0, false));

        req.CertificateExtensions.Add(
            new X509KeyUsageExtension(
                X509KeyUsageFlags.DigitalSignature | X509KeyUsageFlags.NonRepudiation,
                false));

        req.CertificateExtensions.Add(
            new X509EnhancedKeyUsageExtension(
                new OidCollection
                {
                    new Oid("1.3.6.1.5.5.7.3.8")
                },
                true));

        req.CertificateExtensions.Add(
            new X509SubjectKeyIdentifierExtension(req.PublicKey, false));

        using (X509Certificate2 cert = req.Create(
            parentCert,
            DateTimeOffset.UtcNow.AddDays(-1),
            DateTimeOffset.UtcNow.AddDays(90),
            new byte[] { 1, 2, 3, 4 }))
        {
            // Do something with these certs, like export them to PFX,
            // or add them to an X509Store, or whatever.
        }
    }
}

Longer answer if you’re stuck on older versions: To accomplish your goal without adding any new P/Invokes, you would need to read and understand the following documents:

• ITU-T X.680-201508, the ASN.1 language
• IETF RFC 5280 or ITU-T X.509, the documents that explain the fields in X.509 certificates.
• IETF RFC 2986, explains the PKCS#10 certification signing request
• ITU-T X.690, explains the BER encoding family for ASN.1 (including DER) which tells you how to read and write bytes to achieve the semantic meaning from X.509 / PKCS#10.

And then you could write a DER writer/reader, and just emit the bytes for what you want.